3C-like proteinase nsp5
Severe acute respiratory syndrome coronavirus 2
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 3264–3569 | Not recorded | A1D70 (2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-carboxamide × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH6, 10% PEG6000, 3% DMSO | Resolution 1.57 Å R-free 0.221 |
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 8Z46 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 22DR Crystal structure of SARS-CoV-2 3CL protease in complex with compound 7c Deposited 2026-01-07 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1MDL 7-[(3~{R})-3-fluoranylpyrrolidin-1-yl]-5-methoxy-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidine-2,4-dione × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000
|
Resolution 1.90 Å R-free 0.249 |
| 23LY Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with leritrelvir Deposited 2026-02-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.56 Å R-free 0.197 |
| 23MB Crystal structure of SARS-CoV-2 main protease L50F/E166V mutant in complex with leritrelvir Deposited 2026-02-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.246 |
| 23MH Crystal structure of SARS-CoV-2 main protease T21I/E166V mutant in complex with leritrelvir Deposited 2026-02-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.229 |
| 28WF SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative ligand AD1 Deposited 2026-02-24 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1J0V [(2~{S},6~{R})-6-(6-aminopurin-9-yl)morpholin-2-yl]methanol × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 12% PEG 3350, 60 mM magnesium chloride
|
Resolution 1.70 Å R-free 0.278 |
| 6M5I Crystal structure of 2019-nCoV nsp7-nsp8c complex Deposited 2020-03-10 | 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
3860–3941（82 aa）
Chain B
3943–4140（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Magnesium formate dihydrate,15% PEG3350.
|
Resolution 2.50 Å R-free 0.292 |
| 6W9C The crystal structure of papain-like protease of SARS CoV-2 Deposited 2020-03-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1564–1878（315 aa）
Chain B
1564–1878（315 aa）
Chain C
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 4 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate, 10% PEG 8000
|
Resolution 2.70 Å R-free 0.279 |
| 6Y2G 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) Deposited 2020-02-15 | 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
3264–3566（303 aa）
Chain B
3264–3566（303 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.1 M buffer system 3 (1.0 M tris (base), bicine, pH 8.5), pH 8.5, 30% precipitant mix 1 (20% v/v PEG 500 methyl ether, 10% PEG 20,000))
|
Resolution 2.20 Å R-free 0.234 |
| 6YHU Crystal structure of the nsp7-nsp8 complex of SARS-CoV-2 Deposited 2020-03-31 | 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
3860–3930（71 aa）
Chain B
4018–4134（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Magnesium chlorid hexahydrate,
0.1 M Tris pH 8.5,
30% PEG 4000
|
Resolution 2.00 Å R-free 0.239 |
| 6YHU Crystal structure of the nsp7-nsp8 complex of SARS-CoV-2 Deposited 2020-03-31 | 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
3860–3930（71 aa）
Chain D
4018–4134（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Magnesium chlorid hexahydrate,
0.1 M Tris pH 8.5,
30% PEG 4000
|
Resolution 2.00 Å R-free 0.239 |
| 6YVA PLpro-C111S with mISG15 Deposited 2020-04-28 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG4450, 100 mM bis-tris propane pH 6.5, 200 mM Potassium thiocyanate
|
Resolution 3.18 Å R-free 0.290 |
| 6ZCT Nonstructural protein 10 (nsp10) from SARS CoV-2 Deposited 2020-06-12 | 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
4263–4384（122 aa）
|
Mutation：The first 3 residues (TMG) are cloning artefacts. | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5
3 M NaCl
|
Resolution 2.55 Å R-free 0.195 |
| 7BRO Crystal structure of the 2019-nCoV main protease Deposited 2020-03-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；291 K；7% PEG 6000, 100mM MES
|
Resolution 2.00 Å R-free 0.259 |
| 7BRP Crystal structure of the 2019-nCoV main protease complexed with Boceprevir Deposited 2020-03-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | U5G boceprevir (bound form) × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；20% PEG 5000, 0.1M BIS-TRIS
|
Resolution 1.80 Å R-free 0.240 |
| 7C33 Macro domain of SARS-CoV-2 in complex with ADP-ribose Deposited 2020-05-11 | 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
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 3.83 Å R-free 0.268 |
| 7C33 Macro domain of SARS-CoV-2 in complex with ADP-ribose Deposited 2020-05-11 | 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
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 3.83 Å R-free 0.268 |
| 7C33 Macro domain of SARS-CoV-2 in complex with ADP-ribose Deposited 2020-05-11 | 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
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 3.83 Å R-free 0.268 |
| 7C33 Macro domain of SARS-CoV-2 in complex with ADP-ribose Deposited 2020-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 3.83 Å R-free 0.268 |
| 7CZ4 Structure of SARS-CoV-2 macro domain in complex with ADP-ribose Deposited 2020-09-07 | 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
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 2.64 Å R-free 0.215 |
| 7CZ4 Structure of SARS-CoV-2 macro domain in complex with ADP-ribose Deposited 2020-09-07 | 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
1025–1195（171 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
|
Resolution 2.64 Å R-free 0.215 |
| 7D1O Crystal structure of SARS-Cov-2 main protease with narlaprevir Deposited 2020-09-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | NNA (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG5000, 0.1M BIS-TRIS (PH=6.5)
|
Resolution 1.78 Å R-free 0.248 |
| 7D3I Crystal structure of SARS-CoV-2 main protease in complex with MI-23 Deposited 2020-09-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | GQU (3~{S},3~{a}~{S},6~{a}~{R})-2-[3-[3,5-bis(fluoranyl)phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1% w/v n-octyl-beta-D-glucoside,
0.1 M sodium citrate tribasic dihydrate pH 5.5,
22% w/v PEG 3,350
|
Resolution 2.00 Å R-free 0.209 |
| 7D47 Crystal structure of SARS-CoV-2 Papain-like protease C111S Deposited 2020-09-22 | 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
1564–1880（317 aa）
|
Mutation：C111S | ZN ZINC ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；283 K；0.1M Tris 7 , 0.2M CaOAc, 18% PEG 8000
|
Resolution 1.97 Å R-free 0.197 |
| 7D47 Crystal structure of SARS-CoV-2 Papain-like protease C111S Deposited 2020-09-22 | 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
1564–1880（317 aa）
|
Mutation：C111S | ZN ZINC ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；283 K；0.1M Tris 7 , 0.2M CaOAc, 18% PEG 8000
|
Resolution 1.97 Å R-free 0.197 |
| 7D64 The crystal structure of SARS-CoV-2 3CLpro with Zinc Deposited 2020-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Mes pH 6.5, 15 % PEG20000
|
Resolution 2.45 Å R-free 0.265 |
| 7D6H Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant Deposited 2020-09-30 | 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
1563–1878（316 aa）
|
Mutation：C112S | ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；289 K；0.1 M acetate buffer pH 4.5, 0.8 M NaH2PO4/1.2M K2HPO4
|
Resolution 1.60 Å R-free 0.173 |
| 7DAT The crystal structure of COVID-19 main protease treated by AF Deposited 2020-10-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | AU GOLD ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；200mM KF and 15% PEG 3350
|
Resolution 2.75 Å R-free 0.228 |
| 7DAU The crystal structure of COVID-19 main protease treated by GA Deposited 2020-10-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | AU GOLD ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；200mM KF and 15% PEG 3350
|
Resolution 1.72 Å R-free 0.237 |
| 7DAV The native crystal structure of COVID-19 main protease Deposited 2020-10-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；200mM KF and 15% PEG 3350
|
Resolution 1.77 Å R-free 0.247 |
| 7DCD Nonstructural protein 7 and 8 complex of SARS-CoV-2 Deposited 2020-10-24 | 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
3860–3942（83 aa）
Chain B
4019–4140（122 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；200mM sodium chloride, 100mM Tris-HCl, pH 8.2, 25% PEG 3350
|
Resolution 2.57 Å R-free 0.353 |
| 7DCD Nonstructural protein 7 and 8 complex of SARS-CoV-2 Deposited 2020-10-24 | 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
3860–3942（83 aa）
Chain D
4019–4140（122 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；200mM sodium chloride, 100mM Tris-HCl, pH 8.2, 25% PEG 3350
|
Resolution 2.57 Å R-free 0.353 |
| 7DCD Nonstructural protein 7 and 8 complex of SARS-CoV-2 Deposited 2020-10-24 | 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 E
3860–3942（83 aa）
Chain F
4019–4140（122 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；200mM sodium chloride, 100mM Tris-HCl, pH 8.2, 25% PEG 3350
|
Resolution 2.57 Å R-free 0.353 |
| 7DCD Nonstructural protein 7 and 8 complex of SARS-CoV-2 Deposited 2020-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
3860–3942（83 aa）
Chain H
4019–4140（122 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；200mM sodium chloride, 100mM Tris-HCl, pH 8.2, 25% PEG 3350
|
Resolution 2.57 Å R-free 0.353 |
| 7DGB The co-crystal structure of SARS-CoV-2 main protease with (S)-2-cinnamamido-4-methyl-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)pentanamide Deposited 2020-11-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | EOF (2~{S})-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pentanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3% DMSO, 10% PEG 6000
|
Resolution 1.68 Å R-free 0.239 |
| 7DGF The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)hexanamide Deposited 2020-11-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | H60 (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3% DMSO, 10% PEG 6000
|
Resolution 1.64 Å R-free 0.218 |
| 7DGG The co-crystal structure of SARS-CoV-2 main protease with (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)hexanamide Deposited 2020-11-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | H63 (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3% DMSO, 10% PEG 6000
|
Resolution 2.00 Å R-free 0.217 |
| 7DGH The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)-2-naphthamide Deposited 2020-11-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | H6F ~{N}-[(2~{S})-3-methyl-1-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]naphthalene-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3%DMSO, 10% PEG 6000
|
Resolution 1.97 Å R-free 0.235 |
| 7DGI The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)-4-nitrobenzamide Deposited 2020-11-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | H6L ~{N}-[(2~{S})-3-methyl-1-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]-4-nitro-benzamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3% DMSO, 10% PEG 6000
|
Resolution 1.90 Å R-free 0.213 |
| 7DHJ The co-crystal structure of SARS-CoV-2 main protease with the peptidomimetic inhibitor (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)pent-4-ynamide Deposited 2020-11-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | H6R (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pent-4-ynamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1M MES (pH 6.0), 3% DMSO, 10% PEG 6000
|
Resolution 1.96 Å R-free 0.231 |
| 7DJR Crystal structure of SARS-CoV-2 main protease (no ligand) Deposited 2020-11-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.5；289 K；100mM MES, 5% DMSO, 15% PEG 4000
|
Resolution 1.45 Å R-free 0.201 |
| 7DK1 Crystal structure of Zinc bound SARS-CoV-2 main protease Deposited 2020-11-22 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | ZN ZINC ION × 3 DMS DIMETHYL SULFOXIDE × 3 GLY GLYCINE × 2 CL CHLORIDE ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；Bis-Tris (0.1 M), PEG 3350 (20%), DMSO (5%)
|
Resolution 1.90 Å R-free 0.209 |
| 7DPP SARS-CoV-2 3CL protease (3CLpro) in complex with myricetin Deposited 2020-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3564（301 aa）
|
Not recorded | MYC 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH6, 2%PEG6000, 3% DMSO
|
Resolution 2.10 Å R-free 0.220 |
| 7DPU SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-myricetin Deposited 2020-12-21 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | HER 7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH6, 20% PEG6000, 3% DMSO
|
Resolution 1.75 Å R-free 0.199 |
| 7DPV SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihydromyricetin Deposited 2020-12-21 | 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
3264–3569（306 aa）
Chain C
3264–3569（306 aa）
|
Not recorded | HF0 (2S,3S)-3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chroman-4-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100mM MES, pH6, 20% PEG6000, 3% DMSO
|
Resolution 2.35 Å R-free 0.234 |
| 7DPV SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihydromyricetin Deposited 2020-12-21 | 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
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Not recorded | HF0 (2S,3S)-3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chroman-4-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100mM MES, pH6, 20% PEG6000, 3% DMSO
|
Resolution 2.35 Å R-free 0.234 |
| 7EIN SARS-CoV-2 main proteinase complex with microbial metabolite leupeptin Deposited 2021-03-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 1500, 0.1 M BIS-TRIS, pH 6.5
|
Resolution 1.70 Å R-free 0.260 |
| 7EIZ Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading Deposited 2021-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.78 Å |
| 7EN8 Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04 Deposited 2021-04-16 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | J7R ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1.5% v/v Tacsimate pH 4.0, 0.1 M sodium acetate trihydrate pH 4.6, 20% w/v polyethylene glycol 3,350
|
Resolution 1.83 Å R-free 0.274 |
| 7EN9 Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-02 Deposited 2021-04-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | J7O 5-bromanyl-~{N}-methyl-3-nitro-2-[(4~{R},5~{S})-2-(7-oxidanylisoquinolin-4-yl)carbonyl-4-phenyl-2,7-diazaspiro[4.4]nonan-7-yl]benzamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.05 M citric acid, 0.05 M BIS-TRIS propane pH 5.0, 16% w/v polyethylene glycol 3,350
|
Resolution 1.90 Å R-free 0.232 |
| 7EXM The N-terminal crystal structure of SARS-CoV-2 NSP2 Deposited 2021-05-27 | 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
181–456（276 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG
|
Resolution 1.96 Å R-free 0.226 |
| 7EXM The N-terminal crystal structure of SARS-CoV-2 NSP2 Deposited 2021-05-27 | 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
181–456（276 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG
|
Resolution 1.96 Å R-free 0.226 |
| 7EXM The N-terminal crystal structure of SARS-CoV-2 NSP2 Deposited 2021-05-27 | 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
181–456（276 aa）
|
Not recorded | ZN ZINC ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG
|
Resolution 1.96 Å R-free 0.226 |
| 7EXM The N-terminal crystal structure of SARS-CoV-2 NSP2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
181–456（276 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG
|
Resolution 1.96 Å R-free 0.226 |
| 7FAY Crystal structure of SARS-CoV-2 main protease in complex with (R)-1a Deposited 2021-07-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 2XI (2~{R})-~{N}-[(1~{R})-2-(~{tert}-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-~{N}-(4-~{tert}-butylphenyl)-2-oxidanyl-propanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v PEG3350
|
Resolution 2.10 Å R-free 0.234 |
| 7FAZ Crystal structure of the SARS-CoV-2 main protease in complex with Y180 Deposited 2021-07-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 2RI (2~{R})-~{N}-dibenzofuran-3-yl-~{N}-[(1~{R})-2-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]-2-oxidanylidene-1-pyridin-3-yl-ethyl]-2-oxidanyl-propanamide × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v PEG4000
|
Resolution 2.10 Å R-free 0.243 |
| 7JIR The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor Deposited 2020-07-23 | 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
1564–1878（315 aa）
|
Mutation：C111S | TTT 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder457
|
Resolution 2.09 Å R-free 0.200 |
| 7JIT The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor Deposited 2020-07-23 | 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
1564–1878（315 aa）
|
Mutation：C111S | Y95 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder495
|
Resolution 1.95 Å R-free 0.190 |
| 7JIV The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder530 inhibitor Deposited 2020-07-23 | 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
1564–1878（315 aa）
|
Mutation：C111S | VBY 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 3 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder530
|
Resolution 2.05 Å R-free 0.201 |
| 7JIW The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor Deposited 2020-07-23 | 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
1564–1878（315 aa）
|
Not recorded | VBY 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder530
|
Resolution 2.30 Å R-free 0.239 |
| 7JN2 The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441 inhibitor Deposited 2020-08-03 | 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
1564–1878（315 aa）
|
Not recorded | Y41 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 5 CL CHLORIDE ION × 4 ACT ACETATE ION × 1 UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000
|
Resolution 1.93 Å R-free 0.209 |
| 7JRN Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617 Deposited 2020-08-12 | 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
1564–1878（315 aa）
|
Not recorded | TTT 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30 % PEG 4,000
0.2 M Li2SO4
0.1 M Tris pH 8.5
|
Resolution 2.48 Å R-free 0.287 |
| 7JRN Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617 Deposited 2020-08-12 | 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 J
1564–1878（315 aa）
|
Not recorded | TTT 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30 % PEG 4,000
0.2 M Li2SO4
0.1 M Tris pH 8.5
|
Resolution 2.48 Å R-free 0.287 |
| 7KOJ The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494 inhibitor Deposited 2020-11-09 | 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
1564–1878（315 aa）
|
Mutation：C111S | Y94 2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 2 UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder494
|
Resolution 2.02 Å R-free 0.203 |
| 7KOK The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496 inhibitor Deposited 2020-11-09 | 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
1564–1878（315 aa）
|
Mutation：C111S | Y96 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 3 ACT ACETATE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 UNX UNKNOWN LIGAND × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder496
|
Resolution 2.00 Å R-free 0.211 |
| 7KOL The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496 inhibitor Deposited 2020-11-09 | 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
1564–1878（315 aa）
|
Not recorded | Y96 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder496
|
Resolution 2.58 Å R-free 0.206 |
