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9q7s

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13735

Method: X-RAY DIFFRACTION D_max: 72.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q7s
deposition_date	2025-08-25
title	Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13735
keywords	Protease, SARS-CoV-2, Mpro, COVID-19, VIRAL PROTEIN, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	22.33 Å
rg_electron	21.73 Å
i0	38442300.00
molecular_weight	31945.0 kDa
excluded_volume	30795 Å³
envelope_volume	49996 Å³
shell_volume	20031 Å³
envelope_diameter	76.6 Å
shell_rg	27.44 Å
envelope_rg	22.01 Å
shape_rg	21.74 Å
total_rg	22.26 Å
total_atoms	2404
n_residues	306
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	72.7 Å
rg_real	22.99 Å
rg_real_error	0.18 Å
i0_real	3.8120e+07
i0_real_error	4.2740e+05
rg_reciprocal	22.40 Å
i0_reciprocal	38440000.0000
total_estimate	0.6673
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	22.0 Å
skewness	0.478
kurtosis	-0.399
angular_range	— – 0.3550 Å⁻¹
current_alpha	6.9520
highest_alpha	11060000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 0.911; Sysdev: 0.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.434

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2447

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	;methyl {(2S)-1-[(1R,2S,5S)-2-{[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-5-(methylsulfanyl)-1-oxopentan-3-yl]carbamoyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate (non-preferred name) ;
formula_weight	526.7 kDa
src_method	nat
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (1)

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length_a	114.101 Å
length_b	53.189 Å
length_c	45.609 Å
angle_alpha	90.00 °
angle_beta	102.02 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.700 Å
resolution_low	48.060 Å
r_factor	0.1940
r_work	0.1920
r_free	0.2347

fit	/app/data/saxs_computation/q7/9q7s/9q7s.fit
pddf	/app/data/pr_computation/q7/9q7s/9q7s.pr.out
profile	/app/data/saxs_computation/q7/9q7s/9q7s.dat

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13735

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction