← Back to search
9xg4

The crystal structure of SARS-CoV-1 Main protease in complex with inhibitor FD2-21

Method: X-RAY DIFFRACTION Dmax: 81.1 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

3C-like proteinase nsp5

Severe acute respiratory syndrome-related coronavirus

UniProt P0C6X7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 3241–3546 Not recorded A1EZ7 7-(5-azanylpyridin-3-yl)-2-(2-chlorophenyl)-5,7-diazaspiro[3.4]octane-6,8-dione × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289.15 K；1.1 M Ammonium tartrate dibasic pH 7.0 Resolution 1.73 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9XG4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UK4 Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor Deposited 2003-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 3241–3546（306 aa）
Chain B 3241–3546（306 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 6000, MES, DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.231
2XYQ Crystal structure of the nsp16 nsp10 SARS coronavirus complex Deposited 2010-11-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 6776–7065（290 aa） Fragment：RESIDUES 6776-7065
Chain B 4240–4361（122 aa） Fragment：RESIDUES 4240-4361
Not recorded CL CHLORIDE ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1M CHES, 1.52M MGCL2, pH 9
Resolution 2.00 Å R-free 0.227
2XYR Crystal structure of the nsp16 nsp10 SARS coronavirus complex Deposited 2010-11-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 6776–7067（292 aa） Fragment：RESIDUES 6776-7067
Chain B 4240–4361（122 aa） Fragment：RESIDUES 4240-4361
Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 5 SFG SINEFUNGIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1M CHES, 1.52M MGCL2, pH 9
Resolution 2.50 Å R-free 0.235
2XYV Crystal structure of the nsp16 nsp10 SARS coronavirus complex Deposited 2010-11-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 6776–7067（292 aa） Fragment：RESIDUES 6776-7065
Chain B 4240–4361（122 aa） Fragment：RESIDUES 4240-4361
Mutation：YES NA SODIUM ION × 3 CL CHLORIDE ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；67 MM M CHES, 0.99 M MGCL2-HEXAYDRATE, 33 MM TRIS-HCL, 8.3% (V/V) PEG 8000, FROZEN IN THE PRESENCE OF 15% (V/V) GLYCEROL, pH 8.5
Resolution 2.06 Å R-free 0.234
3EBN A Special Dimerization of SARS-CoV Main Protease C-Terminal Domain Due to Domain-swapping Deposited 2008-08-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3429–3546（118 aa） Fragment：UNP residues 3429-3546
Chain C 3429–3546（118 aa） Fragment：UNP residues 3429-3546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% PEG3350, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.40 Å R-free 0.243
3EBN A Special Dimerization of SARS-CoV Main Protease C-Terminal Domain Due to Domain-swapping Deposited 2008-08-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 3429–3546（118 aa） Fragment：UNP residues 3429-3546
Chain D 3429–3546（118 aa） Fragment：UNP residues 3429-3546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% PEG3350, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.40 Å R-free 0.243
3R24 Crystal structure of nsp10/nsp16 complex of SARS coronavirus Deposited 2011-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 6776–7073（298 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2.0M NaCl, 0.1M NaH2PO4, 0.1M K2HPO4, 0.1M MES, pH5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.222
4TWW Structure of SARS-3CL protease complex with a Bromobenzoyl (S,R)-N-decalin type inhibitor Deposited 2014-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Chain B 3241–3546（306 aa）
Not recorded 3A7 (2S)-2-({[(3S,4aR,8aS)-2-(4-bromobenzoyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；9-11%(w/v) of PEG20000, 100mM MES, 5mM DTT
Resolution 2.42 Å R-free 0.261
4TWY Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor Deposited 2014-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Not recorded 3BL (2S)-2-({[(3S,4aR,8aS)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10%(w/v) of PEG20000, 100mM MES, 5mM DTT
Resolution 1.60 Å R-free 0.319
4WY3 Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor Deposited 2014-11-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3241–3546（306 aa）
Not recorded 3X5 (2S)-2-({[(3R,4aS,8aR)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10%(w/v) PEG20000, 100mM MES, 5 mM DTT
Resolution 1.89 Å R-free 0.299
5B6O Crystal structure of MS8104 Deposited 2016-05-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3556（316 aa）
Chain B 3241–3556（316 aa）
Mutation：C145A Mutation：C145A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；Sodium Chloride, PEG 4000 , pH 7.3, temperature 293K
Resolution 2.20 Å R-free 0.254
5C5N Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type inhibitor Deposited 2015-06-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3241–3546（306 aa）
Mutation：R188I SLH (2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10%(w/v) of PEG20000, 100mM MES, 5mM DTT
Resolution 1.69 Å R-free 0.321
5C5N Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type inhibitor Deposited 2015-06-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Mutation：R188I SLH (2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10%(w/v) of PEG20000, 100mM MES, 5mM DTT
Resolution 1.69 Å R-free 0.321
5C5O Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor Deposited 2015-06-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3241–3546（306 aa）
Mutation：R188I SDJ (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% (w/v) PEG 20000, 100mM MES, 5mM DTT
Resolution 1.50 Å R-free 0.271
5C5O Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor Deposited 2015-06-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3241–3546（306 aa）
Mutation：R188I SDJ (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% (w/v) PEG 20000, 100mM MES, 5mM DTT
Resolution 1.50 Å R-free 0.271
5C5O Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor Deposited 2015-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Chain B 3241–3546（306 aa）
Mutation：R188I Mutation：R188I SDJ (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% (w/v) PEG 20000, 100mM MES, 5mM DTT
Resolution 1.50 Å R-free 0.271
5C8S Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligands SAH and GpppA Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 4231–4369（139 aa）
Chain B 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 G3A GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, and 2% (w/v) polyethylene glycol 3350
Resolution 3.33 Å R-free 0.259
5C8S Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligands SAH and GpppA Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 4231–4369（139 aa）
Chain D 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 G3A GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, and 2% (w/v) polyethylene glycol 3350
Resolution 3.33 Å R-free 0.259
5C8T Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligand SAM Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 4231–4369（139 aa）
Chain B 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, and 2% (w/v) polyethylene glycol 3,350
Resolution 3.20 Å R-free 0.265
5C8T Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligand SAM Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 4231–4369（139 aa）
Chain D 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, and 2% (w/v) polyethylene glycol 3,350
Resolution 3.20 Å R-free 0.265
5C8U Crystal structure of the SARS coronavirus nsp14-nsp10 complex Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 4231–4369（139 aa）
Chain B 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 2% (w/v) polyethylene glycol 3350
