SAXSdb — 9pak

▼

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 Chain B； UniProt 3248–3553	Not recorded	A1CHJ (1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M NaCl, Sodium/Potassium Phosphate 6.2, and 18% PEG1000	Resolution 1.86 Å R-free 0.239
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 3248–3553 Chain D； UniProt 3248–3553	Not recorded	A1CHJ (1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M NaCl, Sodium/Potassium Phosphate 6.2, and 18% PEG1000	Resolution 1.86 Å R-free 0.239

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 9PAK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WUR The crystal structure of the MERS-CoV papain-like protease (C111S) with human ubiquitin Deposited 2014-11-03	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 1482–1801（320 aa） Fragment：UNP residues 1482-1801	Mutation：C111S	IPA ISOPROPYL ALCOHOL × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；291 K；22% w/v PEG 4000, 15% v/v 2-propanol, 0.1M tri-sodium citrate pH 4.8 and 10% glycerol	Resolution 3.16 Å R-free 0.252
8PPL MERS-CoV Nsp1 bound to the human 43S pre-initiation complex Deposited 2023-07-07	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 × 50 PDB declaration: 52-meric	Chain Aj 2–193（192 aa）	Not recorded	ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 116 MET METHIONINE × 1 UNX UNKNOWN LIGAND × 129	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.65 Å
9INM Crystal structure of MERS main protease in complex with Bofutrelvir Deposited 2024-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3248–3548（301 aa） Chain D 3248–3548（301 aa）	Not recorded	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, SITTING DROP；298 K；0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000	Resolution 2.34 Å R-free 0.275
9INM Crystal structure of MERS main protease in complex with Bofutrelvir Deposited 2024-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 3248–3548（301 aa） Chain C 3248–3548（301 aa）	Not recorded	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, SITTING DROP；298 K；0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000	Resolution 2.34 Å R-free 0.275
9PAC Crystal structure of MERS-CoV 3CLpro with ALG-097608 (Inhibitor 1) Deposited 2025-06-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3248–3553（306 aa） Chain D 3248–3553（306 aa）	Not recorded	A1CHF (1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M NaCl, Sodium/Potassium Phosphate 6.2, and 18% PEG1000	Resolution 2.28 Å R-free 0.269
9PAC Crystal structure of MERS-CoV 3CLpro with ALG-097608 (Inhibitor 1) Deposited 2025-06-25	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3248–3553（306 aa） Chain B 3248–3553（306 aa）	Not recorded	A1CHF (1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2M NaCl, Sodium/Potassium Phosphate 6.2, and 18% PEG1000	Resolution 2.28 Å R-free 0.269
9XG7 The crystal structure of MERS-CoV Main protease in complex with inhibitor FD2-21 Deposited 2025-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3248–3551（304 aa） Chain B 3248–3551（304 aa）	Not recorded	A1EZ7 7-(5-azanylpyridin-3-yl)-2-(2-chlorophenyl)-5,7-diazaspiro[3.4]octane-6,8-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550	Resolution 2.53 Å R-free 0.298
9XG7 The crystal structure of MERS-CoV Main protease in complex with inhibitor FD2-21 Deposited 2025-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3248–3551（304 aa） Chain D 3248–3551（304 aa）	Not recorded	A1EZ7 7-(5-azanylpyridin-3-yl)-2-(2-chlorophenyl)-5,7-diazaspiro[3.4]octane-6,8-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550	Resolution 2.53 Å R-free 0.298
9Y8W MERS Mpro with EGT710 Deposited 2025-09-11	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 C 3248–3553（306 aa）	Not recorded	A1CBU (4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[6-(trifluoromethyl)pyridin-3-yl]imidazolidin-2-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M Hepes pH 7.5, 8% Ethylene Glycol, 10% Peg 8000	Resolution 3.04 Å R-free 0.278
9Y8W MERS Mpro with EGT710 Deposited 2025-09-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 3248–3553（306 aa） Chain D 3248–3553（306 aa）	Not recorded	A1CBU (4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[6-(trifluoromethyl)pyridin-3-yl]imidazolidin-2-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M Hepes pH 7.5, 8% Ethylene Glycol, 10% Peg 8000	Resolution 3.04 Å R-free 0.278