| 7KRX The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441 inhibitor Deposited 2020-11-20 | 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
1564–1878（315 aa）
|
Mutation：C111S | Y41 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 2 ACT ACETATE ION × 2 UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES buffer pH 6.0, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder441
|
Resolution 2.72 Å R-free 0.249 |
| 7LBR SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89 Deposited 2021-01-08 | 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
1564–1878（315 aa）
Fragment：residues 1564-1878
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 XT7 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1S,3R)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.02M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.20 Å R-free 0.241 |
| 7LBR SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89 Deposited 2021-01-08 | 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
1564–1878（315 aa）
Fragment：residues 1564-1878
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 XT7 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1S,3R)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.02M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.20 Å R-free 0.241 |
| 7LBS SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24 Deposited 2021-01-08 | 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
1564–1878（315 aa）
Fragment：residues 1564-1878
|
Not recorded | XR8 5-[(azetidin-3-yl)amino]-2-methyl-N-[(1R)-1-(3-{5-[(pyrrolidin-1-yl)methyl]thiophen-2-yl}phenyl)ethyl]benzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 2 BO3 BORIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.80 Å R-free 0.260 |
| 7LBS SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24 Deposited 2021-01-08 | 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
1564–1878（315 aa）
Fragment：residues 1564-1878
|
Not recorded | XR8 5-[(azetidin-3-yl)amino]-2-methyl-N-[(1R)-1-(3-{5-[(pyrrolidin-1-yl)methyl]thiophen-2-yl}phenyl)ethyl]benzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 2 BO3 BORIC ACID × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.80 Å R-free 0.260 |
| 7LLF SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83 Deposited 2021-02-03 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 BO3 BORIC ACID × 2 Y54 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1R,3S)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.30 Å R-free 0.260 |
| 7LLF SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83 Deposited 2021-02-03 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 Y54 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1R,3S)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.30 Å R-free 0.260 |
| 7LLZ SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-69 Deposited 2021-02-04 | 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
1564–1878（315 aa）
|
Not recorded | Y61 N-[(1R)-1-(3-{5-[(acetylamino)methyl]thiophen-2-yl}phenyl)ethyl]-5-[(azetidin-3-yl)amino]-2-methylbenzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1M MIB buffer pH 6.5, 0.2 M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.90 Å R-free 0.243 |
| 7LLZ SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-69 Deposited 2021-02-04 | 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
1564–1878（315 aa）
|
Not recorded | Y61 N-[(1R)-1-(3-{5-[(acetylamino)methyl]thiophen-2-yl}phenyl)ethyl]-5-[(azetidin-3-yl)amino]-2-methylbenzamide × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1M MIB buffer pH 6.5, 0.2 M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.90 Å R-free 0.243 |
| 7LOS SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65 Deposited 2021-02-10 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 Y97 5-(azetidin-3-ylamino)-2-methyl-~{N}-[(1~{R})-1-[3-[5-[[[(3~{R})-oxolan-3-yl]amino]methyl]thiophen-2-yl]phenyl]ethyl]benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.2 M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.90 Å R-free 0.293 |
| 7LOS SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65 Deposited 2021-02-10 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 Y97 5-(azetidin-3-ylamino)-2-methyl-~{N}-[(1~{R})-1-[3-[5-[[[(3~{R})-oxolan-3-yl]amino]methyl]thiophen-2-yl]phenyl]ethyl]benzamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MIB buffer pH 6.5, 0.2 M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
|
Resolution 2.90 Å R-free 0.293 |
| 7M1Y The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen Deposited 2021-03-15 | 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
1564–1878（315 aa）
|
Mutation：C111S | 9JT N-phenyl-2-selanylbenzamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 IOD IODIDE ION × 6 FMT FORMIC ACID × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris-Cl, pH 8.5, 3.5 M sodium formate, 0.1 M sodium iodide, 4 mM ebselen
|
Resolution 2.02 Å R-free 0.213 |
| 7M1Y The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen Deposited 2021-03-15 | 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
1564–1878（315 aa）
|
Mutation：C111S | 9JT N-phenyl-2-selanylbenzamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 IOD IODIDE ION × 7 FMT FORMIC ACID × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris-Cl, pH 8.5, 3.5 M sodium formate, 0.1 M sodium iodide, 4 mM ebselen
|
Resolution 2.02 Å R-free 0.213 |
| 7NFV Structure of SARS-CoV-2 Papain-like protease PLpro Deposited 2021-02-07 | 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 AAA
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；1.0M NaH2PO4/1.0MKH2PO4
100mM Tris_HCl pH=7.5
|
Resolution 1.42 Å R-free 0.171 |
| 7NT1 Crystal structure of SARS CoV2 main protease in complex with FSP007 Deposited 2021-03-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 6 UQW [(2R)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxidanylidene-butan-2-yl] prop-2-enoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock FSP007 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
|
Resolution 2.85 Å R-free 0.278 |
| 7NT2 Crystal structure of SARS CoV2 main protease in complex with FSP006 Deposited 2021-03-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 6 CL CHLORIDE ION × 1 URK [(1S)-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock FSP006 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
|
Resolution 2.15 Å R-free 0.251 |
| 7NT3 Crystal structure of SARS CoV2 main protease in complex with FSCU015 Deposited 2021-03-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 4 UQZ ~{N}-[(1~{S})-2-(1,3-benzodioxol-5-ylmethylamino)-1-(3-hydroxyphenyl)-2-oxidanylidene-ethyl]-~{N}-propyl-prop-2-enamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock FSP006 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM FSCU015 by adding the stock to crystallisation drops in
a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
|
Resolution 2.33 Å R-free 0.271 |
| 7NTQ Crystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide Deposited 2021-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 35J N-(pyridin-3-ylmethyl)thioformamide × 2 NA SODIUM ION × 6 FMT FORMIC ACID × 14 DMS DIMETHYL SULFOXIDE × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M NaFormate, 20% PEG 3350, 10% Glycerol, 10% DMSO
|
Resolution 1.50 Å R-free 0.213 |
| 7NTT Crystal structure of the SARS-CoV-2 Main Protease Deposited 2021-03-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | NA SODIUM ION × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol
|
Resolution 1.74 Å R-free 0.255 |
| 7NTV Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map) Deposited 2021-03-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 7 US8 2-acetamido-N-cyclopropyl-5-phenyl-thiophene-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock DN_EG_002 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
|
Resolution 2.06 Å R-free 0.228 |
| 7NTW Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the active site Deposited 2021-03-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | NA SODIUM ION × 6 DMS DIMETHYL SULFOXIDE × 4 FMT FORMIC ACID × 10 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol
|
Resolution 1.81 Å R-free 0.257 |
| 7NUK Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map) Deposited 2021-03-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 4 USH 2-[2-chloranylethanoyl(propyl)amino]-~{N}-(2-methoxyphenyl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock EG009 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM EG009 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
|
Resolution 2.19 Å R-free 0.261 |
| 7NW2 Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-47 Deposited 2021-03-16 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | USZ ~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{R})-2-[2-(3-fluorophenyl)ethylamino]-2-oxidanylidene-1-pyridin-3-yl-ethyl]propanamide × 1 DMS DIMETHYL SULFOXIDE × 9 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；11% PEG 4K, 5% DMSO, 0.1M MES pH 6.5
|
Resolution 2.10 Å R-free 0.224 |
| 7NWX SARS-COV2 NSP5 in the presence of Zn2+ Deposited 2021-03-17 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 20% PEG 3350, 1.5 mM zinc chloride
|
Resolution 1.80 Å R-free 0.244 |
| 7NXH Structure of SARS-CoV2 NSP5 (3C-like proteinase) determined in-house Deposited 2021-03-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium phosphate, 20% PEG 3350, 1.5 mM zinc chloride
|
Resolution 2.10 Å R-free 0.268 |
| 7OFS Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 4-(2-hydroxyethyl)phenol Deposited 2021-05-05 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 3 YRL 4-(2-hydroxyethyl)phenol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.
|
Resolution 1.90 Å R-free 0.214 |
| 7OFT Structure of SARS-CoV-2 Papain-like protease PLpro in complex with p-hydroxybenzaldehyde Deposited 2021-05-05 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 8 HBA P-HYDROXYBENZALDEHYDE × 1 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.
|
Resolution 1.95 Å R-free 0.211 |
| 7OFU Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester Deposited 2021-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
1564–1878（315 aa）
|
Not recorded | HE9 methyl 3,4-bis(oxidanyl)benzoate × 2 GOL GLYCEROL × 4 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 8 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.
|
Resolution 1.72 Å R-free 0.202 |
| 7P51 CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH FRAGMENT F01 Deposited 2021-07-13 | 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
3264–3569（306 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 4 DMS DIMETHYL SULFOXIDE × 4 5P9 N-(5-chloropyridin-2-yl)-3-oxo-2,3-dihydro-1H-indene-1-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M NaFORMATE, 20% PEG 3350, 10%
GLYCEROL, 5% DMSO
|
Resolution 1.47 Å R-free 0.216 |
| 7QCG Structure of SARS-CoV-2 Papain-like Protease bound to N-(2-pyrrolidyl)-3,4,5-trihydroxybenzoylhydrazone Deposited 2021-11-23 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DZI 3,4,5-tris(oxidanyl)-N-[(E)-1H-pyrrol-2-ylmethylideneamino]benzamide × 1 GOL GLYCEROL × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.75 Å R-free 0.198 |
| 7QCH Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,5-dimethoxy-4-hydroxybenzyliden)thiosemicarbazone Deposited 2021-11-24 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A5I N-(3,5-dimetoxy-4-hydroxybenzyliden)thiosemicarbazone × 1 GOL GLYCEROL × 2 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.88 Å R-free 0.235 |
| 7QCI Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,4-dihydroxybenzylidene)-thiosemicarbazone Deposited 2021-11-24 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A6Q N-(3,4-dihydroxybenzylidene)-thiosemicarbazone × 1 GOL GLYCEROL × 2 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.76 Å R-free 0.214 |
| 7QCJ Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,4-dihydroxybenzylidene)-thiosemicarbazone Deposited 2021-11-24 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 5 A4O N-(2,4-dihydroxybenzylidene)-thiosemicarbazone × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 3 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.84 Å R-free 0.198 |
| 7QCK Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,5-dihydroxybenzylidene)-thiosemicarbazone Deposited 2021-11-24 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A7L N-(2,5-dihydroxybenzylidene)-thiosemicarbazone × 1 GOL GLYCEROL × 3 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.92 Å R-free 0.224 |
| 7QCM Structure of SARS-CoV-2 Papain-like Protease bound to N-(3-methoxy-4-hydroxy-acetophenone)thiosemicarbazone Deposited 2021-11-24 | 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
1564–1878（315 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A3X N-(3-metoxy-4-hydroxy-acetophenone)thiosemicarbazone × 1 GOL GLYCEROL × 5 ZN ZINC ION × 1 CL CHLORIDE ION × 3 PO4 PHOSPHATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate
|
Resolution 1.77 Å R-free 0.206 |
| 7QL8 SARS-COV2 Main Protease in complex with inhibitor MG78 Deposited 2021-12-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3564（301 aa）
|
Not recorded | I70 (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；MMT, PEG 1500
|
Resolution 1.81 Å R-free 0.300 |
| 7RBR The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2021-07-06 | Different construct Different mutation/modification 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
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.2 M di-sodium tartrate, 20% PEG-3350,
|
Resolution 1.88 Å R-free 0.228 |
| 7RBS The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 Deposited 2021-07-06 | Different construct Different mutation/modification 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
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
|
Resolution 2.98 Å R-free 0.236 |
| 7RBS The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
|
Resolution 2.98 Å R-free 0.236 |
| 7RBS The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
|
Resolution 2.98 Å R-free 0.236 |
| 7RBS The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
|
Resolution 2.98 Å R-free 0.236 |
| 7RBS The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
1564–1878（315 aa）
|
Mutation：C111S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
|
Resolution 2.98 Å R-free 0.236 |
| 7RZC Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 inhibitor Deposited 2021-08-27 | 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
1564–1878（315 aa）
|
Not recorded | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M magnesium acetate, 20% PEG3350
|
Resolution 2.04 Å R-free 0.212 |
| 7RZC Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 inhibitor Deposited 2021-08-27 | 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
1564–1878（315 aa）
|
Not recorded | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M magnesium acetate, 20% PEG3350
|
Resolution 2.04 Å R-free 0.212 |
| 7RZC Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 inhibitor Deposited 2021-08-27 | 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
1564–1878（315 aa）
|
Not recorded | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M magnesium acetate, 20% PEG3350
|
Resolution 2.04 Å R-free 0.212 |
| 7SDR Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 Inhibitor Deposited 2021-09-29 | 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
1564–1878（315 aa）
|
Not recorded | JW9 4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium citrate, 20% PEG 3350
|
Resolution 2.72 Å R-free 0.212 |
| 7SDR Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 Inhibitor Deposited 2021-09-29 | 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
1564–1878（315 aa）
|
Not recorded | JW9 4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium citrate, 20% PEG 3350
|
Resolution 2.72 Å R-free 0.212 |
| 7SDR Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 Inhibitor Deposited 2021-09-29 | 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
1564–1878（315 aa）
|
Not recorded | JW9 4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium citrate, 20% PEG 3350
|
Resolution 2.72 Å R-free 0.212 |
| 7SGU Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor Deposited 2021-10-07 | 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
1564–1878（315 aa）
|
Mutation：C111S | 9EI 5-amino-N-(naphthalen-1-yl)pyridine-3-carboxamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.1 M sodium acetate pH 4.5, 2 M sodium formate, 4 mM PLP_Snyder608
|
Resolution 1.79 Å R-free 0.188 |
| 7SGV Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor Deposited 2021-10-07 | 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
1564–1878（315 aa）
|
Mutation：C111S | L30 N-(naphthalen-1-yl)pyridine-3-carboxamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；3 M sodium chloride, 0.1 M Bis_tris buffer, pH 5.5
|
Resolution 2.00 Å R-free 0.207 |
| 7SGW Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor Deposited 2021-10-07 | 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
1564–1878（315 aa）
|
Not recorded | L30 N-(naphthalen-1-yl)pyridine-3-carboxamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis_tris propane, pH 7.0, 2.5 M ammonium sulfate, 4 mM PLP_Snyder630
|
Resolution 1.95 Å R-free 0.207 |
| 7SQE Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor Deposited 2021-11-05 | 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
1564–1878（315 aa）
|
Mutation：C111S | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium citrate, 20% PEG3350
|
Resolution 2.00 Å R-free 0.205 |
| 7SQE Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor Deposited 2021-11-05 | 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
1564–1878（315 aa）
|
Mutation：C111S | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium citrate, 20% PEG3350
|
Resolution 2.00 Å R-free 0.205 |
| 7SQE Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor Deposited 2021-11-05 | Different construct Different mutation/modification 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
1564–1878（315 aa）
|
Mutation：C111S | JWX (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium citrate, 20% PEG3350
|
Resolution 2.00 Å R-free 0.205 |
| 7TIA Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-14 Deposited 2022-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | XTP benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate × 2 SCN THIOCYANATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 1.64 Å R-free 0.191 |
| 7TIU Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB46 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | V46 (1S,2S)-2-[(N-{[(3-chlorophenyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 1.65 Å R-free 0.196 |
| 7TIV Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB48 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | W48 (1S,2S)-2-[(N-{[(3-chlorophenyl)methoxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 2.08 Å R-free 0.216 |
| 7TIW Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB54 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | I54 (1S,2S)-2-[(N-{[(2-chlorophenyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 1.68 Å R-free 0.199 |
| 7TIX Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB56 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | Q56 N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 2.00 Å R-free 0.215 |
| 7TIY Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-48 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | Y48 (1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[(N-{[(2,4,5-trifluorophenyl)methoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid × 2 PO4 PHOSPHATE ION × 4 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6；277 K；0.1 M sodium phosphate-monobasic, 0.1 M MES, and 20% (w/v) PEG 4000
