SAXSdb — 9atf

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

3C-like proteinase nsp5

Middle East respiratory syndrome-related coronavirus

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 3248–3553	Fragment：UNP residues 3248-3553	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

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 9ATF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4R3D Crystal structure of MERS Coronavirus papain like protease Deposited 2014-08-15	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 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	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 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	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 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 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 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 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 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 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 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 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
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 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 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 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 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 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 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 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 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 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 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 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 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	R1A_MERS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–313； UniProt 3248–3553

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9atf
Deposition date deposition_date	2024-02-26
Structure title title	Crystal structure of MERS 3CL protease in complex with a 1-methyl-4,4-difluorocyclohexyl 2-pyrrolidone inhibitor
Keywords keywords	MERS, 3CL protease inhibitors, COVID-19, viral protein, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.15 Å
Radius of gyration Rg (electron density) rg_electron	21.62 Å
Forward intensity I(0) i0	19193200.00
Molecular weight molecular_weight	33265.0 kDa
Excluded volume excluded_volume	41535 Å³
Envelope volume envelope_volume	47994 Å³
Hydration-shell volume shell_volume	19495 Å³
Envelope diameter envelope_diameter	76.2 Å
Shell Rg shell_rg	27.20 Å
Envelope Rg envelope_rg	21.66 Å
Shape Rg shape_rg	21.63 Å
Total Rg total_rg	22.32 Å
Total atoms total_atoms	2329
Residues n_residues	305
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	73.2 Å
Rg (real space) rg_real	22.27 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.9190e+07
I(0) uncertainty (real space) i0_real_error	2.8030e+05
Rg (reciprocal space) rg_reciprocal	22.25 Å
I(0) (reciprocal space) i0_reciprocal	19190000.0000
Solution quality estimate total_estimate	0.7914
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.464
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6901000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	3C-like proteinase nsp5
Molecular weight formula_weight	34314.2 kDa
EC 编号 ec_number	3.4.22.69
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2629

MHHHHHHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQ

来源 Source

来源生物 organism	Middle East respiratory syndrome-related coronavirus
NCBI Class编号 ncbi_taxonomy_id	1335626
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	624.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	624.7 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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8. Citations (1)

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Unit-cell length a length_a	101.125 Å
Unit-cell length b length_b	58.034 Å
Unit-cell length c length_c	49.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	23.350 Å
R factor r_factor	0.1564
R_work r_work	0.1552
R_free r_free	0.1786

fit	/app/data/saxs_computation/at/9atf/9atf.fit
pddf	/app/data/pr_computation/at/9atf/9atf.pr.out
profile	/app/data/saxs_computation/at/9atf/9atf.dat

Crystal structure of MERS 3CL protease in complex with a 1-methyl-4,4-difluorocyclohexyl 2-pyrrolidone inhibitor

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

3C-like proteinase nsp5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction