Structures
Our database currently contains information about 941 SARS-CoV-2 protein structures and 64 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. 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 | ||
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1p9s | 2.54 Å | 2003-05-20 | Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs | X-ray | DIO | H-CoV | NSP5 (3CLpro) | Functional ligand | 19.64% | 27.89% | 14.20% | 1,4-DIETHYLENE DIOXIDE | - | 9.1 | ELETTRA (5.2R) | REFMAC | 2003-05-12 | 12746549 | - | - | - | - | N/A | - | - | Replicase polyprotein 1ab - residue 2966-3265, 3C-like proteinase | - | - | No | - | 15.5 | - | 9.1 | - | |||||||
1uk4 | 2.50 Å | 2003-11-18 | Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor | X-ray | ATO | SARS-CoV | NSP5 (3CLpro) | Functional ligand | 21.30% | 23.10% | N/A | 5-mer peptide of inhibitor | CHLOROACETONE | DENZO | 97.40% | - | BSRF (3W1A) | CNS | 2003-08-14 | 14585926 | - | - | - | - | N/A | - | - | 3C-like proteinase; 5-mer peptide of inhibitor | 12.4 | - | No | - | 54.8 | 27.3 | 8.8 | - | |||||
1xjr | 2.70 Å | 2005-02-01 | The Structure of a Rigorously Conserved RNA Element Within the SARS Virus Genome | X-ray | - | SARS-CoV | S2M/RNA | No functional ligands | 23.14% | 24.33% | 5.60% | s2m RNA | - | MOSFLM | 99.40% | 31.3 | SSRL (BL9-1) | REFMAC | 2004-09-24 | 15630477 | 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 | 65.3 | - | Yes | - | 42.7 | 95.5 | 97.5 | s2m RNA | - | ||||
1wof | 2.00 Å | 2005-08-30 | Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor N1 | X-ray | I12 | SARS-CoV | NSP5 (3CLpro) | 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 | HKL-2000 | - | - | ROTATING ANODE () | CNS | 2004-08-18 | 16128623 | - | - | - | - | N/A | - | - | 3C-like proteinase | 20.0 | - | No | - | 46.6 | 42.2 | 21.2 | - | |||||
2ajf | 2.90 Å | 2005-09-20 | Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor | X-ray | NAG | SARS-CoV | Spike | Pathogen-host interaction | 21.80% | 27.50% | N/A | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose; 2-acetamido-2-deoxy-beta-D-glucopyranose | 2-acetamido-2-deoxy-beta-D-glucopyranose | HKL-2000 | 93.10% | 20.5 | ALS (8.2.1) | REFMAC | 2005-08-01 | 16166518 | 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 | - | 17.4 | 34.6 | 12.5 | - | ||||
2d2d | 2.70 Å | 2005-09-20 | Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor I2 | X-ray | ENB | SARS-CoV | NSP5 (3CLpro) | 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 | DENZO | - | - | ROTATING ANODE () | CNS | 2005-09-08 | 16128623 | - | - | - | - | 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 (3CLpro) | 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 | DENZO; HKL-2000 | 98.60% | 32.4 | APS (14-BM-C) | CNS | 2005-08-08 | 16250632 | - | - | 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 | 11.9 | - | ||||
2gx4 | 1.93 Å | 2007-05-08 | Crystal structure of SARS coronavirus 3CL protease inhibitor complex | X-ray | NOL | SARS-CoV | NSP5 (3CLpro) | 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 | DENZO; CrystalClear | - | - | ROTATING ANODE () | CNS | 2006-05-08 | 16884309 | - | - | - | - | N/A | - | - | 3C-like proteinase - residues 1-306 | 38.7 | - | No | - | 37.4 | 67.8 | 43.9 | - | |||||
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 (3CLpro) | 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 | HKL-2000 | - | - | APS (22-BM) | REFMAC | 2007-07-05 | 17855091 | - | - | 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 | 5.0 | significant | Yes | Yes | - | 17.4 | 14.2 | 33.4 | - | ||||