|
Resolution 1.79 Å R-free 0.195 |
| 7TIZ Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-63 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | N63 (1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[3-(trifluoromethyl)phenyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid × 2 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2 SCN THIOCYANATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 1.55 Å R-free 0.191 |
| 7TJ0 Crystal structure of SARS-CoV-2 3CL in complex with inhibitor SL-4-241 Deposited 2022-01-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | S4L (1S,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5；277 K；0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000
|
Resolution 2.17 Å R-free 0.217 |
| 7TLL Structure of SARS-CoV-2 Mpro Omicron P132H in complex with Nirmatrelvir (PF-07321332) Deposited 2022-01-18 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：P132H Mutation：P132H | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20% w/v polyethylene glycol (PEG) 3350 and 0.12 M sodium sulfate
|
Resolution 1.63 Å R-free 0.250 |
| 7TOB Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376 Deposited 2022-01-24 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | K36 (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 PEG DI(HYDROXYETHYL)ETHER × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M KNO3
|
Resolution 2.05 Å R-free 0.213 |
| 7TUU Structure of the SARS-CoV-2 main protease in complex with halicin Deposited 2022-02-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | U88 5-nitro-1,3-thiazole × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium phosphate dibasic, 17% w/v PEG3350, pH8.0
|
Resolution 1.85 Å R-free 0.272 |
| 7TVS The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with demethylated analog of masitinib Deposited 2022-02-05 | 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
3264–3569（306 aa）
|
Mutation：P132H | XNJ N-(4-methyl-3-{[4-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}phenyl)-4-[(piperazin-1-yl)methyl]benzamide × 2 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；286 K；0.1 M HEPES: NaOH, 20 % (w/v) PEG 10000
|
Resolution 1.89 Å R-free 0.225 |
| 7TVX The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with masitinib Deposited 2022-02-06 | 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
3264–3569（306 aa）
|
Mutation：P132H | G65 Masitinib × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；286 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris: HCl, 10 % (w/v) PEG 8000
|
Resolution 2.09 Å R-free 0.212 |
| 7TZJ SARS CoV-2 PLpro in complex with inhibitor 3k Deposited 2022-02-15 | 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
1564–1878（315 aa）
|
Mutation：C111S | S88 N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide × 1 ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.46；281 K；0.117 M Zinc acetate
21.6% PEG 8000
0.1 M bis-tris chloride (pH 5.46)
|
Resolution 2.66 Å R-free 0.257 |
| 7TZJ SARS CoV-2 PLpro in complex with inhibitor 3k Deposited 2022-02-15 | 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
1564–1878（315 aa）
|
Mutation：C111S | S88 N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide × 1 ZN ZINC ION × 5 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.46；281 K；0.117 M Zinc acetate
21.6% PEG 8000
0.1 M bis-tris chloride (pH 5.46)
|
Resolution 2.66 Å R-free 0.257 |
| 7U28 Structure of SARS-CoV-2 Mpro Lambda (G15S) in complex with Nirmatrelvir (PF-07321332) Deposited 2022-02-23 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：G15S Mutation：G15S | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；24.0 %w/v PEG 3350 and 0.2 M sodium sulfate decahydrate
|
Resolution 1.68 Å R-free 0.248 |
| 7U29 Structure of SARS-CoV-2 Mpro mutant (K90R) in complex with Nirmatrelvir (PF-07321332) Deposited 2022-02-23 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：K90R Mutation：K90R | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；20.0 %w/v PEG 3350 and 0.2071428571 M sodium sulfate decahydrate
|
Resolution 2.09 Å R-free 0.266 |
| 7UJ9 Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-199) Deposited 2022-03-30 | 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
3264–3462（199 aa）
Fragment：catalytic domain (MPro1-199)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；283 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 2.25 Å R-free 0.250 |
| 7UJ9 Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-199) Deposited 2022-03-30 | 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 C
3264–3462（199 aa）
Fragment：catalytic domain (MPro1-199)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；283 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 2.25 Å R-free 0.250 |
| 7UJG Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with GC-376 Deposited 2022-03-30 | 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
3268–3458（191 aa）
Fragment：catalytic domain (MPro1-196)
|
Not recorded | K36 (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 1.80 Å R-free 0.179 |
| 7UJG Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with GC-376 Deposited 2022-03-30 | 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
3268–3458（191 aa）
Fragment：catalytic domain (MPro1-196)
|
Not recorded | K36 (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 1.80 Å R-free 0.179 |
| 7UJU Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with nirmatrelvir Deposited 2022-03-31 | 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
3264–3459（196 aa）
Fragment：catalytic domain (MPro1-196)
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 1.85 Å R-free 0.174 |
| 7UJU Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with nirmatrelvir Deposited 2022-03-31 | 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
3264–3459（196 aa）
Fragment：catalytic domain (MPro1-196)
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
|
Resolution 1.85 Å R-free 0.174 |
| 7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 | Different construct Different mutation/modification 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
1564–1878（315 aa）
|
Mutation：C111S, D286N | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
|
Resolution 1.45 Å R-free 0.179 |
| 7V1T A dual Inhibitor Against Main Protease Deposited 2021-08-06 | 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
3264–3569（306 aa）
|
Not recorded | 5IL 5,8-bis(oxidanylidene)-7-[(2-piperazin-1-ylphenyl)amino]naphthalene-1-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；289 K；0.1M BIS-TRIS pH 6.5, 20% PEG 1500
|
Resolution 2.56 Å R-free 0.245 |
| 7V7M crystal structure of SARS-CoV-2 3CL protease Deposited 2021-08-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.05 Sodium citrate tribasic dihydrate, 0.12 M Potassium chloride, 0.08 M Bis-Tris, 14% PEG 4000
|
Resolution 2.08 Å R-free 0.292 |
| 7VFA the complex of SARS-CoV2 3CL and NB1A2 Deposited 2021-09-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
3264–3569（306 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG6000, potassium phosphate
|
Resolution 1.75 Å R-free 0.225 |
| 7VFB the complex of SARS-CoV2 3cl and NB2B4 Deposited 2021-09-11 | 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
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG6000, potassium phosphate
|
Resolution 2.00 Å R-free 0.264 |
| 7VH8 Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332 Deposited 2021-09-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.59 Å R-free 0.205 |
| 7VIC The crystal structure of SARS-CoV-2 3C-like protease in complex with a traditional Chinese Medicine Inhibitors Deposited 2021-09-26 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | ODN (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；100 mM MES, pH6, 12% PEG 6000, 0.5% DMSO
|
Resolution 2.10 Å R-free 0.242 |
| 7VJW Crystal Structure of SARS-CoV-2 Mpro at 2.20 A resolution-10 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris, PEG 4000
|
Resolution 2.20 Å R-free 0.281 |
| 7VJX Crystal Structure of SARS-CoV-2 Mpro at 2.20 A resolution-12 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris, 30% w/v PEG 4000
|
Resolution 2.20 Å R-free 0.287 |
| 7VJY Crystal Structure of Sars-Cov-2 Mpro at 1.90 A resolution-1 Deposited 2021-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6；294 K；0.1 M MMT, 25% w/v PEG 1500
|
Resolution 1.90 Å R-free 0.278 |
| 7VJZ Crystal Structure of SARS-CoV-2 Mpro at 1.90 A resolution-7 Deposited 2021-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6；294 K；0.1M MMT, 25% w/v PEG 1500
|
Resolution 1.90 Å R-free 0.250 |
| 7VK0 Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-6 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris, 30 % w/v PEG 4000
|
Resolution 2.10 Å R-free 0.242 |
| 7VK1 Crystal Structure of SARS-CoV-2 Mpro at 1.93 A resolution-5 Deposited 2021-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6；294 K；0.1M MMT, 25% w/v PEG 1500
|
Resolution 1.93 Å R-free 0.265 |
| 7VK2 Crystal Structure of SARS-CoV-2 Mpro at 2.0 A resolution -9 Deposited 2021-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6；294 K；0.1M MMT, 25% w/v PEG 1500
|
Resolution 2.00 Å R-free 0.275 |
| 7VK3 Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-2 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris, 30% w/v PEG 4000
|
Resolution 2.10 Å R-free 0.278 |
| 7VK4 Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-3 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris, 30% w/v PEG 4000
|
Resolution 2.10 Å R-free 0.266 |
| 7VK5 Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-8 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris 8.5, 30% w/v PEG 4000
|
Resolution 2.17 Å R-free 0.270 |
| 7VK6 Crystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris 8.5, 30% w/v PEG 4000
|
Resolution 2.25 Å R-free 0.266 |
| 7VK7 Crystal Structure of SARS-CoV-2 Mpro at 2.4 A resolution-11 Deposited 2021-09-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8.5；294 K；0.2M Sodium acetate trihydrate, 0.1M Tris 8.5, 30% w/v PEG 4000
|
Resolution 2.40 Å R-free 0.239 |
| 7VK8 Crystal structure of SARS-CoV-2 Mpro at 2.4 A Resolution Deposited 2021-09-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6；294 K；0.1M MMT, 25% w/v PEG 1500
|
Resolution 2.40 Å R-free 0.329 |
| 7VLP Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P1211 Deposited 2021-10-05 | 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
3265–3569（305 aa）
Chain B
3265–3569（305 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.50 Å R-free 0.219 |
| 7VLQ Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P212121 Deposited 2021-10-05 | 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
3266–3565（300 aa）
Chain B
3266–3565（300 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.94 Å R-free 0.228 |
| 7VTH The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1 Deposited 2021-10-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 7XB 2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium citrate tribasic pH 7.0, 20% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.257 |
| 7VU6 The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3 Deposited 2021-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
|
Resolution 1.80 Å R-free 0.279 |
| 7VVT SARS-CoV-2 3CL protease (3CLpro) in complex with a covalent inhibitor Deposited 2021-11-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 80X N-(3-chlorophenyl)-2-[(2R)-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6, 15% PEG6000, 3% DMSO
|
Resolution 2.51 Å R-free 0.253 |
| 7W9G Complex structure of Mpro with ebselen-derivative inhibitor Deposited 2021-12-09 | 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
3264–3569（306 aa）
|
Not recorded | SE SELENIUM ATOM × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG20000, MES
|
Resolution 2.50 Å R-free 0.247 |
| 7WO1 Discovery of SARS-CoV-2 3CLpro peptidomimetic inhibitors through H41-specific protein-ligand interactions Deposited 2022-01-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 3XI N-[(2S)-3-methyl-1-[[(2S)-4-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]cyclohexanecarboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；100 mM MES (pH 6.0), 3% DMSO, 1 mM DTT, 6% polyethylene glycol (PEG) 6000
|
Resolution 2.15 Å R-free 0.223 |
| 7WO2 SARS-CoV-2 3CLPro Peptidomimetic Inhibitor TPM5 Deposited 2022-01-20 | 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
3264–3569（306 aa）
|
Not recorded | 40I N-[(2S)-3-methyl-1-[[(2S)-4-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanylidene-3-[(3S}-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]furan-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；100 mM MES (pH 6.0), 3% DMSO, 1 mM DTT and 5% polyethylene glycol (PEG) 6000
|
Resolution 1.96 Å R-free 0.217 |
| 7WO3 SARS-CoV-2 3CLpro Deposited 2022-01-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 59S (2S)-2-[[(2S)-2-[[(E)-3-(4-methoxyphenyl)prop-2-enoyl]amino]-3-methyl-butanoyl]amino]-4-methyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]pentanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；100 mM MES (pH 6.0), 3% DMSO, 1 mM DTT and 6% polyethylene glycol (PEG) 6000
|
Resolution 2.01 Å R-free 0.243 |
| 7WOF SARS-CoV-2 3CLpro Deposited 2022-01-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 5IZ (2S,3S)-3-methyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；290 K；100 mM MES (pH 6.0), 3% DMSO, 1 mM DTT, 6% polyethylene glycol (PEG) 6000
|
Resolution 1.72 Å R-free 0.204 |
| 7WQB SARS-CoV-2 main protease mutant (P168A) in complex with MG-132 Deposited 2022-01-25 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | ALD N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MMT (Malic acid, MES, Tris) buffer pH 6.0, 25 % w/v PEG 1500
|
Resolution 1.87 Å R-free 0.228 |
| 7WYM Structure of the SARS-COV-2 main protease with 337 inhibitor Deposited 2022-02-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | G7L N-methyl-N-[[4-(trifluoromethyl)-1,3-thiazol-2-yl]methyl]prop-2-enamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；296 K；0.16 M Ammonium acetate, 23% PEG 3350, 0.1 M BIS-TRIS pH 6.9
|
Resolution 2.05 Å R-free 0.221 |
| 7WYP Structure of the SARS-COV-2 main protease with EN102 inhibitor Deposited 2022-02-16 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | G7O N-(1,3-benzothiazol-2-ylmethyl)-N-cyclopropyl-prop-2-enamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；0.1M HEPES SODIUM pH 7.5, 6% 2-Propanol, 16% PEG 4000
|
Resolution 2.30 Å R-free 0.273 |
| 7WZO Crystal structure of the SARS-CoV-2 nucleocapsid protein N-terminal domain in complex with Ubl1 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
819–929（111 aa）
Fragment：ubiquitin-like domain 1
Chain C
819–929（111 aa）
Fragment：ubiquitin-like domain 1
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG 8000
|
Resolution 2.64 Å R-free 0.247 |
| 7X6J SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3af Deposited 2022-03-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | QNC quinoline-2-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 5.5-6.5, 5-25% PEG6000, 3% DMSO
|
Resolution 1.50 Å R-free 0.204 |
| 7X6K SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3w Deposited 2022-03-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 9FF 1H-indole-2-carbaldehyde × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 5.5-6.5, 5-25% PEG6000, 3% DMSO
|
Resolution 2.34 Å R-free 0.270 |
| 7XAR Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor Deposited 2022-03-18 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | NI NICKEL (II) ION × 5 CL CHLORIDE ION × 2 BOV 4-fluoranyl-~{N}-[(2~{S})-1-[2-(2-fluoranylethanoyl)-2-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]hydrazinyl]-4-methyl-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；8 mM Nickel chloride
80 mM TRIS (pH 8.5)
16% PEG-MME 2,000
20% Glycerol
|
Resolution 1.60 Å R-free 0.206 |
| 7XB3 Crystal structure of SARS-Cov-2 main protease D48N mutant Deposited 2022-03-20 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：D48N Mutation：D48N | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 2.08 Å R-free 0.242 |
| 7XB4 Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332 Deposited 2022-03-20 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：D48N Mutation：D48N | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 2.07 Å R-free 0.240 |
| 7XC3 Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique domain-M) Deposited 2022-03-22 | 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
1369–1491（123 aa）
Chain B
1369–1491（123 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；3.5 M sodium formate, pH 6.8
|
Resolution 1.70 Å R-free 0.218 |
| 7XC4 Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique domain-M) in complex with Oxaprozin Deposited 2022-03-22 | 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
1369–1493（125 aa）
Chain B
1369–1493（125 aa）
|
Not recorded | BJ6 3-(4,5-diphenyl-1,3-oxazol-2-yl)propanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；3.5 M sodium formate, pH 6.8, soaking the free-form crystals in 5 mM Oxaprozin buffer (50 mM molecule liquor in DMSO was diluted with the reservoir buffer)
|
Resolution 2.10 Å R-free 0.214 |
| 7XQ6 The complex structure of mutant Mpro with inhibitor Deposited 2022-05-06 | 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
3264–3569（306 aa）
|
Mutation：H41N | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；Ammonium chloride, MES pH6.5, PEG 6000
|
Resolution 2.00 Å R-free 0.233 |
| 7XQ7 The complex structure of WT-Mpro Deposited 2022-05-06 | 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
3264–3569（306 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；MESpH6.5, PEG6000
|
Resolution 2.35 Å R-free 0.238 |
| 7XRS Crystal structure of SARS-Cov-2 main protease in complex with inhibitor YH-53 Deposited 2022-05-11 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | HUR N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.93 Å R-free 0.243 |
| 7YBG Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant) Deposited 2022-06-29 | 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
1564–1877（314 aa）
|
Mutation：C111S | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 MLA MALONIC ACID × 1 ZN ZINC ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；1.4 M sodium malonate dibasic monohydrate
|
Resolution 1.90 Å R-free 0.206 |
| 7Z0P SARS-COV2 Main Protease in complex with inhibitor MG-131 Deposited 2022-02-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3567（304 aa）
|
Not recorded | I8H (1~{R},2~{S},5~{S})-3-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-~{N}-[(2~{S},3~{R})-4-(methylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1 M MMT, pH 9.0 plus 25% w/v polyethylenglycol 1500
|
Resolution 2.52 Å R-free 0.290 |
| 7Z4S Crystal structure of SARS-CoV-2 Mpro in complex with cyclic peptide GM4 including unnatural amino acids. Deposited 2022-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | PEG DI(HYDROXYETHYL)ETHER × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. GM4 was diluted into the protein solution to a final concentration of 10 mM and allowed to incubate for two hours at room temperature prior to dispensing plates. The drop composition was 0.15 ul protein ligand solution, 0.3 ul 11% (v/v) PEG 4K, 0.1 M MES pH 6.5, and 0.05 ul Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5, and vortexing for 60 s with approximately 10 glass beads (1.0 mm diameter, BioSpec products). Reservoir solution was 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 C and appeared within 24 hours, reaching full size within 36 hours. Crystals were looped after one week.
