Structures
Our database currently contains information about 777 SARS-CoV-2 protein structures and 26 additional structures of other coronaviruses. Use the filters below to select rows with attributes of interest. Next to each filter value, the number of shown/total structures from the group is displayed. Multiple values can be selected across multiple panes. To select more than one value within a single search pane, press and hold Ctrl or Shift when selecting filters. By default, the Non-PanDDA structures filter is turned on. To show PanDDA structures, just click on the blue filter in the Presets pane to unselect it, or use the Clear All button. Text search can be performed using the search box on the left below the filters.
| PDB | Resol. | Released | Title | Method | Ligand IDs | Virus | Protein | Ligand category | R-work | R-free | R-merge | Synthetics | Ligand full name | Author List | Processing Software | Completeness | I/σ | Synchrotron/Beamline | Refinement Software | Deposition Date | PubMed ID | Metals | Molstack | Re-refined PDB | Re-refined MTZ | R-free after re-refinement | Re-refinement summary | Validation summary | Polymers | PQ1(PDB) | Issues |  |
Re-refined? | Raw data | Ref. | PR-free | PRSRZ | PGeometry | RNA | Re-refinement comparison | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1p9s | 2.54 Å | 2003-05-20 | Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs | X-ray | DIO | HCoV-229E | NSP5 (Main protease) | Functional ligand | 19.64% | 27.89% | 14.20% | 1,4-DIETHYLENE DIOXIDE | Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J.R., Hilgenfeld, R. | HKL-2000 | 98.22% | 9.1 | ELETTRA (5.2R) | REFMAC | 2003-05-12 | 12746549.0 | - | - | - | - | N/A | - | - | Replicase polyprotein 1ab - residue 2966-3265, 3C-like proteinase | - | - | No | - | 15.6 | - | 9.1 | - | |||||
| 1uk4 | 2.50 Å | 2003-11-18 | Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor | X-ray | ATO | HCoV-229E | NSP5 (Main protease) | Functional ligand | 21.30% | 23.10% | N/A | 5-mer peptide of inhibitor | CHLOROACETONE | Yang, H., Yang, M., Liu, Y., Bartlam, M., Ding, Y., Lou, Z., Sun, L., Zhou, Z., Ye, S., Anand, K., Pang, H., Gao, G.F., Hilgenfeld, R., Rao, Z. | HKL-2000 | - | - | BSRF (3W1A) | CNS | 2003-08-14 | 14585926.0 | - | - | - | - | N/A | - | - | 3C-like proteinase; 5-mer peptide of inhibitor | 12.5 | - | No | - | 54.9 | 27.4 | 8.9 | - | ||||
| 1xjr | 2.70 Å | 2005-02-01 | The Structure of a Rigorously Conserved RNA Element Within the SARS Virus Genome | X-ray | - | SARS-CoV | RNA | No functional ligands | 23.14% | 24.33% | 5.60% | s2m RNA | - | Robertson, M.P., Igel, H., Baertsch, R., Haussler, D., Ares Jr., M., Scott, W.G. | MOSFLM | 99.40% | 31.3 | SSRL (BL9-1) | REFMAC | 2004-09-24 | 15630477.0 | MG | - | http://covid19.bioreproducibility.org/static/data/1xjr/1xjr-refined.pdb | http://covid19.bioreproducibility.org/static/data/1xjr/1xjr-refined.mtz | N/A | - | - | s2m RNA | 65.2 | - | Yes | - | 42.8 | 95.5 | 97.5 | s2m RNA | - | |||
| 1wof | 2.00 Å | 2005-08-30 | Crystal Structure Of SARS-CoV Mpro in FL N1 | X-ray | I12 | SARS-CoV | NSP5 (Main protease) | Functional ligand | 20.10% | 23.90% | N/A | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]-L-ALANYL-L-VALYL-N~1~-((1S)-4-ETHOXY-4-OXO-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]-L-ALANYL-L-VALYL-N~1~-((1S)-4-ETHOXY-4-OXO-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE | Yang, H., Bartlam, M., Xue, X., Yang, K., Liang, W., Rao, Z. | HKL-2000 | - | - | ROTATING ANODE () | CNS | 2004-08-18 | 16128623.0 | - | - | - | - | N/A | - | - | 3C-like proteinase | 20.1 | - | No | - | 46.7 | 42.2 | 21.3 | - | ||||
| 2ajf | 2.90 Å | 2005-09-20 | Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor | X-ray | NAG, BMA | SARS-CoV | Spike protein | Pathogen-host interaction | 21.80% | 27.50% | N/A | N-ACETYL-D-GLUCOSAMINE | N-ACETYL-D-GLUCOSAMINE;BETA-D-MANNOSE | Li, F., Li, W., Farzan, M., Harrison, S.C. | HKL-2000 | 93.10% | 20.5 | ALS (8.2.1) | REFMAC | 2005-08-01 | 16166518.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/2ajf/2ajf_refined.pdb | http://covid19.bioreproducibility.org/static/data/2ajf/2ajf_refined.mtz | 27.60% | Placed the coordinates in a standardized location in the unit cell. | The coordinates are NOT in a standardized location in the unit cell. | Angiotensin-converting enzyme-Related Carboxypeptidase (Ace2) - residues 19-615; SARS-coronavirus spike protein - receptor-binding domain, residues 323-502 | 4.9 | minimal | Yes | Yes | - | 17.5 | 34.7 | 12.6 | - | |||
| 2d2d | 2.70 Å | 2005-09-20 | Crystal Structure Of SARS-CoV Mpro in FL I2 | X-ray | ENB | SARS-CoV | NSP5 (Main protease) | Functional ligand | 20.90% | 28.20% | N/A | ETHYL (2E,4S)-4-[((2R)-2-{[N-(TERT-BUTOXYCARBONYL)-L-VALYL]AMINO}-2-PHENYLETHANOYL)AMINO]-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE | ETHYL (2E,4S)-4-[((2R)-2-{[N-(TERT-BUTOXYCARBONYL)-L-VALYL]AMINO}-2-PHENYLETHANOYL)AMINO]-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE | Yang, H., Bartlam, M., Xue, X., Yang, K., Liang, W., Ding, Y., Rao, Z. | HKL-2000 | - | - | ROTATING ANODE () | CNS | 2005-09-08 | 16128623.0 | - | - | - | - | N/A | - | - | 3C-like proteinase | 15.6 | - | No | - | 13.9 | 80.3 | 5.5 | - | ||||
