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9tpg

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 1

Method: X-RAY DIFFRACTION D_max: 66.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tpg
deposition_date	2025-12-18
title	Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 1
keywords	Zika virus, NS2B-NS3 Protease, allosteric inhibitor, compound 1, HYDROLASE, 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	18.72 Å
rg_electron	17.98 Å
i0	14942400.00
molecular_weight	19090.0 kDa
excluded_volume	18308 Å³
envelope_volume	32524 Å³
shell_volume	15717 Å³
envelope_diameter	64.9 Å
shell_rg	23.93 Å
envelope_rg	19.04 Å
shape_rg	17.98 Å
total_rg	18.77 Å
total_atoms	1439
n_residues	181
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	66.0 Å
rg_real	18.80 Å
rg_real_error	0.61 Å
i0_real	1.4940e+07
i0_real_error	1.8990e+05
rg_reciprocal	18.79 Å
i0_reciprocal	14940000.0000
total_estimate	0.7144
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	20.8 Å
skewness	0.542
kurtosis	0.063
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	2555000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.497; Stabil: 0.960; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Genome polyprotein
formula_weight	23950.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1470

MVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEDDGPPMAGGGGSGGGGSGALWDVPAPKEVKKGETTDGVYRVMTRGLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRR

Source

organism	Zika virus
ncbi_taxonomy_id	64320
host_organism	Escherichia coli

Entity 2 non-polymer

description	(1~{E})-1-[3-[(2~{R})-1-phenylpropan-2-yl]-2~{H}-1,2,3-oxadiazol-3-ium-5-ylidene]-3-[3-(trifluoromethyl)phenyl]urea
formula_weight	391.4 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 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

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6. Citations (1)

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length_a	59.575 Å
length_b	91.546 Å
length_c	103.844 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	2.480 Å
resolution_low	68.671 Å
r_factor	—
r_work	0.2470
r_free	0.2959

fit	/app/data/saxs_computation/tp/9tpg/9tpg.fit
pddf	/app/data/pr_computation/tp/9tpg/9tpg.pr.out
profile	/app/data/saxs_computation/tp/9tpg/9tpg.dat