|
Resolution 1.70 Å R-free 0.234 |
| 8AJ1 SARS-CoV-2 Mpro in Complex with RK-107 Deposited 2022-07-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3567（304 aa）
|
Not recorded | A1IMU (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(phenylcarbamoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M PCTP pH7.0, 25% w/vPEG 1500
|
Resolution 2.60 Å R-free 0.275 |
| 8AZC Structure of SARS-CoV-2 NSP3 macrodomain in the apo form Deposited 2022-09-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1024–1197（174 aa）
|
Not recorded | CL CHLORIDE ION × 2 MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 0.93 Å R-free 0.153 |
| 8AZD Structure of SARS-CoV-2 NSP3 macrodomain in complex with ADPR Deposited 2022-09-05 | 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
1024–1197（174 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.00 Å R-free 0.250 |
| 8AZD Structure of SARS-CoV-2 NSP3 macrodomain in complex with ADPR Deposited 2022-09-05 | 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
1024–1197（174 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.00 Å R-free 0.250 |
| 8AZI Structure of SARS-CoV-2 NSP3 macrodomain in complex with 2'-deoxy-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OHR 2'-deoxyadenosine 5'-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.90 Å R-free 0.266 |
| 8AZI Structure of SARS-CoV-2 NSP3 macrodomain in complex with 2'-deoxy-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OHR 2'-deoxyadenosine 5'-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.90 Å R-free 0.266 |
| 8AZL Structure of SARS-CoV-2 NSP3 macrodomain in complex with 2'-deoxy-2'-fluoro-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OI3 2'-deoxyadenosine 5'-fluoro-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.20 Å R-free 0.273 |
| 8AZL Structure of SARS-CoV-2 NSP3 macrodomain in complex with 2'-deoxy-2'-fluoro-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OI3 2'-deoxyadenosine 5'-fluoro-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.20 Å R-free 0.273 |
| 8AZM Structure of SARS-CoV-2 NSP3 macrodomain in complex with 8Br-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OI6 8-bromoadenosine 5'-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.10 Å R-free 0.281 |
| 8AZM Structure of SARS-CoV-2 NSP3 macrodomain in complex with 8Br-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OI6 8-bromoadenosine 5'-diphosphoribose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 2.10 Å R-free 0.281 |
| 8AZN Structure of SARS-CoV-2 NSP3 macrodomain in complex with alpha-1-O-Me-ADPR Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | RVK Adenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl] estere × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.60 Å R-free 0.174 |
| 8AZO Structure of SARS-CoV-2 NSP3 macrodomain in complex with beta-ethyl-ADP Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OIG beta-ethyl-adenosine diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.90 Å R-free 0.232 |
| 8AZO Structure of SARS-CoV-2 NSP3 macrodomain in complex with beta-ethyl-ADP Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OIG beta-ethyl-adenosine diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.90 Å R-free 0.232 |
| 8AZP Structure of SARS-CoV-2 NSP3 macrodomain in complex with beta-methyl-ADP Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OH9 beta-methyl-adenosine diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.60 Å R-free 0.211 |
| 8AZP Structure of SARS-CoV-2 NSP3 macrodomain in complex with beta-methyl-ADP Deposited 2022-09-06 | 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
1024–1197（174 aa）
|
Not recorded | OH9 beta-methyl-adenosine diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；1.8 M K2HPO4/NaH2PO4
|
Resolution 1.60 Å R-free 0.211 |
| 8B0S SARS-COV-2 Main Protease adduct with Au(NHC)Cl Deposited 2022-09-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3564（301 aa）
|
Not recorded | AU GOLD ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Ammonium Acetate, 20% PEG3350
|
Resolution 2.42 Å R-free 0.273 |
| 8B0T SARS-CoV-2 Main Protease adduct with Au(PEt3)Br Deposited 2022-09-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3564（301 aa）
|
Not recorded | AU GOLD ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Ammonium Acetate, 20% PEG 3350
|
Resolution 2.40 Å R-free 0.276 |
| 8C9L Crystal structure of SARS-CoV-2 Mpro-S144A mutant, free enzyme Deposited 2023-01-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3565（302 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1MBis Tris Propane pH 6.50.02 MSodium potassium phosphate pH 7.520 % w/vPEG 335010% v/vEthylene glycol
|
Resolution 1.70 Å R-free 0.244 |
| 8C9O Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K Deposited 2023-01-23 | 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 AAA
3264–3569（306 aa）
Chain BBB
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Ethylene glycols, HEPES, PEG 500 MME, PEG 20000
|
Resolution 1.69 Å R-free 0.234 |
| 8C9P Crystal structure of SARS-CoV-2 Mpro-E166V mutant, free enzyme Deposited 2023-01-23 | 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 AAA
3264–3568（305 aa）
|
Mutation：E166V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1MBis Tris Propane pH 6.50.2 MPotassium thiocyanate20 % w/vPEG 335010% v/vEthylene glycol
|
Resolution 2.00 Å R-free 0.277 |
| 8C9Q Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with 13b-K Deposited 2023-01-23 | 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 AAA
3264–3566（303 aa）
Chain BBB
3264–3566（303 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M PCTP, pH8.0, 25% w/vPEG 1500
|
Resolution 1.86 Å R-free 0.266 |
| 8C9U Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with nirmatrelvir Deposited 2023-01-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3568（305 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium citrate tribasic dihydrate, 20% w/vPEG 3350
|
Resolution 1.75 Å R-free 0.210 |
| 8CA6 Crystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme Deposited 2023-01-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain AAA
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium formate, 0.1M Bis-Tris propane pH6.5, 20% w/v PEG 3350
|
Resolution 1.92 Å R-free 0.294 |
| 8CA6 Crystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme Deposited 2023-01-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain BBB
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium formate, 0.1M Bis-Tris propane pH6.5, 20% w/v PEG 3350
|
Resolution 1.92 Å R-free 0.294 |
| 8CA8 Crystal structure of SARS-CoV-2 Mpro-H172Y mutant, free enzyme Deposited 2023-01-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3565（302 aa）
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M Bis Tris Propane pH 6.5, 0.2 MSodium acetate trihydrate, 20 % w/vPEG 3350, 10% v/vEthylene glycol
|
Resolution 2.00 Å R-free 0.271 |
| 8CAC Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K Deposited 2023-01-24 | 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 AAA
3264–3565（302 aa）
Chain BBB
3264–3565（302 aa）
|
Not recorded | O6K ~{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 × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；Bis-Tris, Potassium citrate tribasic monohydrate, PEG 3350, Ethylene glycol
|
Resolution 2.13 Å R-free 0.272 |
| 8CAE Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with nirmatrelvir Deposited 2023-01-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3566（303 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M MMT pH8.0, 25% w/vPEG 1500
|
Resolution 2.65 Å R-free 0.258 |
| 8CAJ Crystal structure of SARS-CoV-2 Mpro-E166V mutant in complex with 13b-K Deposited 2023-01-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
3264–3565（302 aa）
|
Not recorded | UAX ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.2M Ammonium chloride, 0.1M Tris pH8.0, 20% w/vPEG 6000
|
Resolution 2.20 Å R-free 0.364 |
| 8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 | 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 B
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 BR BROMIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1,
20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
|
Resolution 3.50 Å R-free 0.270 |
| 8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 | 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 A
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 BR BROMIDE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1,
20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
|
Resolution 3.50 Å R-free 0.270 |
| 8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1,
20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
|
Resolution 3.50 Å R-free 0.270 |
| 8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 BR BROMIDE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1,
20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
|
Resolution 3.50 Å R-free 0.270 |
| 8DI3 Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates Deposited 2022-06-28 | 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
3264–3569（306 aa）
|
Mutation：P132H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium Phosphate, 0.1 M Tris, 50 % MPD
|
Resolution 1.50 Å R-free 0.218 |
| 8DKJ Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates Deposited 2022-07-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M LiCl, 0.1 M Tris pH 8.0, 20% PEG 6000
|
Resolution 2.11 Å R-free 0.248 |
| 8EIR SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction Deposited 2022-09-15 | 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 C
3860–4392（533 aa）
Chain D
3860–4392（533 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.49 Å |
| 8FIG Room-temperature X-ray structure of SARS-CoV-2 main protease double mutant E290A/R298A in complex with GC373 Deposited 2022-12-16 | 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
3264–3569（306 aa）
|
Mutation：E290A, R298A | 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, SITTING DROP；pH 7；287 K；18-21% PEG3350, 0.1 M Bis-Tris pH 7.0, microseeding
|
Resolution 1.75 Å R-free 0.185 |
| 8G62 Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004 Deposited 2023-02-14 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 YOO 3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 2 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand
|
Resolution 2.17 Å R-free 0.214 |
| 8G62 Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004 Deposited 2023-02-14 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 YOO 3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand
|
Resolution 2.17 Å R-free 0.214 |
| 8G62 Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004 Deposited 2023-02-14 | 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
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 1 YOO 3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide × 2 CL CHLORIDE ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand
|
Resolution 2.17 Å R-free 0.214 |
| 8GQC Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.35 angstrom resolution) Deposited 2022-08-30 | 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
1231–1494（264 aa）
Fragment：SUD domain
|
Mutation：L492C, Y623C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.20 M Lithium sulfate monohydrate, 0.10 M Tris pH= 8.50, 25% PEG3350
|
Resolution 1.35 Å R-free 0.162 |
| 8GQT Structure of Mpro complexed with Quercetin Deposited 2022-08-30 | 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 D
3264–3566（303 aa）
|
Not recorded | QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG
|
Resolution 2.09 Å R-free 0.253 |
| 8GTV SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-07 Deposited 2022-09-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | KAE 4-[(2~{S})-4-(3,4-dichlorophenyl)-2-(morpholin-4-ylmethyl)piperazin-1-yl]carbonyl-1~{H}-quinolin-2-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.80 Å R-free 0.247 |
| 8GTW SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-26 Deposited 2022-09-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | K9U (2S)-4-(3,4-dichlorophenyl)-1-[(2-oxidanylidene-1H-quinolin-4-yl)carbonyl]-N-[3,3,3-tris(fluoranyl)propyl]piperazine-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.85 Å R-free 0.227 |
| 8GVD SARS-CoV-2 Mpro in complex with D-4-38 Deposited 2022-09-14 | 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
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.2 m ammonium fluoride, 0.2 peg3350, ph=6.2
|
Resolution 2.00 Å R-free 0.248 |
| 8GVY SARS CoV-2 Mpro in complex with D-3-149 Deposited 2022-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；0.2M sodium fluoride, 20% PEG 3350
|
Resolution 2.50 Å R-free 0.271 |
| 8GW1 A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Deposited 2022-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 U5P URIDINE-5'-MONOPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.31 Å |
| 8GWB SARS-CoV-2 E-RTC complex with RNA-nsp9 Deposited 2022-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: decameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8GWE SARS-CoV-2 E-RTC complex with RNA-nsp9 and GMPPNP Deposited 2022-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: decameric |
Chain C
3860–3937（78 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 8GWF A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 8GWG SARS-CoV-2 E-RTC complex with SMP-nsp9 and GMPPNP Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 6GS 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8GWI SARS-CoV-2 E-RTC complex with SMP-nsp9 and GTP Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 6GS 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 8GWK SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 F86 [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 8GWM SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 6GS 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8GWN A mechanism for SARS-CoV-2 RNA capping and its inhibitor of AT-527 Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 8GWO A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Deposited 2022-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 8 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 U5P URIDINE-5'-MONOPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8GXG The crystal structure of SARS-CoV-2 main protease in complex with 14a Deposited 2022-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 06Q N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.69 Å R-free 0.206 |
| 8GXH The crystal structure of SARS-CoV-2 main protease in complex with 14b Deposited 2022-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 0AX N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.59 Å R-free 0.194 |
| 8GXI The crystal structure of SARS-CoV-2 main protease in complex with 14c Deposited 2022-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 0BO N-[(2S)-3-cyclohexyl-1-[[(2S,3R)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.69 Å R-free 0.203 |
| 8GY6 Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypol binding Deposited 2022-09-21 | Different construct 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 C
3860–3942（83 aa）
|
Not recorded | GO3 Gossypol × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 8GZB SARS-CoV-2 3CLpro Deposited 2022-09-26 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 KM6 2-(4-chlorophenyl)-1,3,4-oxadiazole × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；25% PEG 3350, 0.2M ammonium sulfate, 0.1M HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.256 |
| 8H3G Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Enstrelvir Deposited 2022-10-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：E166V Mutation：E166V | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Sodium formate, 0.1M BICINE pH 8.5, 20% w/v PEG monomethyl ether 5000
|
Resolution 1.46 Å R-free 0.162 |
| 8H3K Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Enstrelvir Deposited 2022-10-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：E166V, L50F Mutation：E166V, L50F | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 VIB 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.3% w/v Sodium-L ascorbate, 0.3% w/v Choline Chloride, 0.3% v/v D-Panthenol, 0.3% w/v Pyridoxine hydrochloride, 0.3% w/v Thiamine hydrochloride
20% v/v PEG 500* MME; 10% w/v PEG 20000;
0.1 M 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid)
|
Resolution 1.80 Å R-free 0.201 |
| 8H3L Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Enstrelvir Deposited 2022-10-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：T21I, E166V Mutation：T21I, E166V | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M HEPES pH 7.5, 2% v/v Tacsimate pH 7.0, 20% w/v Polyethylene glycol 3350
|
Resolution 2.30 Å R-free 0.231 |
| 8H3L Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Enstrelvir Deposited 2022-10-08 | 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
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Mutation：T21I, E166V Mutation：T21I, E166V | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M HEPES pH 7.5, 2% v/v Tacsimate pH 7.0, 20% w/v Polyethylene glycol 3350
|
Resolution 2.30 Å R-free 0.231 |
| 8H4Y Crystal Structure of SARS-CoV-2 Main Protease (Mpro) F140L Mutant in Complex with Inhibitor Nirmatrelvir Deposited 2022-10-11 | 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
3264–3569（306 aa）
|
Mutation：F140L | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.05% w/v (-)-Menthol, 0.05% w/v Caffeic acid, 0.05% w/v D-Quinic acid, 0.05% w/v Shikimic acid, 0.05% w/v Gallic acidmonohydrate, 0.05% w/v N-Vanillylnonanamide, 0.05% w/v Thymol, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8,000
|
Resolution 2.25 Å R-free 0.248 |
| 8H51 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir Deposited 2022-10-11 | 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
3264–3569（306 aa）
|
Mutation：T21I, E166V | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 3 pH 8.5 (Tris base, BICINE), 20% v/v Glycerol, 10% w/v PEG 4,000
|
Resolution 2.18 Å R-free 0.234 |
| 8H57 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) A193P Mutant in Complex with Inhibitor Nirmatrelvir Deposited 2022-10-12 | 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
3264–3569（306 aa）
|
Mutation：A193P | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.05% w/v D-Salicin, 0.05% w/v Esculin hydrate, 0.05% w/v Quinine hemisulfate salt monohydrate, 0.05% w/v Tryptamine, 0.05% w/v Arbutin, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8,000
|
Resolution 1.55 Å R-free 0.204 |
| 8H5F Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir Deposited 2022-10-13 | 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
3264–3569（306 aa）
|
Mutation：L167F | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 3 pH 8.5 (Tris base, BICINE), 20% v/v ethylene glycol, 10% w/v PEG 8,000
|
Resolution 1.79 Å R-free 0.227 |
| 8H5P Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir Deposited 2022-10-13 | 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
3264–3569（306 aa）
|
Mutation：L50F,E166V | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8,000
|
Resolution 1.67 Å R-free 0.207 |
| 8H6I The crystal structure of SARS-CoV-2 3C-like protease Double Mutant (L50F and E166V) in complex with a traditional Chinese Medicine Inhibitors Deposited 2022-10-17 | 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
3264–3569（306 aa）
|
Mutation：E166V, L50F | ODN (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8,000
|
Resolution 1.90 Å R-free 0.227 |
| 8H6N Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (T21I) in complex with protease inhibitor Nirmatrelvir Deposited 2022-10-18 | 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
3264–3569（306 aa）
|
Mutation：T21I | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 LQZ 2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v Glycerol, 10% w/v PEG 4,000
|
Resolution 1.65 Å R-free 0.216 |
| 8H7K SARS-CoV-2 Mpro Double Mutant (H41A and T21I) in complex with nsp4/5 peptidyl substrate Deposited 2022-10-20 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Mutation：H41A/T21I | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v Glycerol, 10% w/v PEG 4,000
|
Resolution 1.45 Å R-free 0.184 |
| 8H7W Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (S144A) in complex with protease inhibitor Nirmatrelvir Deposited 2022-10-21 | 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
3264–3568（305 aa）
|
Mutation：S144A | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M Tris pH 7.0, 16% v/v ethylene glycol, 8% w/v PEG 8,000
|
Resolution 1.60 Å R-free 0.197 |
| 8H82 Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (E166V) in complex with protease inhibitor Nirmatrelvir Deposited 2022-10-21 | 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
3264–3569（306 aa）
|
Mutation：E166V | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M Tris pH 7.6, 14% v/v ethylene glycol, 7% w/v PEG 8,000
|
Resolution 1.93 Å R-free 0.216 |
| 8HBK The crystal structure of SARS-CoV-2 3CL protease in complex with Ensitrelvir Deposited 2022-10-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M Tris pH 7.0, 16% v/v ethylene glycol, 8% w/v PEG 8,000
|
Resolution 1.80 Å R-free 0.232 |
| 8HBL Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.58 angstrom resolution) Deposited 2022-10-29 | 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
1235–1494（260 aa）
|
Mutation：L516C, Y647C | PO4 PHOSPHATE ION × 1 LI LITHIUM ION × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.20 M Lithium sulfate monohydrate, 0.10 M Tris pH 8.50, 25% PEG3350
|
Resolution 1.58 Å R-free 0.180 |
| 8HHT Crystal structure of the SARS-CoV-2 main protease in complex with Hit-1 Deposited 2022-11-17 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | LV0 ~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(1,3-thiazol-2-ylmethylamino)butan-2-yl]benzamide × 2 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350
|
Resolution 1.95 Å R-free 0.245 |
| 8HHU Crystal structure of the SARS-CoV-2 main protease in complex with SY110 Deposited 2022-11-17 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | LVX (1~{R})-3,3-bis(fluoranyl)-~{N}-[(2~{R})-3-methoxy-1-oxidanylidene-1-[[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(1,3-thiazol-2-ylmethylamino)butan-2-yl]amino]propan-2-yl]cyclohexane-1-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M BIS-TRIS pH 5.5, 25% w/v PEG 3350
|
Resolution 2.26 Å R-free 0.227 |
| 8HI9 SARS-CoV-2 3CL protease (3CLpro) in complex with Robinetin Deposited 2022-11-19 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | LKR 3,7-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 2.28 Å R-free 0.255 |
| 8HOL Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) Deposited 2022-12-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M Tris pH 7.0, 16% v/v ethylene glycol, 8% w/v PEG 8,000
|
Resolution 1.82 Å R-free 0.213 |
| 8HOM Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir Deposited 2022-12-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M Tris pH 7.6, 14% v/v ethylene glycol, 7% w/v PEG 8000
|
Resolution 1.56 Å R-free 0.196 |
| 8HOZ Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir Deposited 2022-12-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2% w/v Lidocaine hydrochloride monohydrate, 0.2% w/v Procaine hydrochloride, 0.2% w/v Proparacaine hydrochloride, 0.2% w/v tetracaine hydrochloride, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8000
|
Resolution 2.83 Å R-free 0.258 |
| 8HQG Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53 Deposited 2022-12-13 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：K90R Mutation：K90R | HUR N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.88 Å R-free 0.264 |
| 8HQH Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with inhibitor YH-53 Deposited 2022-12-13 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：M49I Mutation：M49I | HUR N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.58 Å R-free 0.227 |
| 8HQI Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53 Deposited 2022-12-13 | 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
3265–3563（299 aa）
Chain B
3265–3563（299 aa）
|
Mutation：P132H Mutation：P132H | HUR N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.55 Å R-free 0.240 |
| 8HQJ Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53 Deposited 2022-12-13 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：Y54C Mutation：Y54C | HUR N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.74 Å R-free 0.236 |
| 8HTV SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3a Deposited 2022-12-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | UZF 1-(5,6-dihydrobenzo[b][1]benzazepin-11-yl)-2-sulfanyl-ethanone × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 2.04 Å R-free 0.236 |
| 8HUR Crystal structure of SARS-Cov-2 main protease in complex with S217622 Deposited 2022-12-24 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Not recorded | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 10,000
|
Resolution 1.64 Å R-free 0.226 |
| 8HUV Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with S217622 Deposited 2022-12-24 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G15S Mutation：G15S | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate;
|
Resolution 1.97 Å R-free 0.247 |
| 8HUW Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with S217622 Deposited 2022-12-24 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：K90R Mutation：K90R | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M glycine pH8.5, 20% polyethylene glycol
|
Resolution 1.75 Å R-free 0.228 |
| 8HUX Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with S217622 Deposited 2022-12-24 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：P132H Mutation：P132H | 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.74 Å R-free 0.245 |
| 8HVK Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF07321332 Deposited 2022-12-27 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.63 Å R-free 0.215 |
| 8HVL Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF07321332 Deposited 2022-12-27 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：M49I Mutation：M49I | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
|
Resolution 1.45 Å R-free 0.230 |
| 8HVM Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF07321332 Deposited 2022-12-27 | 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
3266–3566（301 aa）
Chain B
3266–3566（301 aa）
|
Mutation：K90R Mutation：K90R | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M glycine pH8.5, 20% polyethylene glycol
|
Resolution 1.48 Å R-free 0.242 |
| 8HVN Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF07321332 Deposited 2022-12-27 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Mutation：P132H Mutation：P132H | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.90 Å R-free 0.243 |
| 8HVO Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF07321332 Deposited 2022-12-27 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Na2SO4, 20%PEG3350
|
Resolution 1.65 Å R-free 0.258 |
| 8HVU Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G15S Mutation：G15S | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate;
|
Resolution 2.29 Å R-free 0.257 |
| 8HVV Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.1M Na2SO4
|
Resolution 1.95 Å R-free 0.238 |
| 8HVW Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
|
Resolution 2.05 Å R-free 0.251 |
| 8HVX Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：Y54C Mutation：Y54C | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 1.75 Å R-free 0.236 |
| 8HVY Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：K90R Mutation：K90R | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M glycine pH8.5, 20% polyethylene glycol
|
Resolution 1.97 Å R-free 0.247 |
| 8HVZ Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF07304814 Deposited 2022-12-28 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：V186F Mutation：V186F | 80I [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
|
Resolution 1.70 Å R-free 0.239 |
| 8HZR Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07321332 Deposited 2023-01-09 | 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
3266–3561（296 aa）
Chain B
3266–3561（296 aa）
|
Mutation：S46F Mutation：S46F | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.1M Na2SO4
|
Resolution 1.92 Å R-free 0.242 |
| 8I30 Crystal structure of the SARS-CoV-2 main protease in complex with 32j Deposited 2023-01-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | OF9 (2~{R})-1-[4,4-bis(fluoranyl)cyclohexyl]carbonyl-4,4-bis(fluoranyl)-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]pyrrolidine-2-carboxamide × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.1 M sodium acetate trihydrate pH 4.5, 25% w/v PEG 3350
|
Resolution 2.00 Å R-free 0.226 |
| 8IFP SARS-CoV-2 3CL protease (3CLpro) in complex with compound 1 Deposited 2023-02-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | OZ6 (1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.78 Å R-free 0.292 |
| 8IFQ SARS-CoV-2 3CL protease (3CLpro) in complex with compound 2 Deposited 2023-02-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | I1Z (1R,2S,5S)-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.96 Å R-free 0.214 |
| 8IFR SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3 Deposited 2023-02-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | P0O (1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-5-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]hex-3-en-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.66 Å R-free 0.216 |
| 8IFS SARS-CoV-2 3CL protease (3CLpro) in complex with compound 7 Deposited 2023-02-19 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | OZL (8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 2.46 Å R-free 0.295 |
| 8IFT SARS-CoV-2 3CL protease (3CLpro) in complex with compound 10 Deposited 2023-02-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | OZB (8S)-N-[(1S)-1-cyano-2-[(3S)-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2S)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.80 Å R-free 0.205 |
| 8IG4 Crystal structure of SARS-Cov-2 main protease in complex with GC376 Deposited 2023-02-20 | 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
3266–3566（301 aa）
Chain B
3266–3566（301 aa）
|
Not recorded | 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, HANGING DROP；293 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 1.80 Å R-free 0.240 |
| 8IG7 Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with GC376 Deposited 2023-02-20 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 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, HANGING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.69 Å R-free 0.241 |
| 8IG8 Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with GC376 Deposited 2023-02-20 | 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
3265–3567（303 aa）
Chain B
3265–3567（303 aa）
|
Mutation：S46F Mutation：S46F | 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, HANGING DROP；293 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.73 Å R-free 0.234 |
| 8IG9 Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with GC376 Deposited 2023-02-20 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 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, HANGING DROP；293 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.68 Å R-free 0.247 |
| 8IGA Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with GC376 Deposited 2023-02-20 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 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, HANGING DROP；293 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.63 Å R-free 0.242 |
| 8IGB Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with GC376 Deposited 2023-02-20 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | 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, HANGING DROP；293 K；0.1 M BICINE pH 8.5, 20% w/v Polyethylene glycol 10,000
|
Resolution 1.72 Å R-free 0.244 |
| 8IGN Crystal structure of SARS-CoV-2 main protease in complex with RAY1216 Deposited 2023-02-21 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 7ON Leritrelvir bound form × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000. Protein concentration 10mg/ml.
|
Resolution 2.02 Å R-free 0.231 |
| 8IGO Crystal structure of apo SARS-CoV-2 main protease Deposited 2023-02-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350. Protein concentration 10mg/ml
|
Resolution 2.00 Å R-free 0.249 |
| 8IGX SARS-CoV-2 3CL protease (3CLpro) in complex with compound 9 (simnotrelvir, SIM0417, SSD8432) Deposited 2023-02-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | PQL (8~{S})-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.90 Å R-free 0.212 |
| 8IGY SARS-CoV-2 3CL protease (3CLpro) in complex with nirmatrelvir Deposited 2023-02-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
|
Resolution 1.96 Å R-free 0.206 |
| 8IHO Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1564–1878（315 aa）
Chain C
1564–1878（315 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v PEG 3350
|
Resolution 2.55 Å R-free 0.305 |
| 8ILC Crystal structure of Se-Met CoV-Y domain of Nsp3 in SARS-CoV-2 Deposited 2023-03-03 | 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
2485–2763（279 aa）
Fragment：CoV-Y domain
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2 M Ammonium sulfate, 0.1M BIS-TRIS pH6.5, 2mM TCEP
|
Resolution 2.20 Å R-free 0.239 |
| 8J35 Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF00835231 Deposited 2023-04-16 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G15S Mutation：G15S | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.79 Å R-free 0.228 |
| 8J36 Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF00835231 Deposited 2023-04-16 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Mutation：M491I Mutation：M491I | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 2.21 Å R-free 0.254 |
| 8J37 Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF00835231 Deposited 2023-04-16 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.68 Å R-free 0.242 |
| 8J3A Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF00835231 Deposited 2023-04-16 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：Y54C Mutation：Y54C | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Na2SO4, 20%PEG3350
|
Resolution 1.91 Å R-free 0.235 |
| 8J3B Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF00835231 Deposited 2023-04-16 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：S46F Mutation：S46F | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.64 Å R-free 0.230 |
| 8JCJ The crystal structure of SARS-CoV-2 main protease in complex with Compound 18 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | PBP p-Bromophenacyl bromide × 2 H2S HYDROSULFURIC ACID × 2 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.70 Å R-free 0.188 |
| 8JCK The crystal structure of SARS-CoV-2 main protease in complex with Compound 32 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A8J tert-butyl 3-ethanoylbenzoate × 2 GOL GLYCEROL × 2 H2S HYDROSULFURIC ACID × 2 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.61 Å R-free 0.175 |
| 8JCL The crystal structure of SARS-CoV-2 main protease in complex with Compound 52 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | AIE 3-ethanoyl-N-phenyl-benzamide × 2 H2S HYDROSULFURIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.59 Å R-free 0.177 |
| 8JCM The crystal structure of SARS-CoV-2 main protease in complex with Compound 55 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | AJF methyl (2S)-2-[(3-ethanoylphenyl)carbonylamino]-3-phenyl-propanoate × 2 DMS DIMETHYL SULFOXIDE × 6 H2S HYDROSULFURIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.61 Å R-free 0.183 |
| 8JCN The crystal structure of SARS-CoV-2 main protease in complex with Compound 58 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | AO0 1-[3-(diphenoxyphosphorylamino)phenyl]ethanone × 2 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.61 Å R-free 0.184 |
| 8JCO The crystal structure of SARS-CoV-2 main protease in complex with Compound 65 Deposited 2023-05-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | B7Y methyl (2S)-2-[[3-(4-chloranylbutanoyl)phenyl]carbonylamino]-3-methyl-butanoate × 2 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.69 Å R-free 0.193 |
| 8JOP Crystal structure of the SARS-CoV-2 main protease in complex with 11a Deposited 2023-06-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | UWO methyl (6~{R})-5-ethanoyl-7-oxidanylidene-6-[4-(trifluoromethyl)phenyl]-8,9,10,11-tetrahydro-6~{H}-benzo[b][1,4]benzodiazepine-2-carboxylate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5000
|
Resolution 2.70 Å R-free 0.248 |
| 8R0V SARS-CoV-2 Mpro (Omicron, P132H) in complex with alpha-ketoamide 13b-K at pH 6.5 Deposited 2023-11-01 | 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 C
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；0.1 BisTris
25% PEG3350
|
Resolution 2.48 Å R-free 0.247 |
| 8R0V SARS-CoV-2 Mpro (Omicron, P132H) in complex with alpha-ketoamide 13b-K at pH 6.5 Deposited 2023-11-01 | 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 A
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；0.1 BisTris
25% PEG3350
|
Resolution 2.48 Å R-free 0.247 |
| 8R11 Structure of compound 7 bound to SARS-CoV-2 main protease Deposited 2023-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XI0 1-[(2~{S})-2-(3-chlorophenyl)pyrrolidin-1-yl]-2-(5-methylpyridin-3-yl)ethanone × 2 GOL GLYCEROL × 1 BR BROMIDE ION × 2 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 4000, 20% glycerol , 0.03 M of each halide: sodium fluoride, sodium bromide, sodium iodide, 0.1 M MES/imidazole pH 6.5
|
Resolution 1.31 Å R-free 0.193 |
| 8R12 Structure of compound 8 bound to SARS-CoV-2 main protease Deposited 2023-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XH9 2-[[4-(5-chloranylpyridin-3-yl)carbonyl-1,4-diazepan-1-yl]methyl]benzenecarbonitrile × 2 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 4000, 20% glycerol , 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide),0.1 M MES/imidazole pH 6.5
|
Resolution 1.59 Å R-free 0.238 |
| 8R14 Structure of compound 11 bound to SARS-CoV-2 main protease Deposited 2023-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XHW (5-chloranylpyridin-3-yl)-[4-[(2-chlorophenyl)methyl]-1,4-diazepan-1-yl]methanone × 2 PGE TRIETHYLENE GLYCOL × 1 BR BROMIDE ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 4000, 20% glycerol , 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide), 0.1 M MES/imidazole pH 6.5
|
Resolution 1.34 Å R-free 0.238 |
| 8R16 Structure of compound 12 bound to SARS-CoV-2 main protease Deposited 2023-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XJ9 1-[6,7-bis(chloranyl)-3,4-dihydro-1H-isoquinolin-2-yl]-2-(5-methylpyridin-3-yl)ethanone × 2 CL CHLORIDE ION × 4 BR BROMIDE ION × 2 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 4000, 20% glycerol , 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide),0.1 M MES/imidazole pH 6.5
|
Resolution 1.30 Å R-free 0.206 |
| 8R19 SARS-CoV-2 Mpro (Omicron, P132H) free enzyme Deposited 2023-11-01 | 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
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；296 K；PEG 3350 20%
Ethylene glycol 10%
|
Resolution 1.91 Å R-free 0.237 |
| 8R1Q SARS-CoV-2 Mpro (Omicron, P132H+T169S) in complex with alpha-ketoamide 13b-K Deposited 2023-11-02 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；296 K；PEG3350 25%
|
Resolution 1.70 Å R-free 0.223 |
| 8R24 SARS-CoV-2 Mpro (Omicron, P132H+T169S) free enzyme Deposited 2023-11-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；296 K；PEG 3350 25%
|
Resolution 1.80 Å R-free 0.264 |
| 8R26 SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5 Deposited 2023-11-03 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；296 K；0.1 BisTris
25% PEG3350
|
Resolution 2.30 Å R-free 0.245 |
| 8R26 SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5 Deposited 2023-11-03 | 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
