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11ro

Crystal Structure of SARS-CoV-2 Mpro with UM-005

Method: X-RAY DIFFRACTION D_max: 82.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ro
deposition_date	2026-03-10
last_revision	2026-04-22
title	Crystal Structure of SARS-CoV-2 Mpro with UM-005
keywords	Mpro, SARS2, coronavirus, viral protease, main protease, VIRAL PROTEIN; VIRAL PROTEIN
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	26.08 Å
rg_electron	25.23 Å
i0	138183000.00
molecular_weight	61832.0 kDa
excluded_volume	59706 Å³
envelope_volume	98739 Å³
shell_volume	32207 Å³
envelope_diameter	85.8 Å
shell_rg	33.00 Å
envelope_rg	25.40 Å
shape_rg	25.22 Å
total_rg	25.86 Å
total_atoms	4678
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	82.1 Å
rg_real	25.95 Å
rg_real_error	0.43 Å
i0_real	1.3820e+08
i0_real_error	1.9480e+06
rg_reciprocal	26.00 Å
i0_reciprocal	138200000.0000
total_estimate	0.9057
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.7 Å
skewness	0.151
kurtosis	-0.544
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	41650000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5041

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	N-(trifluoroacetyl)-D-phenylalanyl-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide
formula_weight	545.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	307

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6. Citations (1)

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length_a	45.671 Å
length_b	54.175 Å
length_c	62.213 Å
angle_alpha	115.81 °
angle_beta	99.97 °
angle_gamma	90.08 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.710 Å
resolution_low	54.960 Å
r_factor	0.1946
r_work	0.1873
r_free	0.2393

fit	/app/data/saxs_computation/1r/11ro/11ro.fit
pddf	/app/data/pr_computation/1r/11ro/11ro.pr.out
profile	/app/data/saxs_computation/1r/11ro/11ro.dat

Crystal Structure of SARS-CoV-2 Mpro with UM-005

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