Resolution 3.40 Å R-free 0.266
5C8U Crystal structure of the SARS coronavirus nsp14-nsp10 complex Deposited 2015-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 4231–4369（139 aa）
Chain D 5903–6429（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 2% (w/v) polyethylene glycol 3350
Resolution 3.40 Å R-free 0.266
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1541–1856（316 aa） Fragment：UNP Residues 1541-1856
Not recorded ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1541–1856（316 aa） Fragment：UNP Residues 1541-1856
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5F22 C-terminal domain of SARS-CoV nsp8 complex with nsp7 Deposited 2015-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 3989–4117（129 aa） Fragment：UNP residues 3989-4117
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2M magnesium acetate, PEG 3350
Resolution 2.15 Å R-free 0.252
5N19 Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide Deposited 2017-02-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Not recorded D03 (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；6 - 8% polyethylene glycol 6000, 0.1 M MES, pH 6.0
Resolution 1.62 Å R-free 0.200
5N5O Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-cyclopropylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (Cinnamoyl-cyclopropylalanine-GlnLactam-CO-CO-NH-benzyl) Deposited 2017-02-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Not recorded 8O5 (2~{R},3~{S})-3-[[(2~{S})-3-cyclopropyl-2-[[(~{E})-3-phenylprop-2-enoyl]amino]propanoyl]amino]-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-~{N}-(phenylmethyl)butanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；6 - 8% polyethylene glycol 6000, 0.1 M MES, pH 6.0
Resolution 2.00 Å R-free 0.252
5TL6 Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain of human ISG15 Deposited 2016-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1541–1855（315 aa） Fragment：UNP residues 1541-1855
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M lithium sulfate, 0.1 M Bis-tris [pH 6.5], 22% PEG 3350, supplemented with 30% (v/v) glycerol additive in a 1:5 dilution
Resolution 2.62 Å R-free 0.250
5TL6 Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain of human ISG15 Deposited 2016-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1541–1855（315 aa） Fragment：UNP residues 1541-1855
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M lithium sulfate, 0.1 M Bis-tris [pH 6.5], 22% PEG 3350, supplemented with 30% (v/v) glycerol additive in a 1:5 dilution
Resolution 2.62 Å R-free 0.250
5TL7 Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15 Deposited 2016-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1541–1855（315 aa） Fragment：UNP residues 1541-1855
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；65% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution
Resolution 2.44 Å R-free 0.267
5TL7 Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15 Deposited 2016-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1541–1855（315 aa） Fragment：UNP residues 1541-1855
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；65% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution
Resolution 2.44 Å R-free 0.267
6JYT Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis Deposited 2019-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5302–5902（601 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；12% w/v polyethylene glycol 20000, 2M ammonium sulfate, 0.1M MES monohydrate pH 6.5
Resolution 2.80 Å R-free 0.292
6JYT Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis Deposited 2019-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 5302–5902（601 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；12% w/v polyethylene glycol 20000, 2M ammonium sulfate, 0.1M MES monohydrate pH 6.5
Resolution 2.80 Å R-free 0.292
6NUR SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors Deposited 2019-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 4370–5300（931 aa） Fragment：UNP residues 4370-5300
Chain C 3837–3919（83 aa） Fragment：UNP residues 3837-3919
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；n-dodecyl-beta-D-maltopyranoside was added just prior to spotting samples onto holey EM grids.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6NUS SARS-Coronavirus NSP12 bound to NSP8 co-factor Deposited 2019-02-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 4370–5300（931 aa） Fragment：UNP residues 4370-5300
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；n-dodecyl-beta-D-maltopyranoside was added just prior to spotting samples onto holey EM grids.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7LCP N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL protease Deposited 2021-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Not recorded UED N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide × 2 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；7% PEG 8000, 1 mM MES pH 6.0, 1mM DTT, 3% ethylene glycol and 3% DMSO
Resolution 1.90 Å R-free 0.221
7LCQ N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL protease Deposited 2021-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3241–3546（306 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 UED N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；295 K；7% PEG 8000, 1 mM MES pH 6.0, 1mM DTT, 3% ethylene glycol and 3% DMSO
Resolution 2.15 Å R-free 0.223
8C0G SARS-CoV nsp16-nsp10 complexed with N7-GTP Deposited 2022-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 6776–7067（292 aa）
Chain B 4240–4361（122 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 SRC [[(2~{R},3~{S},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 NA SODIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；67 MM M CHES, 0.99 M MGCL2-HEXAYDRATE, 33 MM TRIS-HCL, 8.3% (V/V) PEG 8000
Resolution 1.88 Å R-free 0.263
8CB3 SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid Deposited 2023-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1000–1173（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Imidazole, 0.9 M NaCitrate, pH 7.9 0.2 M MOPS
Resolution 1.57 Å R-free 0.203
8CB3 SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid Deposited 2023-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1000–1173（174 aa）
Not recorded MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Imidazole, 0.9 M NaCitrate, pH 7.9 0.2 M MOPS
Resolution 1.57 Å R-free 0.203
8CB3 SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid Deposited 2023-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1000–1173（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Imidazole, 0.9 M NaCitrate, pH 7.9 0.2 M MOPS
Resolution 1.57 Å R-free 0.203
8YKK Crystal structure of SARS main protease in complex with X77 Deposited 2024-03-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3242–3539（298 aa）
Not recorded X77 N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Resolution 2.30 Å R-free 0.248
9LZQ Crystal structure of SARS main protease in complex with Ibuzatrelvir Pomotrelvir Deposited 2025-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3242–3540（299 aa）
Chain B 3242–3540（299 aa）
Not recorded ZQB Pomotrelvir bound form × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Resolution 2.05 Å R-free 0.248
9MBV Crystal structure of SARS main protease complex with CCF0058981 Deposited 2025-03-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3242–3540（299 aa）
Chain B 3242–3540（299 aa）
Not recorded XIU 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(1~{H}-imidazol-5-yl)phenyl]ethanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
Resolution 1.94 Å R-free 0.244