| 2alv | 1.90 Å | 2006-08-08 | X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed anti-viral inhibitors | X-ray | CY6 | SARS-CoV | NSP5 (Main protease) | Functional ligand | 25.50% | 31.50% | 3.80% | N-((3S,6R)-6-((S,E)-4-ETHOXYCARBONYL-1-((S)-2-OXOPYRROLIDIN-3-YL)BUT-3-EN-2-YLCARBAMOYL)-2,9-DIMETHYL-4-OXODEC-8-EN-3-YL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE | N-((3S,6R)-6-((S,E)-4-ETHOXYCARBONYL-1-((S)-2-OXOPYRROLIDIN-3-YL)BUT-3-EN-2-YLCARBAMOYL)-2,9-DIMETHYL-4-OXODEC-8-EN-3-YL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE | Ghosh, A.K., Xi, K., Ratia, K., Santarsiero, B.D., Fu, W., Harcourt, B.H., Rota, P.A., Baker, S.C., Johnson, M.E., Mesecar, A.D. | DENZO; HKL-2000 | 98.60% | 32.4 | APS (14-BM-C) | CNS | 2005-08-08 | 16250632.0 | - | - | http://covid19.bioreproducibility.org/static/data/2alv/2alv_refined.pdb | http://covid19.bioreproducibility.org/static/data/2alv/2alv_refined.mtz | 29.50% | Placed the coordinates in a standardized location in the unit cell. Aded link between the inhibitor and Cys145, corrected. Corrected residues Leu50, Asn51, Val125, Ile286, 301-303. C38 atom of the inhibitor, moved 5-13 oxazol moiety of the inhibitor. | Several residues and the inhibitor can be corrected. The inhibitor is not linked to the protein. The coordinates are NOT in a standardized location in the unit cell. | Replicase polyprotein 1ab - 3CL proteinase, residues 3242-3543 | 1.3 | moderate | Yes | Yes | - | 6.0 | 25.1 | 12.0 | - | |||
| 2gx4 | 1.93 Å | 2007-05-08 | Crystal structure of SARS coronavirus 3CL protease inhibitor complex | X-ray | NOL | SARS-CoV | NSP5 (Main protease) | Functional ligand | 20.53% | 24.88% | N/A | N-[(BENZYLOXY)CARBONYL]-O-(TERT-BUTYL)-L-THREONYL-3-CYCLOHEXYL-N-[(1S)-2-HYDROXY-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}ETHYL]-L-ALANINAMIDE | N-[(BENZYLOXY)CARBONYL]-O-(TERT-BUTYL)-L-THREONYL-3-CYCLOHEXYL-N-[(1S)-2-HYDROXY-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}ETHYL]-L-ALANINAMIDE | Hsu, M.F., Wang, A.H.-J. | HKL-2000; CrystalClear | - | - | ROTATING ANODE () | CNS | 2006-05-08 | 16884309.0 | - | - | - | - | N/A | - | - | 3C-like proteinase - residues 1-306 | 38.8 | - | No | - | 37.5 | 67.8 | 44.2 | - | ||||
| 2qiq | 1.90 Å | 2008-02-12 | Structure-based Design and Synthesis and Biological Evaluation of Peptidomimetic SARS-3CLpro Inhibitors | X-ray | CYV | SARS-CoV | NSP5 (Main protease) | Functional ligand | 23.30% | 27.50% | N/A | ETHYL (4R)-4-{[(2R,5S)-5-{[N-(TERT-BUTOXYCARBONYL)-L-SERYL]AMINO}-6-METHYL-2-(3-METHYLBUT-2-EN-1-YL)-4-OXOHEPTANOYL]AMINO}-5-[(3R)-2-OXOPYRROLIDIN-3-YL]PENTANOATE | ETHYL (4R)-4-{[(2R,5S)-5-{[N-(TERT-BUTOXYCARBONYL)-L-SERYL]AMINO}-6-METHYL-2-(3-METHYLBUT-2-EN-1-YL)-4-OXOHEPTANOYL]AMINO}-5-[(3R)-2-OXOPYRROLIDIN-3-YL]PENTANOATE | Grum-Tokars, V. | HKL-2000 | 91.27% | - | APS (22-BM) | REFMAC | 2007-07-05 | 17855091.0 | - | - | http://covid19.bioreproducibility.org/static/data/2qiq/2qiq_refined.pdb | http://covid19.bioreproducibility.org/static/data/2qiq/2qiq_refined.mtz | 25.30% | Placed the coordinates in a standardized location in the unit cell. The inhibitor was re-refined after truncation to terminal carboxyl groups, assuming that the ester groups had been eliminated by hydrolysis before crystal formation, a supposition that is supported by the well-defined and abrupt limits of the electron density at the ends of both carboxyl groups. | While a large central part of the inhibitor is well defined in the electron density, the ethyl and t-butyl ester groups of the inhibitor molecule lack any electron density. The coordinates are NOT in a standardized location in the unit cell. | Replicase polyprotein 1ab - 3CL proteinase | 5.1 | significant | Yes | Yes | - | 17.5 | 14.3 | 33.6 | - | |||
| 3d0g | 2.80 Å | 2008-07-08 | Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2 | X-ray | NDG, NAG | SARS-CoV | Spike protein | Pathogen-host interaction | 21.40% | 27.90% | N/A | 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE;N-ACETYL-D-GLUCOSAMINE | Li, F. | DENZO | - | - | APS (19-BM) | REFMAC, CNS | 2008-05-01 | 18448527.0 | ZN | https://molstack.bioreproducibility.org/project/view/hnlY2nbqOGN6OoG7s3qz/ | http://covid19.bioreproducibility.org/static/data/3d0g/3d0g_refined.pdb | http://covid19.bioreproducibility.org/static/data/3d0g/3d0g_refined.mtz | 25.50% | Placed the coordinates in a standardized location in the unit cell. Corrected carbohydrate names, added several new carbohydrates. Fixed several rotamer outliers. | Not connected NAG molecules, not satisfactory Zn ion coordination. Unlikely assignment of the carbohydrate moieties bound to asparagine side chains (NDG rather than the expected NAG). Several carbohydrate moieties can be added to those already present, as well as to a few additional asparagine side chains. Coordinates are outside of the unit cell (not according to standardised placement) | Angiotensin-converting enzyme 2; Spike glycoprotein - residues 324-502 | 3.2 | moderate | Yes | Yes | - | 15.3 | 24.8 | 16.0 | - | ||||