9YCK Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P15 RNA, monomeric form Deposited 2025-09-19	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 Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 4238–4377（140 aa） Chain B 5909–6432（524 aa）	Mutation：E191A	ZN ZINC ION × 5 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9YCL Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P15 RNA, dimeric form Deposited 2025-09-19	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 Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 4238–4377（140 aa） Chain B 5909–6432（524 aa） Chain D 4238–4377（140 aa） Chain E 5909–6432（524 aa）	Mutation：E191A Mutation：E191A	ZN ZINC ION × 10 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9YCM Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-U RNA Deposited 2025-09-19	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 Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 4238–4377（140 aa） Chain B 5909–6432（524 aa） Chain D 4238–4377（140 aa） Chain E 5909–6432（524 aa）	Mutation：E191A Mutation：E191A	ZN ZINC ION × 10 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9YCN Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA Deposited 2025-09-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 4238–4377（140 aa） Chain B 5909–6432（524 aa）	Not recorded	ZN ZINC ION × 5 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
9YCO Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-G RNA Deposited 2025-09-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 4238–4377（140 aa） Chain B 5909–6432（524 aa）	Not recorded	ZN ZINC ION × 5 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	R1AB_MERS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 3248–3553 Author chain B； PDBConstruct 1–306； UniProt 3248–3553 Author chain C； PDBConstruct 1–306； UniProt 3248–3553 Author chain D； PDBConstruct 1–306； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pak
Deposition date deposition_date	2025-06-25
最后修订 last_revision	2026-05-06
Structure title title	Crystal structure of MERS-CoV 3CLpro with ALG-097655 (Inhibitor 2)
Keywords keywords	HYDROLASE/INHIBITOR, 3CL Protease, Pan Coronavirus drug, Mpro, Nsp5, ALG-097655, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	36.72 Å
Radius of gyration Rg (electron density) rg_electron	36.62 Å
Forward intensity I(0) i0	526602000.00
Molecular weight molecular_weight	124450.0 kDa
Excluded volume excluded_volume	120190 Å³
Envelope volume envelope_volume	210810 Å³
Hydration-shell volume shell_volume	48215 Å³
Envelope diameter envelope_diameter	127.0 Å
Shell Rg shell_rg	42.71 Å
Envelope Rg envelope_rg	36.24 Å
Shape Rg shape_rg	36.66 Å
Total Rg total_rg	36.82 Å
Total atoms total_atoms	9344
Residues n_residues	1207
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

▼

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

Maximum dimension Dmax dmax	120.2 Å
Rg (real space) rg_real	36.79 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	5.2660e+08
I(0) uncertainty (real space) i0_real_error	8.1220e+06
Rg (reciprocal space) rg_reciprocal	36.75 Å
I(0) (reciprocal space) i0_reciprocal	526600000.0000
Solution quality estimate total_estimate	0.6865
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	25670000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.970; Smooth: 0.828

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	3C-like proteinase nsp5
Molecular weight formula_weight	33354.2 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10126

SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQ

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	;(1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name) ;
Molecular weight formula_weight	579.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	764

▶

8. Citations (1)

▶

Unit-cell length a length_a	63.656 Å
Unit-cell length b length_b	113.793 Å
Unit-cell length c length_c	92.013 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	32.580 Å
R factor r_factor	0.1996
R_work r_work	0.1976
R_free r_free	0.2391

fit	/app/data/saxs_computation/pa/9pak/9pak.fit
pddf	/app/data/pr_computation/pa/9pak/9pak.pr.out
profile	/app/data/saxs_computation/pa/9pak/9pak.dat

Crystal structure of MERS-CoV 3CLpro with ALG-097655 (Inhibitor 2)

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