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Not recorded | O6K ~{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 × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；296 K；0.1 BisTris
25% PEG3350
|
Resolution 2.30 Å R-free 0.245 |
| 8RV4 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 2 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H3C 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-phenyl-benzoic acid × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 5% PEG 3350, 0.24 M magnesium chloride
|
Resolution 2.35 Å R-free 0.233 |
| 8RV5 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 1 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 12% PEG 3350, 0.18 M magnesium chloride
|
Resolution 2.05 Å R-free 0.214 |
| 8RV6 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 2 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H3B 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(4-hydroxyphenyl)benzoic acid × 1 GOL GLYCEROL × 3 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 12% PEG 3350, 0.1 M magnesium chloride
|
Resolution 2.25 Å R-free 0.225 |
| 8RV7 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 4 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H3E 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(3-oxidanylprop-1-ynyl)benzoic acid × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 9% PEG 3350, 0.06 M magnesium chloride
|
Resolution 1.90 Å R-free 0.197 |
| 8RV8 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H28 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-2-chloranyl-benzoic acid × 1 GOL GLYCEROL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 11% PEG 3350, 0.24 M magnesium chloride
|
Resolution 1.70 Å R-free 0.196 |
| 8RV9 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 6 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H3A 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-chloranyl-benzoic acid × 1 GOL GLYCEROL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 5% PEG 3350, 0.24 M magnesium chloride
|
Resolution 1.90 Å R-free 0.208 |
| 8RVA SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 7 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H3D 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]benzoic acid × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 7% PEG 3350, 0.12 M magnesium chloride
|
Resolution 1.80 Å R-free 0.204 |
| 8RVB SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 8 Deposited 2024-01-31 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H29 (2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[2-(1~{H}-1,2,3-triazol-4-yl)ethylsulfanylmethyl]oxolane-3,4-diol × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 5% PEG 3350, 0.22 M magnesium chloride
|
Resolution 1.95 Å R-free 0.203 |
| 8RZC SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 11 Deposited 2024-02-12 | 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
4254–4392（139 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1H4D 3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-imidazol-1-yl-benzoic acid × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 7% PEG 3350, 0.14 M magnesium chloride
|
Resolution 2.35 Å R-free 0.210 |
| 8RZD SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 9 Deposited 2024-02-12 | 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
4254–4392（139 aa）
|
Not recorded | A1H4C 3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(3-hydroxyphenyl)benzoic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 9% PEG 3350, 0.14 M magnesium chloride
|
Resolution 2.10 Å R-free 0.242 |
| 8RZE SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 10 Deposited 2024-02-12 | 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
4254–4392（139 aa）
|
Not recorded | A1H4B 3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-pyridin-3-yl-benzoic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M MES (pH 5.6), 12% PEG 3350, 0.12 M magnesium chloride
|
Resolution 2.00 Å R-free 0.231 |
| 8SPJ Crystal Structure of SARS-CoV-2 Main Protease (Mpro) N28T Mutant Deposited 2023-05-03 | 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
3264–3569（306 aa）
|
Mutation：N28T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
|
Resolution 2.08 Å R-free 0.242 |
| 8SXO Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant Deposited 2023-05-23 | 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
3264–3569（306 aa）
|
Mutation：H164I | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
|
Resolution 2.76 Å R-free 0.244 |
| 8TYK Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T21I Mutant Deposited 2023-08-25 | 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
3264–3569（306 aa）
|
Mutation：T21I | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
|
Resolution 1.98 Å R-free 0.235 |
| 8U25 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant Deposited 2023-09-05 | 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
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Mutation：L50F, E166A, L167F Mutation：L50F, E166A, L167F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
|
Resolution 2.23 Å R-free 0.231 |
| 8U25 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant Deposited 2023-09-05 | 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
3264–3569（306 aa）
Chain C
3264–3569（306 aa）
|
Mutation：L50F, E166A, L167F Mutation：L50F, E166A, L167F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
|
Resolution 2.23 Å R-free 0.231 |
| 8UFM Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2 Deposited 2023-10-04 | 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
1231–1496（266 aa）
Fragment：SARS-Unique Domain (SUD)
|
Mutation：L516C, Y647C Non-standard monomer：Yes (specific site not provided by mmCIF) | FMT FORMIC ACID × 1 ACT ACETATE ION × 1 SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.3；292 K；Protein: 6.45 mg/ml, 0.3M Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 (A2), 0.2M Ammonium acetate, 2.2M Ammonium sulfate; Cryo: 2.0M Lithium sulfate
|
Resolution 1.65 Å R-free 0.208 |
| 8UHO Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A Deposited 2023-10-09 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | WTE N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-[(2S,3Z)-1-[(2S)-oxolan-2-yl]-3-(2-oxooxolan-3-ylidene)propan-2-yl]-L-leucinamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.6；295 K；0.02M CaCl2, 30% MPD, 01 M sodium acetate, pH 4.6
Crystals grew over night with seeding and were left to grow for up to two days before they were harvested
|
Resolution 2.02 Å R-free 0.217 |
| 8UIA Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365097A Deposited 2023-10-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | WTV N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-{(2R)-1-[(2R)-oxolan-2-yl]-3-[(3R)-2-oxooxolan-3-yl]propan-2-yl}-L-leucinamide × 2 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；0.02M CaCl2, 30% MPD, 01 M sodium acetate, pH 4.6
Crystals grew over night with seeding and were left to grow for up to two days before they were harvested
|
Resolution 1.75 Å R-free 0.194 |
| 8UOB SARS-CoV-2 Papain-like protease (PLpro) with Inhibitor Jun12682 Deposited 2023-10-19 | 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
1564–1878（315 aa）
|
Not recorded | XB5 5-[2-(dimethylamino)ethoxy]-N-{(1R)-1-[(3M,5P)-3-(1-ethyl-1H-pyrazol-3-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-2-methylbenzamide × 1 ZN ZINC ION × 6 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；Zinc Acetate, PEG 8000, Bis-Tris 6.3
|
Resolution 2.52 Å R-free 0.244 |
| 8UUF SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun11941 Deposited 2023-11-01 | 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
1564–1878（315 aa）
|
Not recorded | XWO N-{(1R)-1-[(3M,5P)-3,5-bis(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide × 1 ACT ACETATE ION × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；0.2M Zinc acetate, 0.1M Bis Tris, 10% PEG 8000
|
Resolution 2.84 Å R-free 0.234 |
| 8UUH SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12199 Deposited 2023-11-01 | 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
1564–1878（315 aa）
|
Not recorded | XYI 5-[2-(dimethylamino)ethoxy]-2-methyl-N-[(1R)-1-{(3M,5P)-3-(1-methyl-1H-pyrazol-4-yl)-5-[1-(propan-2-yl)-1H-pyrazol-4-yl]phenyl}ethyl]benzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 5 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.2M Zinc Acetate, 0.1M Bis Tris pH 6.0, 10% PEG 8000
|
Resolution 2.80 Å R-free 0.262 |
| 8UUU SARS-Cov-2 papain-like protease (PLpro) with inhibitor Jun12162 Deposited 2023-11-02 | 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
1564–1878（315 aa）
|
Not recorded | XYR N-{(1R)-1-[(3P,5M)-3-[1-(difluoromethyl)-1H-pyrazol-4-yl]-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide × 1 ACT ACETATE ION × 1 ZN ZINC ION × 6 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.9；277 K；0.2M Zinc Acetate, 0.1M BisTris pH 5.9, 12% PEG 8000
|
Resolution 3.01 Å R-free 0.244 |
| 8UUV SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12197 Deposited 2023-11-02 | 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
1564–1878（315 aa）
|
Not recorded | Y2I N-{(1R)-1-[(3P,5P)-3-(1-cyclopropyl-1H-pyrazol-4-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide × 1 ZN ZINC ION × 6 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；0.2M Zinc Acetate, 0.1M BisTris pH 6.4, 8% PEG 8000
|
Resolution 3.01 Å R-free 0.224 |
| 8UUW SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12145 Deposited 2023-11-02 | 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
1564–1878（315 aa）
|
Not recorded | Y2N 5-[2-(dimethylamino)ethoxy]-2-methyl-N-{(1R)-1-[(3P,5M)-3-(1-methyl-1H-pyrazol-4-yl)-5-(1,3-thiazol-5-yl)phenyl]ethyl}benzamide × 1 DMS DIMETHYL SULFOXIDE × 1 ACT ACETATE ION × 1 ZN ZINC ION × 5 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；0.2M Zinc Acetate, 0.1M BisTris pH 5.8, 105 PEG 8000
|
Resolution 3.20 Å R-free 0.305 |
| 8UUY SARS-CoV-2 papain-like protease (PLpro) complex with inhibitor Jun12129 Deposited 2023-11-02 | 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
1564–1878（315 aa）
|
Not recorded | Y2R N-{(1R)-1-[(3P,5P)-3-[5-(aminomethyl)thiophen-2-yl]-5-(thiophen-2-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 ACT ACETATE ION × 1 ZN ZINC ION × 8 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；0.2M Zinc Acetate, 0.1M BisTris pH 6.2, 8% PEG 8000
|
Resolution 3.05 Å R-free 0.250 |
| 8W1T SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit Deposited 2024-02-18 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 4 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 A1A21 (5-bromopyridin-3-yl){4-[(R)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone × 2 A1AFD (5-bromopyridin-3-yl){4-[(S)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M MES pH 6.8, 0.2 M lithium sulfate, 24% PEG3350
|
Resolution 1.76 Å R-free 0.201 |
| 8WS3 Crystal structure of SARS-CoV-2 Main Protease (Mpro) with covalent inhibitor 5,8-Dihydroxy-1,4-naphthoquinone Deposited 2023-10-16 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 X7F 5,8-bis(oxidanyl)naphthalene-1,4-dione × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；MES pH 6.0, polyethylene glycol (PEG) 6000, DMSO, DTT
|
Resolution 2.50 Å R-free 0.252 |
| 8WSI Crystal structure of SARS-Cov-2 main protease, pH=6.0 Deposited 2023-10-17 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M MES pH6.0, 20%PEG4000,10% isopropanol
|
Resolution 2.46 Å R-free 0.287 |
| 8WSJ Crystal structure of SARS-Cov-2 main protease, pH=6.5 Deposited 2023-10-17 | 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
3267–3561（295 aa）
Chain B
3266–3564（299 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Ammonium acetate,0.1M BIS-TRIS pH6.5, 25% PEG3350
|
Resolution 1.74 Å R-free 0.233 |
| 8WSK Crystal structure of SARS-Cov-2 main protease, pH=8.5 Deposited 2023-10-17 | 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
3266–3561（296 aa）
Chain B
3266–3561（296 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M Tris-HCl pH8.5,24%PEG4000
|
Resolution 1.88 Å R-free 0.251 |
| 8WTI Crystal structure of the SARS-CoV-2 main protease in complex with 20j Deposited 2023-10-18 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | X1Z ~{N}-[(1~{R})-1-cyclohexyl-2-[[(2~{R})-3-methoxy-1-oxidanylidene-1-[[1-[(1~{S})-1-oxidanyl-2-oxidanylidene-2-(1,3-thiazol-2-ylmethylamino)ethyl]cyclobutyl]amino]propan-2-yl]amino]-2-oxidanylidene-ethyl]-4,4-bis(fluoranyl)cyclohexane-1-carboxamide × 2 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% PEG3350
|
Resolution 1.50 Å R-free 0.201 |
| 8WUR Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin Deposited 2023-10-21 | 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
3266–3561（296 aa）
Chain B
3266–3561（296 aa）
|
Mutation：D48N Mutation：D48N | FNO 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1M HEPES 7.5, 20% PEG 10000
|
Resolution 2.08 Å R-free 0.238 |
| 8WZ0 SARS-CoV-2 3CLpro bound to covalent inhibitor Deposited 2023-11-01 | 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
3264–3569（306 aa）
|
Not recorded | XQF (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[(2-chloranyl-2-fluoranyl-ethanoyl)-[4-(trifluoromethyloxy)phenyl]amino]-2-pyrimidin-5-yl-propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2M sodium fluoride, 20% PEG 3350
|
Resolution 2.45 Å R-free 0.299 |
| 8WZ0 SARS-CoV-2 3CLpro bound to covalent inhibitor Deposited 2023-11-01 | 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
3264–3569（306 aa）
|
Not recorded | XQF (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[(2-chloranyl-2-fluoranyl-ethanoyl)-[4-(trifluoromethyloxy)phenyl]amino]-2-pyrimidin-5-yl-propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2M sodium fluoride, 20% PEG 3350
|
Resolution 2.45 Å R-free 0.299 |
| 8WZ0 SARS-CoV-2 3CLpro bound to covalent inhibitor Deposited 2023-11-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XQF (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[(2-chloranyl-2-fluoranyl-ethanoyl)-[4-(trifluoromethyloxy)phenyl]amino]-2-pyrimidin-5-yl-propanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2M sodium fluoride, 20% PEG 3350
|
Resolution 2.45 Å R-free 0.299 |
| 8WZP Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with CCF0058981 Deposited 2023-11-02 | 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
3266–3567（302 aa）
Chain B
3266–3567（302 aa）
|
Mutation：M49I Mutation：M49I | XIU 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(1~{H}-imidazol-5-yl)phenyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
|
Resolution 1.76 Å R-free 0.236 |
| 8XCH SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation. Deposited 2023-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 32-meric |
Chain C
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
Chain K
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
Chain S
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
Chain a
3860–3942（83 aa）
Fragment：UNP residues 3860-3942
|
Not recorded | ZN ZINC ION × 32 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.40 Å |
| 8Y42 Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51 Deposited 2024-01-30 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1D51 ~{N}-[(1~{S},2~{R})-2-[[4-cyclopropyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-7.0, 5%-25% PEG6000,
3% DMSO
|
Resolution 2.35 Å R-free 0.274 |
| 8Y42 Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51 Deposited 2024-01-30 | 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
3264–3569（306 aa）
Chain D
3264–3569（306 aa）
|
Not recorded | A1D51 ~{N}-[(1~{S},2~{R})-2-[[4-cyclopropyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-7.0, 5%-25% PEG6000,
3% DMSO
|
Resolution 2.35 Å R-free 0.274 |
| 8Y44 Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 44 Deposited 2024-01-30 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1D50 ~{N}-[(1~{S},2~{R})-2-[(4-bromanyl-2-morpholin-4-ylcarbonyl-6-nitro-phenyl)amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH5.5-7.0, 5%-25%
PEG6000, 3% DMSO
|
Resolution 1.91 Å R-free 0.262 |
| 8Y7T Crystal structure of SARS-CoV-2 main protease in complex with C2 Deposited 2024-02-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1LX1 6-(iminomethyl)-4-(2-pyridin-2-ylethyl)-2-[4-(trifluoromethyl)phenyl]-1,2,4-triazine-3,5-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG3350
|
Resolution 2.50 Å R-free 0.266 |
| 8Y7U Crystal structure of SARS-CoV-2 main protease in complex with C5 Deposited 2024-02-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1LX2 2-(3-fluoro-4-(trifluoromethyl)phenyl)-6-(iminomethyl)-4-(2-oxo-2-(pyridin-2-yl)ethyl)-1,2,4-triazine-3,5(2H,4H)-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M Bis-Tris pH 5.5, 25% w/v PEG3350
|
Resolution 2.20 Å R-free 0.272 |
| 8YA5 Mpro from SARS-CoV-2 Deposited 2024-02-07 | 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
3264–3564（301 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；PEG 25% 800, MES 0.1 M
|
Resolution 2.72 Å R-free 0.273 |
| 8YKJ Crystal structure of SARS-Cov-2 main protease in complex with X77 Deposited 2024-03-05 | 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
3266–3566（301 aa）
Chain B
3266–3566（301 aa）
|
Mutation：N142A Mutation：N142A | 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 7.5, 20% PEG 10000
|
Resolution 1.99 Å R-free 0.252 |
| 8YKM Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with X77 Deposited 2024-03-05 | 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
3266–3563（298 aa）
Chain B
3266–3563（298 aa）
|
Mutation：G15S Mutation：G15S | 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, SITTING DROP；293 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.84 Å R-free 0.237 |
| 8YKN Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77 Deposited 2024-03-05 | 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
3265–3567（303 aa）
|
Mutation：K90R | 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, SITTING DROP；293 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.77 Å R-free 0.234 |
| 8YKP Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77 Deposited 2024-03-05 | 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
3266–3566（301 aa）
|
Mutation：M49I | 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, SITTING DROP；293 K；0.12M-0.21M Na2SO4, 20%-24% PEG3350
|
Resolution 2.40 Å R-free 0.263 |
| 8YKQ Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with X77 Deposited 2024-03-05 | 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
3266–3564（299 aa）
|
Mutation：V186F | 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；0.2M Na2SO4, 20%PEG3350
|
Resolution 2.00 Å R-free 0.233 |
| 8YLS Structure of SARS-CoV-2 Mpro in complex with its degrader Deposited 2024-03-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1LYZ (4-methoxyphenyl)methyl ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]carbamate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.1 K；25 % w/v PEG 1500, 0.1 M SPG 9.0
|
Resolution 1.93 Å R-free 0.222 |
| 8YSA The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H102 Deposited 2024-03-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES monohydrate pH 6.0 and 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.50 Å R-free 0.197 |
| 8YSA The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H102 Deposited 2024-03-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES monohydrate pH 6.0 and 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.50 Å R-free 0.197 |
| 8YWY Crystal structure of SARS-Cov-2 main protease E166N mutant in complex with Bofutrelvir Deposited 2024-04-01 | 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
3266–3567（302 aa）
|
Mutation：E166N | FHR ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1M HEPES pH6.5, 10% isopropanol, 22% PEG3350
|
Resolution 1.95 Å R-free 0.246 |
| 8Z1H Crystal structure of SARS main protease in complex with PF-00835231 Deposited 2024-04-11 | 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
3267–3562（296 aa）
Chain B
3267–3562（296 aa）
|
Not recorded | V2M N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 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 2.61 Å R-free 0.236 |