| 3d0h | 3.10 Å | 2008-07-08 | Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 | X-ray | NDG, NAG | SARS-CoV | Spike protein | Pathogen-host interaction | 22.10% | 30.20% | N/A | 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE;N-ACETYL-D-GLUCOSAMINE | Li, F. | - | - | APS (19-BM) | REFMAC | 2008-05-01 | 18448527.0 | ZN | https://molstack.bioreproducibility.org/project/view/WrI2XslE978LiF95PQYo/ | http://covid19.bioreproducibility.org/static/data/3d0h/3d0h_refined.pdb | http://covid19.bioreproducibility.org/static/data/3d0h/3d0h_refined.mtz | 26.60% | Placed the coordinates in a standardized location in the unit cell. Corrected carbohydrate names, added several new carbohydrates. Fixed several rotamer outliers. | Not connected NAG molecules, not satisfactory Zn ion coordination. Unlikely assignment of the carbohydrate moieties bound to asparagine side chains (NDG rather than the expected NAG). Several carbohydrate moieties can be added to those already present, as well as to a few additional asparagine side chains. Coordinates are outside of the unit cell (not according to standardised placement) | Angiotensin-converting enzyme 2; Spike glycoprotein - residues 324-502 | 11.3 | moderate | Yes | Yes | - | 7.6 | 70.9 | 9.4 | - | |||||
| 3d0i | 2.90 Å | 2008-07-08 | Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 | X-ray | NDG, NAG | SARS-CoV | Spike protein | Pathogen-host interaction | 22.40% | 27.80% | N/A | 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE;N-ACETYL-D-GLUCOSAMINE | Li, F. | - | - | APS (19-BM) | REFMAC | 2008-05-01 | 18448527.0 | ZN | https://molstack.bioreproducibility.org/project/view/tyBAIB4W8gsYJT2boa8Q/ | http://covid19.bioreproducibility.org/static/data/3d0i/3d0i_refined.pdb | http://covid19.bioreproducibility.org/static/data/3d0i/3d0i_refined.mtz | 26.20% | Placed the coordinates in a standardized location in the unit cell. Corrected carbohydrate names, added several new carbohydrates. Fixed several rotamer outliers. | Not connected NAG molecules, not satisfactory Zn ion coordination. Unlikely assignment of the carbohydrate moieties bound to asparagine side chains (NDG rather than the expected NAG). Several carbohydrate moieties can be added to those already present, as well as to a few additional asparagine side chains. Coordinates are outside of the unit cell (not according to standardised placement) | Angiotensin-converting enzyme 2; Spike glycoprotein - residues 324-502 | 4.5 | moderate | Yes | Yes | - | 15.9 | 37.1 | 9.7 | - | |||||
| 3bgf | 3.00 Å | 2008-12-02 | X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab | X-ray | - | SARS-CoV | Spike protein | Pathogen-host interaction | 23.40% | 28.60% | 13.20% | - | Pak, J.E., Sharon, C., Satkunarajah, M., Auperin, T.C., Cameron, C.M., Kelvin, D.J., Seetharaman, J., Cochrane, A., Plummer, F.A., Berry, J.D., Rini, J.M. | HKL-2000 | 94.40% | - | NSLS (X12C) | REFMAC | 2007-11-26 | 19324051.0 | - | - | - | - | N/A | - | - | Spike protein S1; F26G19 Fab | 18.2 | - | No | - | 12.2 | 73.7 | 19.9 | - | |||||
| 3aw0 | 2.30 Å | 2011-12-14 | Structure of SARS 3CL protease with peptidic aldehyde inhibitor | X-ray | - | SARS-CoV | NSP5 (Main protease) | Functional ligand | 22.48% | 28.64% | 8.20% | peptide ACE-SER-ALA-VAL-LEU-HIS-H | - | Akaji, K., Konno, H., Mitsui, H., Teruya, K., Hattori, Y., Ozaki, T., Kusunoki, M., Sanjho, A. | HKL-2000 | 99.28% | 21.786 | Photon Factory (BL-6A) | REFMAC | 2011-03-09 | 22014094.0 | - | - | - | - | N/A | - | - | 3C-Like Proteinase; peptide ACE-SER-ALA-VAL-LEU-HIS-H | 5.7 | - | No | - | 12.1 | 38.4 | 17.4 | - | ||||
| 3sci | 2.90 Å | 2012-02-08 | Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus human strain complexed with human receptor ACE2 | X-ray | - | SARS-CoV | Spike protein | Pathogen-host interaction | 22.59% | 28.26% | N/A | - | Wu, K., Peng, G., Wilken, M., Geraghty, R., Li, F. | HKL-2000 | 93.40% | - | APS (19-ID) | REFMAC; CNS | 2011-06-07 | 22291007.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/3sci/3sci_refined_2_tls.pdb | http://covid19.bioreproducibility.org/static/data/3sci/3sci_refined_2.mtz | 27.70% | Placed the coordinates in a standardized location in the unit cell. Added a water molecule to each Zn cation and added LINKs between Zn and each of the coordinating ligands. Removed Cl ions. Fixed someRamachandran outliers. Many more Ramachandran outliers are left; the refinement is stopped due to availability of better structures for the same proteins. Sugar moieties were not added. | Zinc cations are placed without proper coordination. There are also two Cl ions in the structure, chemically feasible, but with poor/lacking electron density. Multiple Ramachandran outliers. Some residues have electron density for the sugar moieties due to glycosylation. The coordinates are NOT in a standardized location in the unit cell. | Angiotensin-converting enzyme 2 - UNP residues 19-615; Spike glycoprotein - receptor binding domain (UNP residues 306-527) | 2.4 | minimal | Yes | Yes | - | 13.7 | 26.7 | 10.7 | - | ||||
| 3sck | 3.00 Å | 2012-02-08 | Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 | X-ray | - | SARS-CoV | Spike protein | Pathogen-host interaction | 23.92% | 28.53% | N/A | - | Wu, K., Peng, G., Wilken, M., Geraghty, R., Li, F. | HKL-2000 | 91.70% | - | APS (19-ID) | REFMAC; CNS | 2011-06-07 | 22291007.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/3sck/3sck_refined_tls_2.pdb | http://covid19.bioreproducibility.org/static/data/3sck/3sck_refined_tls_2.mtz | 29.50% | Placed the coordinates in a standardized location in the unit cell. Added a water molecule to each Zn cation and added LINKs between Zn and each of the coordinating ligands. Removed Cl ions. Fixed someRamachandran outliers. Many more Ramachandran outliers are left; the refinement is stopped due to availability of better structures for the same proteins. Sugar moieties were not added. | Zinc cations are placed without proper coordination. There are also two Cl ions in the structure, chemically feasible, but with poor/lacking electron density. Multiple Ramachandran outliers. Some residues have electron density for the sugar moieties due to glycosylation. The coordinates are NOT in a standardized location in the unit cell. | Angiotensin-converting enzyme 2 chimera - SEE REMARK 999; Spike glycoprotein - receptor binding domain (UNP residues 324-502) | 11.8 | minimal | Yes | Yes | - | 12.6 | 71.8 | 4.8 | - | ||||