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 | Pathogen-host interaction | 21.40% | 27.90% | N/A | 2-acetamido-2-deoxy-alpha-D-glucopyranose; 2-acetamido-2-deoxy-beta-D-glucopyranose | DENZO | - | - | APS (19-BM) | REFMAC; CNS | 2008-05-01 | 18448527 | 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 | 24.7 | 15.8 | - | |||||
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 | Pathogen-host interaction | 22.10% | 30.20% | N/A | 2-acetamido-2-deoxy-alpha-D-glucopyranose; 2-acetamido-2-deoxy-beta-D-glucopyranose | - | - | APS (19-BM) | REFMAC | 2008-05-01 | 18448527 | 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 | - | 7.5 | 70.9 | 9.3 | - | ||||||
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 | Pathogen-host interaction | 22.40% | 27.80% | N/A | 2-acetamido-2-deoxy-alpha-D-glucopyranose; 2-acetamido-2-deoxy-beta-D-glucopyranose | - | - | APS (19-BM) | REFMAC | 2008-05-01 | 18448527 | 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 | 4.4 | moderate | Yes | Yes | - | 15.8 | 37.0 | 9.6 | - | ||||||
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 | Pathogen-host interaction | 23.40% | 28.60% | 13.20% | - | HKL-2000; DENZO | 94.40% | 6.3 | NSLS (X12C) | REFMAC | 2007-11-26 | 19324051 | - | - | - | - | N/A | - | - | Spike protein S1; F26G19 Fab; F26G19 Fab | 18.1 | - | No | - | 12.1 | 73.7 | 19.8 | - | ||||||
3aw0 | 2.30 Å | 2011-12-14 | Structure of SARS 3CL protease with peptidic aldehyde inhibitor | X-ray | - | SARS-CoV | NSP5 (3CLpro) | Functional ligand | 22.48% | 28.64% | 8.20% | peptide ACE-SER-ALA-VAL-LEU-HIS-H | - | HKL-2000 | 99.90% | 21.786 | Photon Factory (BL-6A) | REFMAC | 2011-03-09 | 22014094 | - | - | - | - | N/A | - | - | 3C-Like Proteinase; peptide ACE-SER-ALA-VAL-LEU-HIS-H | 5.6 | - | No | - | 12.0 | 38.4 | 17.2 | - | |||||
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 | Pathogen-host interaction | 22.59% | 28.26% | N/A | - | HKL-2000 | 93.40% | - | APS (19-ID) | CNS; REFMAC | 2011-06-07 | 22291007 | 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 | 26.6 | 10.6 | - | |||||
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 | Pathogen-host interaction | 23.92% | 28.53% | N/A | - | HKL-2000 | 91.70% | - | APS (19-ID) | CNS; REFMAC | 2011-06-07 | 22291007 | 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 | - | 12.5 | 71.9 | 4.7 | - | |||||
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 | Pathogen-host interaction | 23.88% | 29.18% | N/A | - | HKL-2000 | 97.70% | - | APS (24-ID-E) | REFMAC; CNS | 2011-06-07 | 22291007 | 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 | - | 10.1 | 67.1 | 10.0 | - | |||||
4rsp | 1.62 Å | 2015-06-17 | X-ray structure of MERS-CoV nsp5 protease bound with a designed inhibitor | X-ray | - | MERS-CoV | NSP5 (3CLpro) | Functional ligand | 16.18% | 20.27% | N/A | Peptide inhibitor | - | MOSFLM | 95.00% | - | APS (31-ID) | PHENIX | 2014-11-10 | 26055715 | - | - | 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 | 88.5 | - | ||||
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 | - | H-CoV-229E | Spike | Functional ligand | 20.19% | 24.81% | N/A | - | HKL-3000 | 99.40% | 18.9 | SSRF (BL19U1) | REFMAC | 2018-05-08 | 30989115 | - | - | 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 | - | 37.9 | 43.2 | 87.7 | - | |||||
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-CoV | Spike | Functional ligand | 25.90% | 31.36% | N/A | - | HKL-3000 | 99.90% | 20.7 | SSRF (BL19U1) | PHENIX | 2018-05-11 | 30989115 | - | - | - | - | 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 | - | 6.1 | 23.5 | 47.5 | - | ||||||
