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4r3d

Crystal structure of MERS Coronavirus papain like protease

Method: X-RAY DIFFRACTION Dmax: 122.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Non-structural protein 3

Betacoronavirus England 1

UniProt K9N638

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1481–1811 Fragment：UNP RESIDUES 1481-1811 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M sodium chloride, 0.1M HEPES (pH 7.0), 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.82 Å R-free 0.224
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1481–1811 Fragment：UNP RESIDUES 1481-1811 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M sodium chloride, 0.1M HEPES (pH 7.0), 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.82 Å R-free 0.224

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 4R3D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7T3Y Structure of MERS 3CL protease in complex with inhibitor 8c Deposited 2021-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：Full Length
Chain B 3248–3553（306 aa） Fragment：Full Length
Not recorded F5L (1R,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 F8C (1S,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% (w/v) PEG 3350, 100 mM, 200 mM ammonium sulfate
Resolution 1.90 Å R-free 0.258
7T3Z Structure of MERS 3CL protease in complex with inhibitor 9c Deposited 2021-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：Full Length
Chain B 3248–3553（306 aa） Fragment：Full Length
Not recorded FHS (1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[7-(phenylacetyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid × 2 FEY (1R,2S)-2-{[N-({[(2r,4R)-7-acetyl-7-azaspiro[3.5]non-5-en-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；30% (w/v) PEG 550 MME, 100 mM, 50 mM magnesium chloride
Resolution 1.95 Å R-free 0.206
7T40 Structure of MERS 3CL protease in complex with inhibitor 10c Deposited 2021-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：Full Length
Not recorded FV5 (1R,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 FVE (1S,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；17% (w/v) PEG 10000, 100 mM Bis-Tris, 100 mM ammonium acetate
Resolution 1.70 Å R-free 0.195
7T41 Structure of MERS 3CL protease in complex with inhibitor 14c Deposited 2021-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：Full Length
Not recorded FWI (1R,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid × 2 FZI (1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 100 mM Hepes, 200 mM magnesium chloride
Resolution 2.10 Å R-free 0.237
8R5J Crystal structure of MERS-CoV main protease Deposited 2023-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa）
Chain B 3248–3553（306 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Sodium malonate dibasic monohydrate, 20% w/v PEG 3350
Resolution 1.90 Å R-free 0.242
9ATA Crystal structure of MERS 3CL protease in complex with a phenylethyl 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Chain B 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGG (1S,2S)-1-hydroxy-2-{[N-({[(2S)-5-oxo-1-(2-phenylethyl)pyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGH (1R,2S)-1-hydroxy-2-{[N-({[(2S)-5-oxo-1-(2-phenylethyl)pyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% w/v PEG2000 MME, 150 mM potassium bromide
Resolution 1.65 Å R-free 0.188
9ATD Crystal structure of MERS 3CL protease in complex with a ethylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) inhibitor Deposited 2024-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGL (1S,2S)-2-{[N-({[(2S)-1-(2-cyclohexylethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGK (1R,2S)-2-{[N-({[(2S)-1-(2-cyclohexylethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG3350, 100 mM Bis-Tris, pH 5.5, 200 mM ammonium acetate
Resolution 1.80 Å R-free 0.201
9ATE Crystal structure of MERS 3CL protease in complex with a methylbicyclo[2.2.1]heptane 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Chain B 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGN (1S,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGM (1R,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25% w/v PEG3350, 100 mM HEPES, pH 7.5
Resolution 1.85 Å R-free 0.191
9ATF Crystal structure of MERS 3CL protease in complex with a 1-methyl-4,4-difluorocyclohexyl 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGP (1S,2S)-2-({N-[({(2S)-1-[(4,4-difluorocyclohexyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGO (1R,2S)-2-({N-[({(2S)-1-[(4,4-difluorocyclohexyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG3350, 100 mM Bis-Tris, pH 5.5, 200 mM sodium chloride
Resolution 1.50 Å R-free 0.179
9ATG Crystal structure of MERS 3CL protease in complex with a 2,2-difluoro-5-methylbenzo[1,3]dioxole 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGT (1S,2S)-2-({N-[({(2S)-1-[(2,2-difluoro-2H-1,3-benzodioxol-5-yl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGS (1R,2S)-2-({N-[({(2S)-1-[(2,2-difluoro-2H-1,3-benzodioxol-5-yl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG3350, 100 mM Tris, pH 8.5, 200 mM magnesium chloride hexahydrate
Resolution 1.75 Å R-free 0.199
9ATH Crystal structure of MERS 3CL protease in complex with a methylbicyclo[2.2.1]heptene 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Chain B 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGR (1S,2S)-2-{[N-({[(2S)-1-{[(1R,2S,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGQ (1R,2S)-2-{[N-({[(2S)-1-{[(1R,2S,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；800 mM potassium sodium tartrate tetrahydrate, 100 mM Tris, pH 8.5, 0.5% w/v PEG5000 MME
Resolution 1.65 Å R-free 0.208
9ATI Crystal structure of MERS 3CL protease in complex with a racemic bicyclo[2.2.1]heptenyl-methyl 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGV (1S,2S)-2-{[N-({[(3S)-1-{[(1R,2R,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGU (1R,2S)-2-{[N-({[(3S)-1-{[(1R,2R,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG3350, 100 mM Tris, pH 8.5, 200 mM ammonium acetate
Resolution 1.60 Å R-free 0.196
9ATJ Crystal structure of MERS 3CL protease in complex with a m-chlorobenzyl 2-pyrrolidone inhibitor Deposited 2024-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded MG MAGNESIUM ION × 2 A1AGJ (1S,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGI (1R,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；15% v/v PEG400, 100 mM MES, pH 6.0, 100 mM calcium acetate
Resolution 1.40 Å R-free 0.170
9ATS Crystal structure of MERS 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) Deposited 2024-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGX (1S,2S)-2-{[N-({[(2S)-1-(cyclohexylmethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；28% w/v PEG2000 MME, 100 mM Bis-Tris pH 6.5
Resolution 2.50 Å R-free 0.252
9ATT Crystal structure of MERS 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (R-enantiomer) Deposited 2024-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Chain B 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded A1AGZ (1S,2S)-2-{[N-({[(2R)-1-(cyclohexylmethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 A1AGY (1R,2S)-2-{[N-({[(2R)-1-(cyclohexylmethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10% w/v PEG3350, 100 mM HEPES, pH 7.5, 200 mM L-proline
Resolution 1.70 Å R-free 0.210
9BOO Crystal structure of MERS-CoV Nsp5 in complex with PF-07817883 Deposited 2024-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：residues 3248-3553
Not recorded 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；pH 7；291.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES 7.0, 20 % w/v PEG 6000
Resolution 1.50 Å R-free 0.195
9N9V Main protease of MERS in complex with AVI8122 Deposited 2025-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3550（303 aa）
Chain B 3248–3550（303 aa）
Not recorded A1BWH N-[(2S)-3-cyclopropyl-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}amino)-1-oxopropan-2-yl]-7-fluoro-1H-indole-2-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291.15 K；8% PEG 8K, 0.1 M Tris-HCl pH 7.5
Resolution 2.50 Å R-free 0.287
9ZJ8 Crystal structure of MERS 3CL protease in complex with inhibitor AMJ-II-72 Deposited 2025-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.247
9ZJB Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-46 Deposited 2025-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.88 Å R-free 0.216
9ZJC Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-52 Deposited 2025-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3248–3553（306 aa） Fragment：UNP residues 3248-3553
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.223