| 3scl | 3.00 Å | 2012-02-08 | Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2 | X-ray | - | SARS-CoV | Spike protein | Pathogen-host interaction | 23.88% | 29.18% | N/A | - | Wu, K., Peng, G., Wilken, M., Geraghty, R., Li, F. | HKL-2000 | 97.70% | - | APS (24-ID-E) | REFMAC; CNS | 2011-06-07 | 22291007.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/3scl/3scl_refined_2_tls.pdb | http://covid19.bioreproducibility.org/static/data/3scl/3scl_refined_2_coot.mtz | 29.00% | Placed the coordinates in a standardized location in the unit cell. Added a water molecule to each Zn cation and added LINKs between Zn and each of the coordinating ligands. Replaced Cl with water molecules. Fixed multiple Ramachandran outliers. Many more Ramachandran outliers are left; the refinement is stopped due to availability of better structures for the same proteins. Sugar moieties were not added. | Zinc cations are placed without proper coordination. There are also two Cl ions in the structure, chemically feasible, but with poor/lacking electron density. Multiple Ramachandran outliers. Some residues have electron density for the sugar moieties due to glycosylation. The coordinates are NOT in a standardized location in the unit cell. | Angiotensin-converting enzyme 2 chimera - SEE REMARK 999; Spike glycoprotein - receptor binding domain (UNP residues 324-502) | 11.1 | minimal | Yes | Yes | - | 10.2 | 67.1 | 10.1 | - | ||||
| 4rsp | 1.62 Å | 2015-06-17 | X-ray structure of MERS-CoV nsp5 protease bound with a designed inhibitor | X-ray | - | SARS-CoV | NSP5 (Main protease) | Functional ligand | 16.18% | 20.27% | N/A | Peptide inhibitor | - | Tomar, S., Mesecar, A.D. | MOSFLM | 95.00% | - | APS (31-ID) | PHENIX | 2014-11-10 | 26055715.0 | - | - | http://covid19.bioreproducibility.org/static/data/4rsp/4rsp_refined.pdb | http://covid19.bioreproducibility.org/static/data/4rsp/4rsp_refined.mtz | 21.20% | Placed the coordinates in a standardized location in the unit cell. Reset occupancies to n/m integral values. | Many residues with unbelievable occupancies (0.74/0.26, 0.61/0.39 etc.). The coordinates are NOT in a standardized location in the unit cell. | Orf1a protein; Peptide inhibitor | 81.9 | minimal | Yes | Yes | - | 80.5 | 72.8 | 88.6 | - | |||
| 5zuv | 2.21 Å | 2019-04-10 | Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1 | X-ray | - | HCoV-229E | Spike protein | Functional ligand | 20.19% | 24.81% | N/A | Yan, L., Yang, B., Wilson, I.A. | HKL-3000 | 98.75% | 18.9 | SSRF (BL19U1) | REFMAC | 2018-05-08 | 30989115.0 | - | - | http://covid19.bioreproducibility.org/static/data/5zuv/5zuv_refined.pdb | http://covid19.bioreproducibility.org/static/data/5zuv/5zuv_refined.mtz | 23.00% | Repositioned the coordinates with ACHESYM and improved the model by adding residue Leu8 in chain c (inhibitor peptide), correcting conformations of 13 residues (Lys23b, Gln788B/A, Glu789A, Asn790B, Gln791A/B, Leu794A, Val806C, Gln839C, Thr848B, Gln856A/B), and adding 43 water molecules. | Structure of good quality, without any additional ligands and without missing side chains. Most of the protein residues outside of the reference unit cell. The fusion molecule (HR1 motif and the peptidic inhibitor) is represented in the deposit as a single protein chain with consecutive residue numbering, not as separte chains (as in 5zvk and 5zvm). | Spike glycoprotein,Spike glycoprotein,inhibitor EK1 - UNP residues 785-873 | 49.1 | moderate | Yes | Yes | - | 38.0 | 43.3 | 87.8 | - | |||||
| 5zvk | 3.31 Å | 2019-04-10 | Crystal Structure of the Human Coronavirus MERS HR1 motif in complex with pan-CoVs inhibitor EK1 | X-ray | - | MERS | Spike protein | Functional ligand | 25.90% | 31.36% | N/A | Yan, L., Yang, B., Wilson, I.A. | HKL-3000 | 99.85% | 20.7 | SSRF (BL19U1) | PHENIX | 2018-05-11 | 30989115.0 | - | - | - | - | N/A | - | Structure of good quality, without any additional ligands and with no missing side chains. Most of the protein residues outside of the reference unit cell. | Human Coronavirus MERS HR1 motif - UNP residues 984-1062; pan-CoV inhibitory peptide EK1 | 8.1 | minimal | No | - | 6.2 | 23.6 | 47.7 | - | ||||||
| 5zvm | 3.30 Å | 2019-04-10 | Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs inhibitor EK1 | X-ray | - | SARS-CoV | Spike protein | Functional ligand | 24.76% | 30.14% | N/A | - | Yan, L., Yang, B., Wilson, I.A. | HKL-3000 | 99.90% | 11.9 | SSRF (BL19U1) | REFMAC | 2018-05-11 | 30989115.0 | - | - | - | - | N/A | not done | The coordinates are NOT in a standardized location in the unit cell. | Spike glycoprotein - UNP residues 892-970; pan-CoV inhibitory peptide EK1 | 14.5 | minimal | No | - | 7.7 | 14.2 | 75.0 | - | |||||
| 6u7e | 3.00 Å | 2019-11-13 | HCoV-229E RBD Class III in complex with human APN | X-ray | NAG, BMA | HCoV-229E | Spike protein | Pathogen-host interaction | 20.35% | 24.39% | 7.10% | N-ACETYL-D-GLUCOSAMINE;BETA-D-MANNOSE | Tomlinson, A.C.A., Li, Z., Rini, J.M. | XDS | 99.78% | 11.06 | CLSI (08ID-1) | PHENIX | 2019-09-02 | 31650956.0 | ZN | - | - | - | N/A | - | - | Aminopeptidase N - ectodomain (UNP residues 66-967); Spike glycoprotein | 68.0 | - | No | 42.3 | 86.1 | 78.0 | - | ||||||
