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9vkk

Crystal structure of EV71 3C protease in complex with bofutrelvir

Method: X-RAY DIFFRACTION D_max: 51.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vkk
deposition_date	2025-06-23
last_revision	2026-04-01
title	Crystal structure of EV71 3C protease in complex with bofutrelvir
keywords	Enterovirus, 3C protease, Complex, bofutrelvir, 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	16.54 Å
rg_electron	15.12 Å
i0	7612490.00
molecular_weight	20466.0 kDa
excluded_volume	25778 Å³
envelope_volume	28365 Å³
shell_volume	15414 Å³
envelope_diameter	50.8 Å
shell_rg	21.51 Å
envelope_rg	15.43 Å
shape_rg	15.12 Å
total_rg	16.25 Å
total_atoms	1440
n_residues	182
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	51.8 Å
rg_real	16.39 Å
rg_real_error	0.27 Å
i0_real	7.6120e+06
i0_real_error	8.5940e+04
rg_reciprocal	16.41 Å
i0_reciprocal	7613000.0000
total_estimate	0.8855
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.2 Å
skewness	0.048
kurtosis	-0.440
angular_range	— – 0.4800 Å⁻¹
current_alpha	0.0000
highest_alpha	2329000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protease 3C
formula_weight	20089.1 kDa
ec_number	3.4.22.28
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1541

GSPSLDFALSLLRRNIRQAQTDQGHFTMLGVRDRLAILPRHSQPGKTIWVEHKLINVLDAVELVDEQGVNLELTLVTLDTNEKFRDITKFIPEVITGASDATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKIIGIHIGGNGRQGFCAGLKRSYFASE

Source

organism	Human enterovirus 71 (strain BRCR)
ncbi_taxonomy_id	69153
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide ;
formula_weight	452.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	101

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6. Citations (1)

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length_a	78.205 Å
length_b	46.617 Å
length_c	51.920 Å
angle_alpha	90.00 °
angle_beta	106.64 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	28.920 Å
r_factor	0.1699
r_work	0.1674
r_free	0.2197

fit	/app/data/saxs_computation/vk/9vkk/9vkk.fit
pddf	/app/data/pr_computation/vk/9vkk/9vkk.pr.out
profile	/app/data/saxs_computation/vk/9vkk/9vkk.dat

Crystal structure of EV71 3C protease in complex with bofutrelvir

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