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10dv

Room Temperature X-Ray Structure of SARS CoV-2 Main Protease Intermediate Precursor with Ensitrelvir (ESV)

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10dv
deposition_date	2026-01-14
last_revision	2026-05-06
title	Room Temperature X-Ray Structure of SARS CoV-2 Main Protease Intermediate Precursor with Ensitrelvir (ESV)
keywords	SARS CoV-2 main protease, enzyme-inhibitor complex, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE 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	26.70 Å
rg_electron	25.68 Å
i0	77068300.00
molecular_weight	67486.0 kDa
excluded_volume	83893 Å³
envelope_volume	101770 Å³
shell_volume	32680 Å³
envelope_diameter	86.7 Å
shell_rg	33.33 Å
envelope_rg	25.82 Å
shape_rg	25.66 Å
total_rg	26.55 Å
total_atoms	4730
n_residues	602
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	82.8 Å
rg_real	26.57 Å
rg_real_error	0.38 Å
i0_real	7.7070e+07
i0_real_error	9.4470e+05
rg_reciprocal	26.61 Å
i0_reciprocal	77070000.0000
total_estimate	0.7239
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.1 Å
skewness	0.141
kurtosis	-0.571
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	42740000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 0.199; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Replicase polyprotein 1ab,Immunoglobulin G-binding protein G
formula_weight	41332.7 kDa
mutation	C145A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4854

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSAGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVMQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTELEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione ;
formula_weight	531.9 kDa
src_method	nat
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	124

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6. Citations (1)

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length_a	54.890 Å
length_b	68.343 Å
length_c	68.363 Å
angle_alpha	73.99 °
angle_beta	77.12 °
angle_gamma	85.52 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.050 Å
resolution_low	22.320 Å
r_factor	0.2126
r_work	0.2113
r_free	0.2345

fit	/app/data/saxs_computation/0d/10dv/10dv.fit
pddf	/app/data/pr_computation/0d/10dv/10dv.pr.out
profile	/app/data/saxs_computation/0d/10dv/10dv.dat

Room Temperature X-Ray Structure of SARS CoV-2 Main Protease Intermediate Precursor with Ensitrelvir (ESV)

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