| 6u7f | 2.75 Å | 2019-11-13 | HCoV-229E RBD Class IV in complex with human APN | X-ray | NAG | HCoV-229E | Spike protein | Pathogen-host interaction | 19.04% | 22.51% | 6.80% | N-ACETYL-D-GLUCOSAMINE | Tomlinson, A.C.A., Li, Z., Rini, J.M. | XDS | 99.86% | 16.24 | CLSI (08ID-1) | PHENIX | 2019-09-02 | 31650956.0 | ZN | - | - | - | N/A | - | - | Aminopeptidase N - ectodomain (UNP residues 66-967); Spike glycoprotein | 78.5 | - | No | 61.0 | 85.9 | 84.7 | - | ||||||
| 6u7g | 2.35 Å | 2019-11-13 | HCoV-229E RBD Class V in complex with human APN | X-ray | NAG | HCoV-229E | Spike protein | Pathogen-host interaction | 17.86% | 21.84% | 5.20% | N-ACETYL-D-GLUCOSAMINE | Tomlinson, A., Li, Z., Rini, J.M. | HKL-2000 | 96.03% | 14.9 | APS (23-ID-B) | PHENIX | 2019-09-02 | 31650956.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/6u7g/6u7g_refined.pdb | http://covid19.bioreproducibility.org/static/data/6u7g/6u7g_refined.mtz | 22.40% | Fixed minor issues with geometry and solvent | - | Aminopeptidase N - ectodomain (UNP residues 66-967); Spike protein - receptor-binding domain (UNP residues 292-432) | 57.1 | minimal | Yes | 67.5 | 33.3 | 83.6 | - | ||||||
| 6u7h | 3.10 Å | 2019-11-13 | Cryo-EM structure of the HCoV-229E spike glycoprotein | Cryo-EM | NAG, BMA, MAN | HCoV-229E | Spike protein | No functional ligands | N/A | N/A | N/A | N-ACETYL-D-GLUCOSAMINE;BETA-D-MANNOSE;ALPHA-D-MANNOSE | Li, Z., Benlekbir, S., Rubinstein, J.L., Rini, J.M. | - | - | () | 2019-09-02 | 31650956.0 | - | - | - | - | N/A | - | - | spike glycoprotein | N/A | - | No | - | N/A | N/A | N/A | - | |||||||
| 6lu7 | 2.16 Å | 2020-02-05 | The crystal structure of COVID-19 main protease in FL N3 | X-ray | PRD_002214 | SARS-CoV-2 | NSP5 (Main protease) | Functional ligand | 20.20% | 23.50% | 18.90% | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE | Liu, X., Zhang, B., Jin, Z., Yang, H., Rao, Z. | xia2 | 99.49% | 6.3 | SSRF (BL17U1) | PHENIX | 2020-01-26 | 32272481.0 | - | https://molstack.bioreproducibility.org/project/view/x9jJQnlGN25TRBSRdxJm/ | http://covid19.bioreproducibility.org/static/data/6lu7/6lu7_refined.pdb | http://covid19.bioreproducibility.org/static/data/6lu7/6lu7_refined.mtz | 22.50% | The phenyl group was removed from the inhibitor. After re-refinement of the model negative density disappeared. A few minor model corrections. | The terminal phenyl group of the inhibitor with negative difference electron density, possible hydrolysis. | SARS-CoV-2 main protease; N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE | 36.7 | moderate | Yes | Yes | - | 50.9 | 27.4 | 66.9 | - | ||||
| 6lvn | 2.47 Å | 2020-02-26 | Structure of the 2019-nCoV HR2 Domain | X-ray | - | SARS-CoV-2 | Spike protein | No functional ligands | 21.48% | 25.80% | 13.24% | Zhu, Y., Sun, F. | XDS | 99.26% | 19.06 | ROTATING ANODE () | PHENIX | 2020-02-04 | - | - | - | http://covid19.bioreproducibility.org/static/data/6lvn/6lvn_refined_tls.pdb | http://covid19.bioreproducibility.org/static/data/6lvn/6lvn_refined.mtz | 26.90% | Brought all four chains in one bundle. Modified residues: 18, 30, 2, 29. Added 34water molecules. | Structure of good quality. No ligands bound. No Ramachandran outliers, no rotamer outliers, and no missing side chains. Four helices are not placed in the ASU as a single oligomer, but as two independent dimers | SARS-coV-2 S2 subunit - HR2 domain | 51.7 | minimal | Yes | Yes | - | - | 29.1 | 75.4 | 69.5 | - | ||||
| 6lxt | 2.90 Å | 2020-02-26 | Structure of post fusion core of 2019-nCoV S2 subunit | X-ray | PG4 | SARS-CoV-2 | Spike protein | No functional ligands | 25.93% | 28.96% | 16.00% | TETRAETHYLENE GLYCOL | Zhu, Y., Sun, F. | MOSFLM | 94.02% | 6.3 | ROTATING ANODE () | REFMAC | 2020-02-11 | 32231345.0 | ZN | - | - | - | N/A | not done | Structure of good quality. It has one Ramachandran outlier, probably justified. No missing side-chains. Several side-chain outliers, but most are not trivial to fix - a common problem at low resolution (% outliers is low). Most of the protein is outside of the unit cell. A metal cation (Zn2+) is missing between Asp1199 of chain B and Asp1199 of chain F. At the interface between Asp1163 and Asp1165 of chain B and a symmetry mate of Glu1188 and Asp1184 of chain A (crystallographic interface between two six-helix bundles), a molecule of PEG is modeled instead of, most probably, one or two Zn2+ ions. This PEG molecule is hilariously mismodelled: it has severe clashes with the protein residues, all contacts are polar-to-nonpolar, and it is too curled-up | SARS-CoV-2 S2 subunit, SARS-CoV-2 S2 subunit - HR1 domain,HR2 domain | 11.3 | moderate | No | - | 10.8 | 48.1 | 29.0 | - | |||||
| 6vsb | 3.46 Å | 2020-02-26 | Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up | Cryo-EM | NAG | SARS-CoV-2 | Spike protein | No functional ligands | N/A | N/A | N/A | N-ACETYL-D-GLUCOSAMINE | Wrapp, D., Wang, N., Corbett, K.S., Goldsmith, J.A., Hsieh, C., Abiona, O., Graham, B.S., McLellan, J.S. | - | - | () | 2020-02-10 | 32075877.0 | - | - | - | - | N/A | - | - | SARS-CoV-2 spike glycoprotein | N/A | - | No | - | N/A | N/A | N/A | - | |||||||
