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9pkr

SARS-CoV2 main protease bound to compound 26

Method: X-RAY DIFFRACTION D_max: 83.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pkr
deposition_date	2025-07-14
title	SARS-CoV2 main protease bound to compound 26
keywords	Protease, Mpro, SARS, SARS-CoV2, Inhibitor, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex; VIRAL PROTEIN/INHIBITOR
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	26.33 Å
rg_electron	25.45 Å
i0	143881000.00
molecular_weight	63108.0 kDa
excluded_volume	60848 Å³
envelope_volume	99632 Å³
shell_volume	32303 Å³
envelope_diameter	88.9 Å
shell_rg	33.24 Å
envelope_rg	25.65 Å
shape_rg	25.43 Å
total_rg	26.06 Å
total_atoms	4747
n_residues	610
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	83.7 Å
rg_real	26.20 Å
rg_real_error	0.58 Å
i0_real	1.4390e+08
i0_real_error	2.3150e+06
rg_reciprocal	26.24 Å
i0_reciprocal	143900000.0000
total_estimate	0.9039
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.165
kurtosis	-0.543
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	48170000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33697.4 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5386

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 polymer

description	(BOC)F(ALC)(ELL) peptide
formula_weight	556.7 kDa
src_method	syn
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

FAX

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	620

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6. Citations (1)

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length_a	49.670 Å
length_b	106.298 Å
length_c	54.470 Å
angle_alpha	90.00 °
angle_beta	103.65 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.540 Å
resolution_low	43.950 Å
r_factor	0.1729
r_work	0.1721
r_free	0.2009

fit	/app/data/saxs_computation/pk/9pkr/9pkr.fit
pddf	/app/data/pr_computation/pk/9pkr/9pkr.pr.out
profile	/app/data/saxs_computation/pk/9pkr/9pkr.dat

SARS-CoV2 main protease bound to compound 26

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)