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name R1A_CVEMC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–336； UniProt 1481–1811 Author chain B； PDBConstruct 6–336； UniProt 1481–1811

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

SAXS scattering curve SAXS Profile

SAXS profile for 4r3d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4r3d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4r3d
Deposition date deposition_date2014-08-15
Structure title titleCrystal structure of MERS Coronavirus papain like protease
Keywords keywordsBETA STRANDS, ZINC FINGER, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.82 Å
Radius of gyration Rg (electron density) rg_electron35.26 Å
Forward intensity I(0) i078626000.00
Molecular weight molecular_weight71318.0 kDa
Excluded volume excluded_volume89514 ų
Envelope volume envelope_volume121520 ų
Hydration-shell volume shell_volume30375 ų
Envelope diameter envelope_diameter128.0 Å
Shell Rg shell_rg39.00 Å
Envelope Rg envelope_rg35.21 Å
Shape Rg shape_rg35.15 Å
Total Rg total_rg35.92 Å
Total atoms total_atoms4995
Residues n_residues639
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.0 Å
Rg (real space) rg_real36.13 Å
Rg uncertainty (real space) rg_real_error1.16 Å
I(0) (real space) i0_real7.8630e+07
I(0) uncertainty (real space) i0_real_error1.1610e+06
Rg (reciprocal space) rg_reciprocal35.94 Å
I(0) (reciprocal space) i0_reciprocal78610000.0000
Solution quality estimate total_estimate0.6292
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.0 Å
Skewness Skewness skewness0.473
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4558000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.737; Smooth: 0.579
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4r3da1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4r3da2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain
Domain ID domain_idd4r3db1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4r3db2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain

CATH v4.4 (6 domains)

Domain ID domain_id4r3dA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id4r3dA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id4r3dA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
Domain ID domain_id4r3dB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id4r3dB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id4r3dB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
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9. Files and Curves (10)