| 6vw1 | 2.68 Å | 2020-03-04 | Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 | X-ray | NAG, BMA | SARS-CoV-2 | Spike protein | Pathogen-host interaction | 19.70% | 22.88% | 8.10% | N-ACETYL-D-GLUCOSAMINE;BETA-D-MANNOSE | Shang, J., Ye, G., Shi, K., Wan, Y.S., Aihara, H., Li, F. | HKL-2000 | 98.97% | 12.08 | APS (24-ID-E) | PHENIX, REFMAC | 2020-02-18 | 32225175.0 | ZN | - | http://covid19.bioreproducibility.org/static/data/6vw1/6vw1_refined.pdb | http://covid19.bioreproducibility.org/static/data/6vw1/6vw1_refined.mtz | 24.00% | Placed the coordinates in a standardized location in the unit cell. MC - refined the structure | Zn2+ cations have abnormally high B factors (135 and 196 Å2) and do not make any contacts with their environment that would indicate proper coordination. Otherwise the structure seems to be in good agreement with the electron density. The coordinates are NOT in a standardized location in the unit cell. | Angiotensin-converting enzyme 2; SARS-CoV-2 chimeric RBD | 54.3 | minimal | Yes | Yes | - | 57.3 | 75.5 | 46.1 | http://covid19.bioreproducibility.org/static/data/6vw1/6vw1_refinement_report.pdf | ||||
| 6vww | 2.20 Å | 2020-03-04 | Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2. | X-ray | ACY | SARS-CoV-2 | NSP15 | No functional ligands | 15.77% | 17.77% | 17.40% | ACETIC ACID | Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 98.08% | 10.0 | APS (19-ID) | PHENIX | 2020-02-20 | 32304108.0 | MG | - | - | - | N/A | - | - | NSP15 endoribnuclease | 87.9 | - | No | 93.3 | 95.1 | 83.2 | - | ||||||
| 6vxs | 2.03 Å | 2020-03-04 | Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 | X-ray | NHE | SARS-CoV-2 | NSP3: X-domain | No functional ligands | 18.64% | 23.35% | N/A | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID | Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mececar, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 84.84% | 8.44 | APS (19-ID) | PHENIX | 2020-02-24 | 32939273.0 | - | - | - | - | N/A | - | - | ADP-ribose-1"-monophosphatase | 76.9 | - | No | 52.6 | 89.2 | 85.3 | - | |||||
| 6y2e | 1.75 Å | 2020-03-04 | Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease | X-ray | - | SARS-CoV-2 | NSP5 (Main protease) | No functional ligands | 17.12% | 22.24% | 8.20% | Zhang, L., Sun, X., Hilgenfeld, R. | XDS | 99.97% | 15.0 | BESSY (14.2) | REFMAC | 2020-02-15 | 32198291.0 | - | - | http://covid19.bioreproducibility.org/static/data/6y2e/6y2e_refined.pdb | http://covid19.bioreproducibility.org/static/data/6y2e/6y2e_refined.mtz | 22.06% | Fixed minor issues with side chain rotamers. | Protein chains are modeled well. | SARS-CoV-2 (2019-nCoV) main protease | 65.0 | minimal | Yes | Yes | - | 63.7 | 63.2 | 73.2 | - | |||||
| 6y2f | 1.95 Å | 2020-03-04 | Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) | X-ray | O6K | SARS-CoV-2 | NSP5 (Main protease) | Functional ligand | 17.79% | 21.91% | 7.60% | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | Zhang, L., Lin, D., Sun, X., Hilgenfeld, R. | XDS | 99.95% | 15.5 | BESSY (14.2) | REFMAC | 2020-02-15 | 32198291.0 | - | - | http://covid19.bioreproducibility.org/static/data/6y2f/6y2f_refined.pdb | http://covid19.bioreproducibility.org/static/data/6y2f/6y2f_refined.mtz | 20.60% | Re-refinement with a sodium cation modeled at the highest peak site. A few side chain rotamer corrections. Application of TLS parameters. | Structure of good quality. High positive peak coordinated by five carbonyl oxygen atoms and one water molecule; octahedral coordination. | SARS-CoV-2 (2019-nCoV) main protease | 44.1 | moderate | Yes | Yes | - | 66.7 | 35.0 | 57.9 | - | |||
| 6y2g | 2.20 Å | 2020-03-04 | Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) | X-ray | O6K | SARS-CoV-2 | NSP5 (Main protease) | Functional ligand | 18.62% | 24.73% | 17.00% | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | Zhang, L., Lin, D., Sun, X., Hilgenfeld, R. | XDS | 99.95% | 13.1 | BESSY (14.2) | REFMAC | 2020-02-15 | 32198291.0 | - | - | http://covid19.bioreproducibility.org/static/data/6y2g/6y2g_refined.pdb | http://covid19.bioreproducibility.org/static/data/6y2g/6y2g_refined.mtz | 24.00% | Fixed minor issues with side chain rotamers and a couple of orphaned solvent molecules. | Protein chains are modeled well. | SARS-CoV-2 (2019-nCoV) main protease | 49.4 | minimal | No | Yes | - | 38.8 | 77.7 | 53.1 | - | |||
| 5r7y | 1.65 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z45617795 | X-ray | JFM | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 17.94% | 23.67% | 11.30% | N-(2-phenylethyl)methanesulfonamide | N-(2-phenylethyl)methanesulfonamide | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 98.82% | 5.8 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | N/A | not done | Weak density for the ligand on the primary 2Fo-Fc map. | SARS-CoV-2 main protease | - | moderate | No | - | 49.3 | - | 51.4 | - | ||||
| 5r7z | 1.59 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1220452176 | X-ray | HWH | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 24.47% | 27.65% | 9.60% | ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide | ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 98.87% | 6.2 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | https://molstack.bioreproducibility.org/collection/view/GqjIgzdHOk3yuQaO0ukE/ | - | - | 24.30% | not done | Weak density for the ligand on the primary 2Fo-Fc map. | SARS-CoV-2 main protease | 42.8 | moderate | No | - | 52.9 | 40.5 | 63.7 | - | ||||
