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9xz6

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13699

Method: X-RAY DIFFRACTION D_max: 75.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xz6
deposition_date	2025-08-26
title	Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13699
keywords	Protease, SARS-CoV-2, Mpro, Apo, 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	22.32 Å
rg_electron	21.70 Å
i0	37987400.00
molecular_weight	31730.0 kDa
excluded_volume	30602 Å³
envelope_volume	50036 Å³
shell_volume	20039 Å³
envelope_diameter	76.9 Å
shell_rg	27.57 Å
envelope_rg	22.02 Å
shape_rg	21.70 Å
total_rg	22.26 Å
total_atoms	2388
n_residues	305
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	75.7 Å
rg_real	22.42 Å
rg_real_error	0.63 Å
i0_real	3.7990e+07
i0_real_error	5.5700e+05
rg_reciprocal	22.40 Å
i0_reciprocal	37990000.0000
total_estimate	0.7783
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.8 Å
skewness	0.476
kurtosis	-0.350
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	11730000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.000

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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	2442

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)-6,6-dimethyl-2-{[(2S)-4-(methylsulfanyl)-1-oxobutan-2-yl]carbamoyl}-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate ;
formula_weight	441.6 kDa
src_method	nat
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

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6. Citations (1)

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length_a	113.732 Å
length_b	52.847 Å
length_c	45.427 Å
angle_alpha	90.00 °
angle_beta	102.56 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.470 Å
resolution_low	47.760 Å
r_factor	0.2082
r_work	0.2055
r_free	0.2616

fit	/app/data/saxs_computation/xz/9xz6/9xz6.fit
pddf	/app/data/pr_computation/xz/9xz6/9xz6.pr.out
profile	/app/data/saxs_computation/xz/9xz6/9xz6.dat

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) in complex with Jun13699

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