| 8Z4W Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors Deposited 2024-04-17 | 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
1564–1878（315 aa）
|
Not recorded | A1D7X 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5
|
Resolution 2.33 Å R-free 0.235 |
| 8Z4W Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors Deposited 2024-04-17 | 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
1564–1878（315 aa）
|
Not recorded | A1D7X 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5
|
Resolution 2.33 Å R-free 0.235 |
| 8Z4W Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors Deposited 2024-04-17 | 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
1564–1878（315 aa）
|
Not recorded | A1D7X 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone × 1 ZN ZINC ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5
|
Resolution 2.33 Å R-free 0.235 |
| 8Z4W Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors Deposited 2024-04-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1564–1878（315 aa）
|
Not recorded | A1D7X 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5
|
Resolution 2.33 Å R-free 0.235 |
| 8ZBP The crystal structure of SARS-CoV-2 main protease in complex with chebulagic acid (CHLA) Deposited 2024-04-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1D76 2-[(4R,5S,7R,25S,26R,29R,30S,31R)-13,14,15,18,19,20,21,31,35,36-decahydroxy-2,10,23,28,32-pentaoxo-5-(3,4,5-trihydroxybenzoyl)oxy-3,6,9,24,27,33-hexaoxaheptacyclo[28.7.1.04,25.07,26.011,16.017,22.034,38]octatriaconta-1(37),11,13,15,17(22),18,20,34(38),35-nonaen-29-yl]acetic acid × 2 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；5% polyethylene glycol (PEG) 6000, 3% DMSO, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml
|
Resolution 1.41 Å R-free 0.209 |
| 9BBP SARS-CoV-2 Mpro in complex with compound 12d inhibitor Deposited 2024-04-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | GLY GLYCINE × 2 VAL VALINE × 2 THR THREONINE × 2 PHE PHENYLALANINE × 2 A1ALW N-{(2R)-1-amino-3-[(2R,3S)-2-hydroxypyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-fluoropyridin-3-yl)benzoyl]-L-leucinamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium Formate, 20% w/v Polyethylene glycol 3350
|
Resolution 1.81 Å R-free 0.237 |
| 9BNT Crystal Structure of T21I SARS-CoV-2 Main Protease Deposited 2024-05-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；0.1 M MES monohydrate, 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.83 Å R-free 0.240 |
| 9BO0 Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Compound Mpro61 Deposited 2024-05-03 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | XEK (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；10% v/v Polyethylene glycol 200, 0.1 M BIS-TRIS propane, 18% w/v Polyethylene glycol 8,000
|
Resolution 2.16 Å R-free 0.251 |
| 9BO4 Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Nirmatrelvir Deposited 2024-05-03 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；20% v/v 2-Propanol, 0.1 M MES monohydrate, 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.28 Å R-free 0.252 |
| 9BO8 Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376 Deposited 2024-05-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.1 M BIS-TRIS, 16% w/v Polyethylene glycol 10,000
|
Resolution 1.49 Å R-free 0.202 |
| 9BRW SARS-CoV-2 Papain-like Protease (PLpro) with Fragment 7 Deposited 2024-05-11 | 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
1563–1879（317 aa）
|
Mutation：C111S, C270S | A1ARL N-(2-chlorophenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M magnesium formate, 15-25% PEG3350
|
Resolution 2.50 Å R-free 0.237 |
| 9BRW SARS-CoV-2 Papain-like Protease (PLpro) with Fragment 7 Deposited 2024-05-11 | 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
1563–1879（317 aa）
|
Mutation：C111S, C270S | A1ARL N-(2-chlorophenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M magnesium formate, 15-25% PEG3350
|
Resolution 2.50 Å R-free 0.237 |
| 9BRW SARS-CoV-2 Papain-like Protease (PLpro) with Fragment 7 Deposited 2024-05-11 | Different construct Different mutation/modification 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
1563–1879（317 aa）
|
Mutation：C111S, C270S | A1ARL N-(2-chlorophenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M magnesium formate, 15-25% PEG3350
|
Resolution 2.50 Å R-free 0.237 |
| 9BRW SARS-CoV-2 Papain-like Protease (PLpro) with Fragment 7 Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1563–1879（317 aa）
|
Mutation：C111S, C270S | A1ARL N-(2-chlorophenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M magnesium formate, 15-25% PEG3350
|
Resolution 2.50 Å R-free 0.237 |
| 9BRX SARS-CoV-2 Papain-like Protease (PLpro) with Fragment 10 Deposited 2024-05-11 | 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 AA
1563–1879（317 aa）
|
Mutation：C270S | A1ASL (4R)-N-(2,4-dimethylphenyl)-7-methyl[1,2,4]triazolo[4,3-a]pyrimidin-5-amine × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M sodium citrate, 15%-25% PEG3350
|
Resolution 1.80 Å R-free 0.198 |
| 9CSY SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472 Deposited 2024-07-24 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1AZ1 2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide × 1 TFA trifluoroacetic acid × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0
|
Resolution 2.60 Å R-free 0.259 |
| 9CSY SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472 Deposited 2024-07-24 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1AZ1 2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0
|
Resolution 2.60 Å R-free 0.259 |
| 9CSY SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472 Deposited 2024-07-24 | Different construct Different mutation/modification 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
1564–1878（315 aa）
|
Mutation：C111S | A1AZ1 2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0
|
Resolution 2.60 Å R-free 0.259 |
| 9CYB SARS-CoV-2 PLpro in complex with inhibitor WEHI-P1 Deposited 2024-08-01 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1A0T [(3R)-1-cyclopentylpiperidin-3-yl](6-methoxynaphthalen-2-yl)methanone × 1 SIN SUCCINIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.72；281 K；0.2 M Sodium Succinate
10% PEG 8000 (w/v)
0.1 M trisodium citrate-citric acid pH 5.72
|
Resolution 1.98 Å R-free 0.208 |
| 9CYB SARS-CoV-2 PLpro in complex with inhibitor WEHI-P1 Deposited 2024-08-01 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1A0T [(3R)-1-cyclopentylpiperidin-3-yl](6-methoxynaphthalen-2-yl)methanone × 1 SIN SUCCINIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.72；281 K；0.2 M Sodium Succinate
10% PEG 8000 (w/v)
0.1 M trisodium citrate-citric acid pH 5.72
|
Resolution 1.98 Å R-free 0.208 |
| 9CYC SARS-CoV-2 PLpro in complex with inhibitor WEHI-P2 Deposited 2024-08-01 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1A0S (E)-1-[(3R)-1-cyclopentylpiperidin-3-yl]-N-methoxy-1-(6-methoxynaphthalen-2-yl)methanimine × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.4；281 K；0.2 M Sodium Acetate
10% PEG 8000 (w/v)
0.1 M trisodium citrate-citric acid pH 5.4
|
Resolution 2.01 Å R-free 0.237 |
| 9CYC SARS-CoV-2 PLpro in complex with inhibitor WEHI-P2 Deposited 2024-08-01 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1A0S (E)-1-[(3R)-1-cyclopentylpiperidin-3-yl]-N-methoxy-1-(6-methoxynaphthalen-2-yl)methanimine × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.4；281 K；0.2 M Sodium Acetate
10% PEG 8000 (w/v)
0.1 M trisodium citrate-citric acid pH 5.4
|
Resolution 2.01 Å R-free 0.237 |
| 9CYD SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4 Deposited 2024-08-02 | 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
1564–1878（315 aa）
|
Mutation：C111S | A1A0U (1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol × 1 ZN ZINC ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；0.3 M Sodium Malonate
6% w/v PGA-LM
0.05 mM Zinc Chloride
0.1 M Tris pH 7.6
|
Resolution 2.80 Å R-free 0.265 |
| 9CYK SARS-CoV-2 PLpro in complex with inhibitor WEHI-P24 Deposited 2024-08-02 | 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
1564–1878（315 aa）
Chain B
1564–1878（315 aa）
|
Mutation：C111S Mutation：C111S | A1A0V {(3R)-1-[(1s,4S)-4-hydroxycyclohexyl]piperidin-3-yl}(6-methoxynaphthalen-2-yl)methanone × 2 ACY ACETIC ACID × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.97；281 K；0.2 M Lithium Acetate
10% w/v PEG 8000
0.1 M trisodium citrate-citric acid pH 5.97
0.44 mM Inhibitor
|
Resolution 1.88 Å R-free 0.212 |
| 9EPL Mpro from SARS-CoV-2 with 298Q mutation Deposited 2024-03-18 | 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
3264–3563（300 aa）
|
Mutation：R298Q | GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate
|
Resolution 1.80 Å R-free 0.228 |
| 9EPM Mpro from SARS-CoV-2 with 4A mutation Deposited 2024-03-19 | 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
3264–3563（300 aa）
|
Mutation：R4A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% Polyethylene glycol monomethyl ether 5.000, 200 mM Potassium formate
|
Resolution 1.98 Å R-free 0.266 |
| 9EWM Mpro from SARS-CoV-2 with R4Q R298Q double mutations Deposited 2024-04-04 | 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
3264–3563（300 aa）
|
Mutation：R4Q, R298Q | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate
|
Resolution 2.63 Å R-free 0.336 |
| 9EWN Mpro from SARS-CoV-2 with 4Q mutation Deposited 2024-04-04 | 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
3264–3563（300 aa）
|
Mutation：R4Q | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 200 mM magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 5.5
|
Resolution 2.11 Å R-free 0.281 |
| 9EWO Mpro from SARS-CoV-2 with R4A R298A double mutations Deposited 2024-04-04 | 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
3264–3563（300 aa）
|
Mutation：R4A, R298A | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.12 mM benzamidine hydrochloride, 200 mM potassium formate
|
Resolution 3.00 Å R-free 0.275 |
| 9FQ9 Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21110 (compound 29b in publication) Deposited 2024-06-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1IF1 (5-chloranylpyridin-3-yl) 4-ethoxy-2-fluoranyl-benzoate × 2 BR BROMIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.0 M imidazole/MES (pH 6.5), 0.3 M NaF, 0.3 M NaBr, 0.3 M NaI; 30% (v/v), 12% (v/v) PEG500 MME, 6% (w/v) PEG20000
|
Resolution 1.25 Å R-free 0.213 |
| 9FQA Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21101 (compound 30b in publication) Deposited 2024-06-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1IEY (5-chloranylpyridin-3-yl) 2-fluoranyl-4-phenylmethoxy-benzoate × 2 MG MAGNESIUM ION × 2 BR BROMIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；1.0 M imidazole/MES (pH 6.5), 0.3 M NaF, 0.3 M NaBr, 0.3 M NaI; 30% (v/v), 12% (v/v) PEG500 MME, 6% (w/v) PEG20000
|
Resolution 1.47 Å R-free 0.241 |
| 9FW2 SARS CoV-2 nsp10 in complex with the ExoN domain from nsp14 Deposited 2024-06-28 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 GOL GLYCEROL × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.04-0.24 M Amino acids, 0.1 M buffer system 2 (pH 7.5), 16-38% v/v precipitant mix 2.
|
Resolution 1.77 Å R-free 0.183 |
| 9FWH Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019 Deposited 2024-06-30 | 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
4254–4383（130 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGQ (4R)-4-phenyl-1,2-thiazolidine 1,1-dioxide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 24.50%w/v Morpheus Amino acids: 0.09M
|
Resolution 2.35 Å R-free 0.247 |
| 9FWI Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | A1IGP (3-oxidanylazetidin-1-yl)-phenyl-methanone × 1 ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 36.50%w/v Morpheus Amino acids: 0.09M
|
Resolution 1.53 Å R-free 0.199 |
| 9FWJ Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00079 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 MG MAGNESIUM ION × 1 UYY 2-methoxybenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 27.50%w/v Morpheus Amino acids: 0.20M
|
Resolution 2.42 Å R-free 0.254 |
| 9FWK Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGT (4S)-4-pyridin-4-ylpyrrolidin-2-one × 1 DMS DIMETHYL SULFOXIDE × 1 A1IGS (4R)-4-pyridin-4-ylpyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 36.50%w/v Morpheus Amino acids: 0.11M
|
Resolution 1.51 Å R-free 0.199 |
| 9FWL Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00167 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 4 A1IGO 3-phenylthiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 36.50%w/v Morpheus Amino acids: 0.09M
|
Resolution 2.09 Å R-free 0.229 |
| 9FWM Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00180 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 A1IGR 1H-indole-3-carboxamide × 1 ZN ZINC ION × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 36.50%w/v Morpheus Amino acids: 0.14M
|
Resolution 1.57 Å R-free 0.213 |
| 9FWN Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 MG MAGNESIUM ION × 2 A1IGN 1-methyl-1-(phenylmethyl)urea × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 30.50%w/v Morpheus Amino acids: 0.20M
|
Resolution 1.87 Å R-free 0.231 |
| 9FWO Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00216 Deposited 2024-06-30 | 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
4254–4383（130 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGM 1-methylpyrrole-2-carboxamide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 27.50%w/v Morpheus Amino acids: 0.17M
|
Resolution 2.18 Å R-free 0.249 |
| 9FWP Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00198 Deposited 2024-06-30 | 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
4254–4383（130 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGK N-methylbenzamide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 21.50%w/v Morpheus Amino acids: 0.06M
|
Resolution 2.38 Å R-free 0.246 |
| 9FWQ Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00218 Deposited 2024-06-30 | 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
4254–4383（130 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGJ 5,6,7,8-tetrahydro-[1,2,4]triazolo[4,3-a]pyridine × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 29.00%w/v Morpheus Amino acids: 0.20M
|
Resolution 2.32 Å R-free 0.260 |
| 9FWR Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00249 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 A1IGL (4R)-4-phenyl-1,3-oxazolidin-2-one × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 23.00%w/v Morpheus Amino acids: 0.09M
|
Resolution 2.29 Å R-free 0.251 |
| 9FWS Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00258 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | MI7 7-METHOXY-1H-INDAZOLE × 1 DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 21.50%w/v Morpheus Amino acids: 0.11M
|
Resolution 1.43 Å R-free 0.213 |
| 9FWT Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259 Deposited 2024-06-30 | 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
4254–4384（131 aa）
|
Not recorded | VSL methyl 4,5,6,7-tetrahydro-2H-indazole-3-carboxylate × 1 DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 32.00%w/v Morpheus Amino acids: 0.11M
|
Resolution 1.64 Å R-free 0.214 |
| 9FWU Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00421 Deposited 2024-06-30 | 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
4254–4383（130 aa）
|
Not recorded | A1IGI N,N-dimethyl-3-oxidanyl-benzamide × 1 ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 32.00%w/v Morpheus Amino acids: 0.11M
|
Resolution 1.43 Å R-free 0.201 |
| 9FX6 Crystal structure of Cryo2RT SARS-CoV-2 main protease at 100K Deposited 2024-07-01 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 5 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；300 mM sodium nitrate, 300 mM disodium hydrogen phosphate, 300 mM ammonium sulphate, 100 mM MES/imidazole pH 6.5, 10% (w/v) PEG550 MME and 20% (w/v) PEG 20K
|
Resolution 2.23 Å R-free 0.267 |
| 9FZ4 SARS CoV-2 nsp10 in complex with theExoN domain from nsp14 Deposited 2024-07-04 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.04-0.24 M Amino acids, 0.1 M buffer system 2 (pH 7.5), 16-38% v/v precipitant mix 2.
|
Resolution 2.44 Å R-free 0.229 |
| 9FZK SARS CoV-2 nsp10 in complex with theExoN domain from nsp14 Deposited 2024-07-05 | 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
4254–4384（131 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.04-0.24 M Amino acids, 0.1 M buffer system 2 (pH 7.5), 16-38% v/v precipitant mix 2
|
Resolution 1.30 Å R-free 0.185 |
| 9G0H Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17A Deposited 2024-07-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 4 A1IHT [(1~{S},5~{R})-8-[(~{S})-(3-fluorophenyl)-[1-(2-thiophen-3-ylethyl)-1,2,3-triazol-4-yl]methyl]-3,8-diazabicyclo[3.2.1]octan-3-yl]-(5-methylpyridin-3-yl)methanone × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；1.5 mM inhibitor, 24% PEG1500, 0.05 M sodium malonate, 0.075 M imidazole, 0.075 M boric acid, 5 % DMSO, 1 mM DTT, 1.58 mM EDTA, 26.67 mM Tris, 20 mM NaCl, 1.33 mM TCEP, pH 7.8
|
Resolution 1.65 Å R-free 0.222 |
| 9G0I Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17B Deposited 2024-07-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 4 A1IHV [(1~{S},5~{R})-8-[(~{R})-(3-fluorophenyl)-[1-(2-thiophen-3-ylethyl)-1,2,3-triazol-4-yl]methyl]-3,8-diazabicyclo[3.2.1]octan-3-yl]-(5-methylpyridin-3-yl)methanone × 1 IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；1.5 mM inhibitor, 24% PEG1500, 0.05 M sodium malonate, 0.075 M imidazole, 0.075 M boric acid, 5 % DMSO, 1 mM DTT, 1.58 mM EDTA, 26.67 mM Tris, 20 mM NaCl, 1.33 mM TCEP, pH 7.8
|
Resolution 1.67 Å R-free 0.233 |
| 9GF7 SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a Deposited 2024-08-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1IYL ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]quinoline-8-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290.15 K；22-27% PEG1500, 100mM MTT buffer [DL-Malic acid, 4-Morpholine
Ethane Sulfonic acid (MES) monohydrate, 2-Amino-2-
(hydroxymethyl)-1,3- propanediol (TRIS)-HCl), pH=6.0].
|
Resolution 1.90 Å R-free 0.293 |
| 9GHN Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A Deposited 2024-08-15 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Mutation：Q256A Mutation：Q256A | EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20 % (w/v) PEG 1500, 0.1 M MMT, 5 % ethylene glycol
|
Resolution 1.40 Å R-free 0.218 |
| 9GHO Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of S284A Deposited 2024-08-15 | 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
3264–3569（306 aa）
|
Mutation：S284A | CL CHLORIDE ION × 2 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；27.5 PEG 1500, 5 % DMSO, 0.1 M MIB
|
Resolution 1.86 Å R-free 0.241 |
| 9GIJ Crystal structure of SARS-CoV-2 Mpro with compound 5 Deposited 2024-08-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1IL0 (2~{R})-3-(4-chlorophenyl)-2-[2-[(2~{R})-1-isoquinolin-4-ylcarbonylpyrrolidin-2-yl]ethanoyl-methyl-amino]-~{N}-methyl-propanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；PCB: 0.100000 M pH:6.00 ; PEG 1500: 25.000000 %w/v
|
Resolution 1.48 Å R-free 0.177 |
| 9GIL Crystal structure of SARS-CoV-2 Mpro with compound 12 Deposited 2024-08-19 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1IL7 (7~{R},11~{R},19~{E})-11-[(4-chlorophenyl)methyl]-13-oxa-3,10,23-triazatricyclo[19.3.1.0^{3,7}]pentacosa-1(24),19,21(25),22-tetraene-2,9,12-trione × 2 SO4 SULFATE ION × 7 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；(NH4)2SO4: 1.6 M ; Dioxane: 10 %v/v ; MES: 0.1 M pH: 6.50
|
Resolution 1.85 Å R-free 0.236 |
| 9GLV Crystal structure of SARS-CoV-2 Mpro with AB-343. Deposited 2024-08-28 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1IMY (1S,3S,4S)-N-[(2S)-1-azanylidene-3-[(3S)-5,5-dimethyl-2-oxidanylidene-pyrrolidin-3-yl]propan-2-yl]-2-[(2R)-3-cyclobutyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]propanoyl]-5,5-bis(fluoranyl)-2-azabicyclo[2.2.2]octane-3-carboxamide × 2 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；2M Calcium Acetate, 100mM Sodium Cacodylate pH 6.50 and 40% PEG 600.