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 | Functional ligand | 24.76% | 30.14% | N/A | - | HKL-3000 | 99.90% | 11.9 | SSRF (BL19U1) | REFMAC | 2018-05-11 | 30989115 | - | - | - | - | 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 | 14.4 | minimal | No | - | 7.7 | 14.2 | 74.8 | - | ||||||
6u7e | 3.00 Å | 2019-11-13 | HCoV-229E RBD Class III in complex with human APN | X-ray | NAG | H-CoV-229E | Spike | Pathogen-host interaction | 20.35% | 24.39% | 7.10% | 2-acetamido-2-deoxy-beta-D-glucopyranose | XDS | 99.80% | 11.06 | CLSI (08ID-1) | PHENIX | 2019-09-02 | 31650956 | ZN | - | - | - | N/A | - | - | Aminopeptidase N - ectodomain (UNP residues 66-967); Spike glycoprotein | 68.0 | - | No | 42.2 | 86.1 | 77.8 | - | |||||||
6u7f | 2.75 Å | 2019-11-13 | HCoV-229E RBD Class IV in complex with human APN | X-ray | NAG | H-CoV-229E | Spike | Pathogen-host interaction | 19.04% | 22.51% | 6.80% | 2-acetamido-2-deoxy-beta-D-glucopyranose | XDS | 99.80% | 16.24 | CLSI (08ID-1) | PHENIX | 2019-09-02 | 31650956 | ZN | - | - | - | N/A | - | - | Aminopeptidase N - ectodomain (UNP residues 66-967); Spike glycoprotein | 78.5 | - | No | 60.9 | 86.0 | 84.6 | - | |||||||
6u7g | 2.35 Å | 2019-11-13 | HCoV-229E RBD Class V in complex with human APN | X-ray | NAG | H-CoV-229E | Spike | Pathogen-host interaction | 17.86% | 21.84% | 5.20% | 2-acetamido-2-deoxy-beta-D-glucopyranose | HKL-2000 | 99.70% | 14.9 | APS (23-ID-B) | PHENIX | 2019-09-02 | 31650956 | 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 | 67.4 | 33.2 | 83.5 | - | |||||||
6u7h | 3.10 Å | 2019-11-13 | Cryo-EM structure of the HCoV-229E spike glycoprotein | Cryo-EM | NAG | H-CoV-229E | Spike | No functional ligands | N/A | N/A | N/A | 2-acetamido-2-deoxy-beta-D-glucopyranose | - | - | () | 2019-09-02 | 31650956 | - | - | - | - | N/A | - | - | spike glycoprotein | N/A | - | No | - | N/A | N/A | N/A | - | ||||||||
6jx7 | 3.31 Å | 2020-01-15 | Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4 | Cryo-EM | MAN, NAG | FIPV | Spike | No functional ligands | N/A | N/A | N/A | alpha-D-mannopyranose; 2-acetamido-2-deoxy-beta-D-glucopyranose | - | - | () | 2019-04-22 | 31900356 | - | - | - | - | N/A | - | - | Feline Infectious Peritonitis Virus Spike Protein | N/A | - | No | - | N/A | N/A | N/A | - | ||||||||
6noz | 1.95 Å | 2020-01-22 | X-ray structure of PEDV papain-like protease 2 | X-ray | - | PEDV | NSP3: PLpro | No functional ligands | 14.47% | 19.31% | 16.40% | - | HKL-2000 | 100.00% | 6.4 | APS (31-ID) | PHENIX | 2019-01-16 | - | ZN | - | - | - | N/A | - | - | Polyprotein - UNP Residues 1688-1933 | 87.6 | - | No | - | - | 86.5 | 92.0 | 90.1 | - | |||||
6lu7 | 2.16 Å | 2020-02-05 | The crystal structure of COVID-19 main protease in complex with an inhibitor N3 | X-ray | - | SARS-CoV-2 | NSP5 (3CLpro) | 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 | - | xia2 | 100.00% | 6.3 | SSRF (BL17U1) | PHENIX | 2020-01-26 | 32272481 | - | 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. | main protease - 3C-like proteinase; 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 | 36.6 | moderate | Yes | Yes | - | 50.8 | 27.3 | 66.7 | - | ||||
6lvn | 2.47 Å | 2020-02-26 | Structure of the 2019-nCoV HR2 Domain | X-ray | - | SARS-CoV-2 | Spike | No functional ligands | 21.48% | 25.80% | 13.24% | - | XDS | 99.22% | 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 | Spike protein S2 - HR2 domain | 51.6 | minimal | Yes | Yes | - |