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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：K9N638 New Search
21PDB entries
22Biological assembly
30chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
4R3D Crystal structure of MERS Coronavirus papain like protease Deposited 2014-08-15 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1481–1811（331 aa） Fragment：UNP RESIDUES 1481-1811
Not recorded 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
4R3D Crystal structure of MERS Coronavirus papain like protease Deposited 2014-08-15 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1481–1811（331 aa） Fragment：UNP RESIDUES 1481-1811
Not recorded 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
7T3Y Structure of MERS 3CL protease in complex with inhibitor 8c Deposited 2021-12-09 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.