|
Resolution 1.93 Å R-free 0.238 |
| 9GMQ Crystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor Deposited 2024-08-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | MXU ~{tert}-butyl ~{N}-[1-[(2~{S})-1-[[(2~{S},3~{R})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.02 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH8.5, 20 % w/v PEG 3350
|
Resolution 2.19 Å R-free 0.218 |
| 9H0F SARS-CoV-2 Mpro in complex with a silicon-containing inhibitor Deposited 2024-10-08 | 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
3264–3568（305 aa）
Chain B
3264–3568（305 aa）
|
Not recorded | GOL GLYCEROL × 1 A1IRW methyl-N-[(2S)-1-[(5R)-5-[[(2S)-1-azanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3-dimethyl-1,3-azasilolidin-1-yl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate × 2 SO4 SULFATE ION × 14 CL CHLORIDE ION × 9 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 15% PEG4K, 5% DMSO
|
Resolution 2.09 Å R-free 0.233 |
| 9HAJ Structure of compound 1 bound to SARS-CoV-2 main protease Deposited 2024-11-04 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1ITJ (5~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-1-(5-chloranylpyridin-3-yl)carbonyl-~{N}-ethyl-1,4-diazepane-5-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；Morpheus B3
|
Resolution 1.28 Å R-free 0.192 |
| 9HAK Structure of compound 119 bound to SARS-CoV-2 main protease Deposited 2024-11-04 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1ITI (5~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-~{N}-ethyl-1-thieno[2,3-c]pyridin-4-ylcarbonyl-1,4-diazepane-5-carboxamide × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus screen, condition A4
|
Resolution 1.25 Å R-free 0.176 |
| 9HHG A rare open conformation for Ubl2 domain of papain-like protease of SARS-CoV2 Deposited 2024-11-21 | 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
1564–1879（316 aa）
Chain B
1564–1879（316 aa）
|
Not recorded | GOL GLYCEROL × 2 ZN ZINC ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；1.45 M Ammonium Sulfate, 0.1 M Bicine pH 8, 10 % Glycerol
|
Resolution 1.95 Å R-free 0.221 |
| 9HHH A rare open conformation for Ubl2 domain of papain-like protease C111S of SARS-CoV2 Deposited 2024-11-21 | 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
1564–1879（316 aa）
Chain B
1564–1879（316 aa）
|
Mutation：C111S Mutation：C111S | GOL GLYCEROL × 3 ZN ZINC ION × 2 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；1.45 M Ammonium Sulfate, 0.1 M Bicine pH 8, 10 % Glycerol
|
Resolution 1.98 Å R-free 0.215 |
| 9HHI A rare open conformation for Ubl2 domain of papain-like protease without zinc of SARS-CoV2 Deposited 2024-11-21 | 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
1564–1879（316 aa）
Chain B
1564–1879（316 aa）
|
Not recorded | GOL GLYCEROL × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；1.45 M Ammonium Sulfate, 0.1 M Bicine pH 8, 10 % Glycerol
|
Resolution 2.70 Å R-free 0.284 |
| 9HJH Structure of compound 1 bound to SARS-CoV-2 main protease Deposited 2024-11-29 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1IVK (2~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-1-(5-chloranylpyridin-3-yl)carbonyl-~{N}-ethyl-1,4-diazepane-2-carboxamide × 2 EDO 1,2-ETHANEDIOL × 4 BR BROMIDE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350,
0.1M HEPES pH 7.0
|
Resolution 1.20 Å R-free 0.159 |
| 9IK2 The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H109 Deposited 2024-06-26 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1D9H tert-butyl N-[(2S)-1-[[(2S)-1-[[(2S)-1-azanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES monohydrate pH 6.0 and 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.80 Å R-free 0.212 |
| 9IKZ SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3- Deposited 2024-06-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain C
3860–3937（78 aa）
|
Not recorded | ZN ZINC ION × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 9IMK SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (dRTC) in post-capping state Deposited 2024-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: octadecameric |
Chain C
3860–3942（83 aa）
Chain J
3860–3942（83 aa）
|
Not recorded | ZN ZINC ION × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.01 Å |
| 9IMM SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (local dRTC) in post-capping state Deposited 2024-07-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: undecameric |
Chain C
3860–3942（83 aa）
|
Not recorded | ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 9IR9 SARS-CoV-2 3CL protease (3CLpro) in complex with compound 6 Deposited 2024-07-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1D7M (2~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]amino]-4-methyl-pentanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2-8% PEG6000, 100 mM MES, pH 6.0-7.25, 3% DMSO
|
Resolution 1.49 Å R-free 0.230 |
| 9IZB Crystal structure of SARS-CoV-2 main protease in complex with TMP1 Deposited 2024-08-01 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v PEG3350
|
Resolution 2.60 Å R-free 0.253 |
| 9J8T Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2 Deposited 2024-08-21 | 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
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG5000, 0.1M BIS-TRIS (pH6.5)
|
Resolution 2.39 Å R-free 0.265 |
| 9J8T Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2 Deposited 2024-08-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG5000, 0.1M BIS-TRIS (pH6.5)
|
Resolution 2.39 Å R-free 0.265 |
| 9J8U Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7 Deposited 2024-08-21 | 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
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG5000, 0.1M BIS-TRIS (pH6.5)
|
Resolution 2.71 Å R-free 0.245 |
| 9J8U Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7 Deposited 2024-08-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
3264–3569（306 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG5000, 0.1M BIS-TRIS (pH6.5)
|
Resolution 2.71 Å R-free 0.245 |
| 9JGV Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with Ibuzatrelvir Deposited 2024-09-08 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G15S Mutation：G15S | YDL N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.76 Å R-free 0.205 |
| 9JGW Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with Ibuzatrelvir Deposited 2024-09-08 | 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：K90R Mutation：K90R | YDL N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.49 Å R-free 0.216 |
| 9L09 SARS-CoV-2 C-RTC with 13-TP Deposited 2024-12-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
3860–3942（83 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9LVT Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4 Deposited 2025-02-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1L7Q 1-(2-azanylideneethyl)-6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-5-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
|
Resolution 1.90 Å R-free 0.237 |
| 9LVV Crystal structure of SARS-CoV-2 3CL protease in complex with compound 17 (S-892216) Deposited 2025-02-12 | 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
3264–3569（306 aa）
|
Not recorded | A1L7R 1-(2-azanylideneethyl)-6-[6,6-bis(fluoranyl)-2-azaspiro[3.3]heptan-2-yl]-5-(3-chloranyl-4-fluoranyl-phenyl)-3-(5-chloranylpyridin-3-yl)pyrimidine-2,4-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Lithium sulfate monohydrate, 20% w/v Polyethylene glycol 3,350
|
Resolution 1.90 Å R-free 0.242 |
| 9M6Q Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with Pomotrelvir Deposited 2025-03-07 | 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
3265–3568（304 aa）
Chain B
3265–3568（304 aa）
|
Mutation：S46F Mutation：S46F | ZQB Pomotrelvir bound form × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.95 Å R-free 0.271 |
| 9M9N Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Mutant del23. Deposited 2025-03-13 | 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
3264–3564（301 aa）
|
Mutation：del23 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES (pH 7.5),
8% (v/v) ethylene glycol
10% (v/v) PEG 8000
|
Resolution 1.75 Å R-free 0.239 |
| 9M9R Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Mutant del23 in Complex with Nirmatrelvir Deposited 2025-03-13 | 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
3264–3564（301 aa）
|
Mutation：del23 | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；100 mM imidazole (pH 8.0) and 10% (v/v) PEG 8000
|
Resolution 2.11 Å R-free 0.230 |
| 9MA3 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Mutant del23T45I in Complex with Nirmatrelvir (C2 space group) Deposited 2025-03-14 | 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
3264–3564（301 aa）
|
Mutation：del23,T45I | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；200 mM ammonium acetate and 20% (v/v) PEG 3350
|
Resolution 2.40 Å R-free 0.251 |
| 9MA6 Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Mutant del23T45I in Complex with Nirmatrelvir (P21 space group) Deposited 2025-03-14 | 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
3264–3564（301 aa）
Chain B
3264–3564（301 aa）
|
Mutation：del23,T45I Mutation：del23,T45I | 4WI (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；200 mM ammonium acetate and 20% (v/v) PEG 3350
|
Resolution 2.36 Å R-free 0.244 |
| 9MCI Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with Leritrelvir 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G3278S Mutation：G3278S | A1EN0 (3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20~24%PEG3350,0.12~0.21M sodium sulfate
|
Resolution 1.74 Å R-free 0.250 |
| 9MCJ Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with Leritrelvir 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
3266–3564（299 aa）
Chain B
3266–3564（299 aa）
|
Mutation：G3278S Mutation：G3278S | 7ON Leritrelvir bound form × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 1.74 Å R-free 0.250 |
| 9MCL Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with Leritrelvir 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
3266–3565（300 aa）
Chain B
3266–3565（300 aa）
|
Mutation：K3353R Mutation：K3353R | A1EN0 (3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.12~0.21M PEG3350,20%~24%Na2SO4
|
Resolution 2.10 Å R-free 0.229 |
| 9MDQ Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) Complex with Azapeptide Inhibitor 20a Deposited 2024-12-05 | 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
3264–3569（306 aa）
Fragment：UNP residues 3264-3569
|
Mutation：P132H | A1BKV N-[(2S)-1-{2-(dichloroacetyl)-2-[(2-oxo-1,2-dihydropyridin-3-yl)methyl]hydrazin-1-yl}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% w/v PEG 20000, 20% v/v PEG MME 550, 0.1M MOPS/HEPES-Na pH 7.5, 0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol
|
Resolution 1.60 Å R-free 0.203 |
| 9N3M SARS-CoV-2 Mpro L50F/E166A/L167F triple mutant bound to inhibitor Deposited 2025-01-31 | 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
3264–3569（306 aa）
|
Mutation：L50F, E166A, L167F | A1BVV (1S,2S,4S)-2-{[3-cyclopropyl-N-(4-methoxy-1H-indole-2-carbonyl)-L-alanyl]amino}-1-hydroxy-4-methyl-5-(methylamino)-5-oxopentane-1-sulfonic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.22 M potassium thiocyanate, 20% w/v PEG3500
|
Resolution 1.90 Å R-free 0.243 |
| 9OR4 Crystal structure of SARS-CoV2 PLpro in complex with a covalent inhibitor Deposited 2025-05-21 | 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 D
1565–1879（315 aa）
|
Not recorded | ZN ZINC ION × 1 A1CEE (2S)-3-amino-2-{1-[(1R)-1-(7-ethoxynaphthalen-1-yl)ethyl]piperidin-4-yl}-N-(2-oxo-2-{[(2Z)-4,4,4-trifluorobut-2-en-1-yl]amino}ethyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-32% PEG 3350, 0.1-0.38M K/Na tartrate tetrahydrate, 0.1M Bis-Tris propane, pH 7.5
|
Resolution 2.43 Å R-free 0.266 |
| 9OR4 Crystal structure of SARS-CoV2 PLpro in complex with a covalent inhibitor Deposited 2025-05-21 | 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 A
1565–1879（315 aa）
|
Not recorded | ZN ZINC ION × 1 A1CEE (2S)-3-amino-2-{1-[(1R)-1-(7-ethoxynaphthalen-1-yl)ethyl]piperidin-4-yl}-N-(2-oxo-2-{[(2Z)-4,4,4-trifluorobut-2-en-1-yl]amino}ethyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-32% PEG 3350, 0.1-0.38M K/Na tartrate tetrahydrate, 0.1M Bis-Tris propane, pH 7.5
|
Resolution 2.43 Å R-free 0.266 |
| 9P0F Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2 Deposited 2025-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
3173–3263（91 aa）
Chain B
3173–3263（91 aa）
Chain C
3173–3263（91 aa）
|
Not recorded | NA SODIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；Protein: 2.8 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3;
Screen: ComPAS (H8), 0.2M Sodium acetate, 0.1M MES (pH 6.5), 2.0M Sodium chloride;
Cryo: 4.0M Sodium formate.
|
Resolution 2.35 Å R-free 0.259 |
| 9PFH Crystal structure of SARS-CoV-2 Mpro Mutant P132H with C5a Deposited 2025-07-04 | 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
3264–3569（306 aa）
Fragment：UNP residues 3264-3569
Chain B
3264–3569（306 aa）
Fragment：UNP residues 3264-3569
|
Not recorded | WZK N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(5-hydroxyisoquinolin-4-yl)acetamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；296 K；0.1 M Tris, pH 8, 15% PEG8000, 10% ethylene glycol
|
Resolution 2.69 Å R-free 0.283 |
| 9PFI Crystal structure of SARS-CoV-2 Mpro Mutant P132H Deposited 2025-07-04 | 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
3264–3569（306 aa）
Fragment：UNP residues 3264-3569
Chain B
3264–3569（306 aa）
Fragment：UNP residues 3264-3569
|
Mutation：P132H Mutation：P132H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；296 K；0.1 M Tris, pH 8, 15% PEG8000, 10% ethylene glycol
|
Resolution 1.81 Å R-free 0.237 |
| 9RHS Structure of 3CL protease with a bound inhibitor Deposited 2025-06-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JF7 ~{N}-(4-bromanyl-3-nitro-phenyl)-2-(1,2,3-triazol-1-yl)ethanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.64 Å R-free 0.248 |
| 9RHT Structure of 3CL protease with a bound inhibitor Deposited 2025-06-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JF8 ~{N}-(5-cyclopentyl-1~{H}-pyrazol-3-yl)-4-fluoranyl-2-nitro-benzamide × 2 DMS DIMETHYL SULFOXIDE × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.62 Å R-free 0.226 |
| 9RHX SARS-CoV-2 main protease with a bound inhibitor Deposited 2025-06-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGE 2-pyridin-3-ylquinazoline × 2 DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.62 Å R-free 0.223 |
| 9RI0 SARS-CoV-2 3CL protease with a bound inhibitor Deposited 2025-06-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGF [1-[[5-chloranyl-1-(phenylmethyl)benzimidazol-2-yl]methyl]-1,2,4-triazol-3-yl]methanamine × 2 DMS DIMETHYL SULFOXIDE × 4 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.39 Å R-free 0.198 |
| 9RI1 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-10 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGD (4~{R})-~{N}-(3,4-dipropoxyphenyl)-2-oxidanylidene-3,4-dihydro-1~{H}-quinoline-4-carboxamide × 2 PG4 TETRAETHYLENE GLYCOL × 1 BR BROMIDE ION × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.31 Å R-free 0.180 |
| 9RI3 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGG [1-(2-methylsulfanyl-[1,3]thiazolo[4,5-d]pyrimidin-7-yl)-1,2,4-triazol-3-yl]methanimine × 2 DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.72 Å R-free 0.238 |
| 9RI4 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGC 2-azanyl-~{N}-[(1~{R},2~{S})-2-(4-chloranyl-3-fluoranyl-phenyl)cyclopropyl]-6-nitro-benzamide × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.76 Å R-free 0.257 |
| 9RI5 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGB ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-2-pyridin-3-yl-~{N}-(thiophen-2-ylmethyl)ethanamide × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.63 Å R-free 0.231 |
| 9RI8 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGH 4-(azetidin-1-yl)-2-isoquinolin-4-yl-thieno[2,3-d]pyrimidine × 1 SO4 SULFATE ION × 1 NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.78 Å R-free 0.250 |
| 9RID SARS-CoV-2 with a bound inhibitor Deposited 2025-06-11 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGI (2~{R})-2-[2-(benzotriazol-1-yl)ethanoyl-methyl-amino]-2-(3-fluorophenyl)ethanamide × 2 SO4 SULFATE ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.63 Å R-free 0.262 |
| 9RIX SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGK (4~{R})-~{N}-[2-(1-benzothiophen-3-yl)ethyl]-7-fluoranyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinoline-4-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 2 SO4 SULFATE ION × 2 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.73 Å R-free 0.257 |
| 9RIY SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGM [6-(4-iodanylphenoxy)pyrimidin-4-yl]methanimine × 2 DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.79 Å R-free 0.258 |
| 9RIZ SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGN (4~{R})-~{N}-(3-cyclopropylphenyl)-2-oxidanylidene-3,4-dihydro-1~{H}-1,8-naphthyridine-4-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.73 Å R-free 0.228 |
| 9RJ0 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGO 1-(benzimidazol-1-yl)-3-[(4~{S})-6-fluoranyl-3,4-dihydro-2~{H}-thiochromen-4-yl]urea × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.71 Å R-free 0.242 |
| 9RJ3 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGP (2~{R})-1-[3-(aminomethyl)-1,2,4-triazol-1-yl]-3-[2,5-bis(chloranyl)phenoxy]propan-2-ol × 2 DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.62 Å R-free 0.224 |
| 9RJ5 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1JGR 1-(2-cyclohexylethyl)-3-cyclopropyl-1-[(5-methyl-1,2-oxazol-3-yl)methyl]urea × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.25 Å R-free 0.176 |
| 9RJ7 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGS 4-fluoranyl-~{N}-(pyridin-3-ylmethyl)-2,3-dihydroindole-1-carboxamide × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.90 Å R-free 0.252 |
| 9RJ8 SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGT 4-fluoranyl-~{N}-(3-phenoxypropyl)-~{N}-(1,2-thiazol-5-ylmethyl)-2,3-dihydroindole-1-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.43 Å R-free 0.217 |
| 9RJF SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGU 3-(5-bromanylpyridin-3-yl)-1-[(1~{R})-1-phenylethyl]imidazolidine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.89 Å R-free 0.271 |
| 9RJR SARS-CoV-2 with a bound inhibitor Deposited 2025-06-12 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JGV 1-[[3,4-bis(fluoranyl)phenyl]methyl]-3-(5-bromanylpyridin-3-yl)imidazolidine-2,4-dione × 2 SO4 SULFATE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
|
Resolution 1.71 Å R-free 0.229 |
| 9RME Hybrid NMR/Xray structure of SARS-CoV2 macrodomain (nsp3b) in complex with the sulfamoyl derivative of GS-441524 Deposited 2025-06-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1025–1194（170 aa）
|
Not recorded | A1JHT [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 180；Pressure atmospheric
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 9SDM Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor GUE-4303 (compound 12 in publication) Deposited 2025-08-14 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1JNF N-[(2S)-1-[[(2S)-1-[2-[(3-chlorophenyl)methyl]-2-ethanoyl-hydrazinyl]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]thiophene-2-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 3 CO3 CARBONATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.7；295 K；23.5% PEG1500, 0.1M MIB (sodium malonate, imidazole and boric acid) pH 7.7, 5% DMSO, 1mM DTT, 0.25 mM EDTA
|
Resolution 1.55 Å R-free 0.231 |
| 9UCN Monomer of SARS-CoV-2 nsp4CTD Deposited 2025-04-04 | 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
3171–3263（93 aa）
Fragment：Nsp4C,CTD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.8 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate, at pH 4.6.
|
Resolution 1.44 Å R-free 0.236 |
| 9UCN Monomer of SARS-CoV-2 nsp4CTD Deposited 2025-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3171–3263（93 aa）
Fragment：Nsp4C,CTD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.8 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate, at pH 4.6.
|
Resolution 1.44 Å R-free 0.236 |
| 9UOQ Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 8 Deposited 2025-04-26 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3264–3569（306 aa）
|
Not recorded | A1EPZ (2~{S})-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]pentanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2-8% PEG6000, 100 mM MES, pH 6.0-7.25, 3% DMSO
|
Resolution 1.89 Å R-free 0.258 |
| 9VS1 Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15 Deposited 2025-07-08 | 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
3264–3569（306 aa）
Chain B
3264–3569（306 aa）
|
Not recorded | A1MA2 4-chloranyl-3-[6-methyl-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-2,4,5-tris(oxidanylidene)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidin-7-yl]benzenecarbonitrile × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05M Calcium chloride dihydrate, 0.1M BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol monomethyl ether 550
|
Resolution 1.70 Å R-free 0.223 |
440 other PDB entries and 508 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | R1A_SARS2 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–306； UniProt 3264–3569 |