| 5r80 | 1.93 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z18197050 | X-ray | RZG | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 22.16% | 27.57% | 11.30% | methyl 4-sulfamoylbenzoate | methyl 4-sulfamoylbenzoate | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 98.85% | 6.0 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | N/A | - | - | SARS-CoV-2 main protease | 25.7 | - | No | - | 51.5 | 30.7 | 40.5 | - | ||||
| 5r81 | 1.95 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110 | X-ray | RZJ | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 18.20% | 24.94% | 16.20% | 1-methyl-3,4-dihydro-2~{H}-quinoline-7-sulfonamide | 1-methyl-3,4-dihydro-2~{H}-quinoline-7-sulfonamide | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 99.77% | 4.0 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | N/A | - | - | SARS-CoV-2 main protease | 39.3 | - | No | - | 36.7 | 63.0 | 50.6 | - | ||||
| 5r82 | 1.31 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z219104216 | X-ray | RZS | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 18.03% | 21.16% | 5.00% | 6-(ethylamino)pyridine-3-carbonitrile | 6-(ethylamino)pyridine-3-carbonitrile | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 87.51% | 9.7 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | 21.20% | not done | Weak density for the ligand on the primary 2Fo-Fc map. | SARS-CoV-2 main protease | - | moderate | No | - | 73.5 | - | 50.1 | - | ||||
| 5r83 | 1.58 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z44592329 | X-ray | K0G | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 23.27% | 26.52% | 10.00% | N-phenyl-N'-pyridin-3-ylurea | N-phenyl-N'-pyridin-3-ylurea | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 99.39% | 6.7 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | N/A | - | - | SARS-CoV-2 main protease | 60.7 | - | No | - | 70.8 | 58.4 | 62.2 | - | ||||
| 5r84 | 1.83 Å | 2020-03-11 | PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168 | X-ray | GWS | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 21.67% | 29.26% | 14.00% | 2-cyclohexyl-~{N}-pyridin-3-yl-ethanamide | 2-cyclohexyl-~{N}-pyridin-3-yl-ethanamide | Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F. | XDS | 99.04% | 5.6 | Diamond (I04-1) | REFMAC | 2020-03-03 | - | - | - | - | - | N/A | - | - | SARS-CoV-2 main protease | 13.8 | - | No | - | 9.9 | 43.5 | 41.4 | - | ||||
| 6m03 | 2.00 Å | 2020-03-11 | The crystal structure of COVID-19 main protease in apo form | X-ray | - | SARS-CoV-2 | NSP5 (Main protease) | No functional ligands | 19.62% | 24.58% | 3.90% | Zhang, B., Zhao, Y., Jin, Z., Liu, X., Yang, H., Rao, Z. | XDS | 99.71% | 16.29 | SSRF (BL18U) | PHENIX | 2020-02-19 | - | - | - | http://covid19.bioreproducibility.org/static/data/6m03/6m03_refined.pdb | http://covid19.bioreproducibility.org/static/data/6m03/6m03_refined.mtz | 24.21% | Placed the coordinates in a standardized location in the unit cell. Added TLS (9 groups), added waters, fixed ramachandran outliers, Flipped side chains GLN 74, HIS 164, ASN 203. Changed rotamers MET 17, MET 165, ARG 298, GLN 189. Added alternative conformation for PHE 294. | Flipped sidechains, missing rotamers. The coordinates are NOT in a standardized location in the unit cell. No ligands, no metals. | SARS-CoV-2 main protease | 54.1 | moderate | Yes | Yes | - | - | 40.5 | 67.8 | 70.5 | - | ||||
| 6m17 | 2.90 Å | 2020-03-11 | The 2019-nCoV RBD/ACE2-B0AT1 complex | Cryo-EM | NAG | SARS-CoV-2 | Spike protein | Pathogen-host interaction | N/A | N/A | N/A | N-ACETYL-D-GLUCOSAMINE | Yan, R.H., Zhang, Y.Y., Li, Y.N., Xia, L., Guo, Y.Y., Zhou, Q. | - | - | () | 2020-02-24 | 32132184.0 | ZN | - | - | - | N/A | - | Poor map | Sodium-dependent neutral amino acid transporter B(0)AT1; Angiotensin-converting enzyme 2; SARS-coV-2 Receptor Binding Domain | N/A | moderate | No | - | N/A | N/A | N/A | - | |||||||
| 6vxx | 2.80 Å | 2020-03-11 | Structure of the SARS-CoV-2 spike glycoprotein (closed state) | Cryo-EM | NAG | SARS-CoV-2 | Spike protein | No functional ligands | N/A | N/A | N/A | N-ACETYL-D-GLUCOSAMINE | Walls, A.C., Park, Y.J., Tortorici, M.A., Wall, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), McGuire, A.T., Veesler, D. | - | - | () | 2020-02-25 | 32155444.0 | - | - | - | - | N/A | - | - | SARS-CoV-2 spike glycoprotein - ectodomain | N/A | - | No | - | N/A | N/A | N/A | - | |||||||
| 6vyb | 3.20 Å | 2020-03-11 | SARS-CoV-2 spike ectodomain structure (open state) | Cryo-EM | NAG | SARS-CoV-2 | Spike protein | No functional ligands | N/A | N/A | N/A | N-ACETYL-D-GLUCOSAMINE | Walls, A.C., Park, Y.J., Tortorici, M.A., Wall, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), McGuire, A.T., Veesler, D. | - | - | () | 2020-02-25 | 32155444.0 | - | - | - | - | N/A | - | - | SARS-CoV-2 spike glycoprotein - ectodomain | N/A | - | No | - | N/A | N/A | N/A | - | |||||||
| 6vyo | 1.70 Å | 2020-03-11 | Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 | X-ray | MES | SARS-CoV-2 | Nucleocapsid | No functional ligands | 15.99% | 20.49% | 13.10% | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID | Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 87.28% | 6.9 | APS (19-ID) | PHENIX | 2020-02-27 | - | ZN | - | http://covid19.bioreproducibility.org/static/data/6vyo/6vyo_refined.pdb | http://covid19.bioreproducibility.org/static/data/6vyo/6vyo_refined.mtz | 21.20% | - | - | RNA binding domain of nucleocapsid protein | 78.6 | - | Yes | - | 78.6 | 67.2 | 85.9 | - | ||||