31 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name R1AB_SARS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–306； UniProt 3241–3546

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9xg4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xg4
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9xg4
Deposition date deposition_date2025-10-29
最后修订 last_revision2026-05-27
Structure title titleThe crystal structure of SARS-CoV-1 Main protease in complex with inhibitor FD2-21
Keywords keywordsSARS-CoV-1, Main protease, Inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.78 Å
Radius of gyration Rg (electron density) rg_electron22.09 Å
Forward intensity I(0) i020529200.00
Molecular weight molecular_weight34185.0 kDa
Excluded volume excluded_volume42623 ų
Envelope volume envelope_volume50534 ų
Hydration-shell volume shell_volume20015 ų
Envelope diameter envelope_diameter80.0 Å
Shell Rg shell_rg27.77 Å
Envelope Rg envelope_rg22.34 Å
Shape Rg shape_rg22.15 Å
Total Rg total_rg22.63 Å
Total atoms total_atoms4731
Residues n_residues306
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.1 Å
Rg (real space) rg_real22.89 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real2.0530e+07
I(0) uncertainty (real space) i0_real_error3.4730e+05
Rg (reciprocal space) rg_reciprocal22.87 Å
I(0) (reciprocal space) i0_reciprocal20530000.0000
Solution quality estimate total_estimate0.8297
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.1 Å
Skewness Skewness skewness0.488
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8883000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.656; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.989
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)