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9ri5

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 83.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ri5
deposition_date	2025-06-11
last_revision	2025-07-09
title	SARS-CoV-2 with a bound inhibitor
keywords	protease, inhibitor, 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	26.60 Å
rg_electron	25.54 Å
i0	75621700.00
molecular_weight	67649.0 kDa
excluded_volume	84445 Å³
envelope_volume	100390 Å³
shell_volume	32456 Å³
envelope_diameter	87.0 Å
shell_rg	33.15 Å
envelope_rg	25.67 Å
shape_rg	25.59 Å
total_rg	26.19 Å
total_atoms	9365
n_residues	605
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	83.1 Å
rg_real	26.47 Å
rg_real_error	0.51 Å
i0_real	7.5620e+07
i0_real_error	1.1120e+06
rg_reciprocal	26.51 Å
i0_reciprocal	75620000.0000
total_estimate	0.7440
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.156
kurtosis	-0.547
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	39180000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.291; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9724

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-2-pyridin-3-yl-~{N}-(thiophen-2-ylmethyl)ethanamide
formula_weight	348.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	359

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6. Citations (1)

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length_a	67.840 Å
length_b	100.030 Å
length_c	104.140 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.634 Å
resolution_low	72.141 Å
r_factor	—
r_work	0.1979
r_free	0.2312

fit	/app/data/saxs_computation/ri/9ri5/9ri5.fit
pddf	/app/data/pr_computation/ri/9ri5/9ri5.pr.out
profile	/app/data/saxs_computation/ri/9ri5/9ri5.dat

SARS-CoV-2 with a bound inhibitor

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