| 6w01 | 1.90 Å | 2020-03-11 | The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate | X-ray | - | SARS-CoV-2 | NSP15 | No functional ligands | 16.05% | 18.49% | 11.20% | Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 98.70% | 13.11 | APS (19-ID) | PHENIX | 2020-02-28 | 32304108.0 | - | - | - | - | N/A | z | - | NSP15 Endoribonuclease | 82.8 | - | No | 90.6 | 71.3 | 83.2 | - | |||||||
| 6w02 | 1.50 Å | 2020-03-11 | Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose | X-ray | APR | SARS-CoV-2 | NSP3: X-domain | Functional ligand | 14.96% | 17.29% | 7.50% | ADENOSINE-5-DIPHOSPHORIBOSE | ADENOSINE-5-DIPHOSPHORIBOSE | Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mececar, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 79.80% | 25.3 | APS (19-ID) | PHENIX | 2020-02-28 | 32939273.0 | - | - | - | - | N/A | - | - | ADP ribose phosphatase | 87.4 | - | No | 94.7 | 89.2 | 83.8 | - | |||||
| 6y84 | 1.39 Å | 2020-03-11 | COVID-19 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, SARS-CoV-2) | X-ray | - | SARS-CoV-2 | NSP5 (Main protease) | No functional ligands | 17.79% | 20.00% | 5.90% | Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D., McAauley, K., Stuart, D.I., von Delft, F., Walsh, M.A. | DIALS; xia2 | 97.50% | 9.7 | Diamond (I04-1) | BUSTER, REFMAC | 2020-03-03 | - | - | - | http://covid19.bioreproducibility.org/static/data/6y84/6y84_refined_1.pdb | http://covid19.bioreproducibility.org/static/data/6y84/6y84_refined_1.mtz | 18.60% | - | Structure of good quality. | Non-structural polyprotein 1ab | 66.3 | minimal | Yes | - | - | 82.3 | 37.7 | 82.9 | - | |||||
| 6lzg | 2.50 Å | 2020-03-18 | Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2 | X-ray | NAG | SARS-CoV-2 | Spike protein | Pathogen-host interaction | 18.46% | 21.42% | 12.90% | N-ACETYL-D-GLUCOSAMINE | Wang, Q.H., Song, H., Qi, J.X. | HKL-2000 | 99.88% | 26.7 | SSRF (BL17U1) | PHENIX | 2020-02-19 | 32275855.0 | ZN | - | - | - | N/A | - | - | Angiotensin-converting enzyme 2; SARS-CoV-2 Spike receptor-binding domain | 42.7 | - | No | - | 70.1 | 30.9 | 55.9 | - | |||||
| 6m0j | 2.45 Å | 2020-03-18 | Crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2 | X-ray | NAG | SARS-CoV-2 | Spike protein | Pathogen-host interaction | 19.57% | 23.75% | 12.00% | N-ACETYL-D-GLUCOSAMINE | Wang, X., Lan, J., Ge, J., Yu, J., Shan, S. | XDS | 99.91% | 24.2 | SSRF (BL17U1) | PHENIX | 2020-02-21 | 32225176.0 | ZN | - | - | - | N/A | - | - | Angiotensin-converting enzyme 2; SARS-CoV-2 receptor-binding domain | 54.7 | - | No | - | 59.3 | 58.2 | 62.2 | - | |||||
| 6m3m | 2.70 Å | 2020-03-18 | Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain | X-ray | - | SARS-CoV-2 | Nucleocapsid | No functional ligands | 25.78% | 29.34% | 10.43% | Chen, S., Kang, S. | CrysalisPro | 99.00% | 14.97 | ROTATING ANODE () | PHENIX | 2020-03-04 | 32363136.0 | - | - | - | - | 28.90% | not done | Structure of good quality. No ligands. Some ramachandran outliers at the C-terminus. Many slashed side chains due to the lack of electron density – some can be built. | SARS-CoV-2 nucleocapsid protein - N-terminal RNA binding domain | 4.8 | minimal | No | - | 9.7 | 22.6 | 32.0 | - | ||||||
| 6w4b | 2.95 Å | 2020-03-18 | The crystal structure of Nsp9 replicase protein of COVID-19 | X-ray | - | SARS-CoV-2 | NSP9 | No functional ligands | 23.98% | 27.60% | 19.00% | Tan, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 97.09% | 17.4 | APS (19-BM) | PHENIX | 2020-03-10 | - | - | - | - | - | N/A | - | - | Nsp9 replicase protein | 7.2 | - | No | - | 16.9 | 21.4 | 35.9 | - | ||||||
| 6w4h | 1.80 Å | 2020-03-18 | 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 | X-ray | SO3, SAM, BDF | SARS-CoV-2 | NSP10/NSP16 | Protein-protein complex | 14.90% | 16.27% | 6.00% | S-ADENOSYLMETHIONINE | SULFITE ION;S-ADENOSYLMETHIONINE;BETA-D-FRUCTOPYRANOSE | Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Wiersum, G., Godzik, A., Jaroszewski, L., Stogios, P.J., Skarina, T., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID) | HKL-3000 | 99.97% | 29.3 | APS (21-ID-F) | REFMAC | 2020-03-10 | - | ZN | - | - | - | N/A | - | - | SARS-CoV-2 NSP16; SARS-CoV-2 NSP10 | 63.7 | - | No | - | 96.8 | 13.4 | 87.2 | - | ||||
| 6y7m | 1.90 Å | 2020-03-18 | Crystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate | X-ray | OEW | SARS-CoV | NSP5 (Main protease) | Functional ligand | 20.62% | 25.76% | 4.80% | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclohexyl-1-[[(2~{S},3~{R})-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclohexyl-1-[[(2~{S},3~{R})-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate | Zhang, L., Lin, D., Hilgenfeld, R. | XDS | 98.99% | 12.8 | PETRA III, DESY (P11) | REFMAC | 2020-03-01 | - | - | - | http://covid19.bioreproducibility.org/static/data/6y7m/6y7m_refined.pdb | http://covid19.bioreproducibility.org/static/data/6y7m/6y7m_refined.mtz | 25.60% | Added one water molecule. Some minor difficult to correction issues. | Structure of good quality. | Replicase polyprotein 1a | 31.0 | minimal | Yes | Yes | - | - | 29.6 | 43.8 | 60.4 | - | ||
| 5re4 | 1.88 Å | 2020-03-25 | PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193 | X-ray | SZY | SARS-CoV-2 | NSP5 (Main protease) | PanDDA fragment screening | 19.91% | 26.64% | 22.80% | N-(4-methylpyridin-3-yl)acetamide | N-(4-methylpyridin-3-yl)acetamide | Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft | XDS | 99.50% | 3.3 | Diamond (I04-1) | REFMAC | 2020-03-15 | - | - | - | - | - | N/A | - | - | SARS-CoV-2 main protease | 32.1 | - | No | - | 22.9 | 58.4 | 54.6 | - | ||||