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9rga

Crystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS87208 from ECBL

Method: X-RAY DIFFRACTION D_max: 77.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rga
deposition_date	2025-06-06
title	Crystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS87208 from ECBL
keywords	crystallographic fragment screening, NS2B-NS3 Zika protease, ECBL-96 fragment library, 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	23.59 Å
rg_electron	22.65 Å
i0	29385300.00
molecular_weight	41393.0 kDa
excluded_volume	51750 Å³
envelope_volume	63453 Å³
shell_volume	23372 Å³
envelope_diameter	80.0 Å
shell_rg	29.33 Å
envelope_rg	22.88 Å
shape_rg	22.65 Å
total_rg	23.48 Å
total_atoms	5783
n_residues	383
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	77.2 Å
rg_real	23.56 Å
rg_real_error	0.66 Å
i0_real	2.9390e+07
i0_real_error	4.5510e+05
rg_reciprocal	23.57 Å
i0_reciprocal	29390000.0000
total_estimate	0.8158
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.8 Å
skewness	0.287
kurtosis	-0.454
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	8975000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Serine protease subunit NS2B
formula_weight	5865.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	6053

MTGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEEDGPPMRE

Source

organism	Zika virus
ncbi_taxonomy_id	64320
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Genome polyprotein
formula_weight	18877.4 kDa
mutation	C143S, R107K
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

GALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKSGRVIGLYGNGVVIKNGSYVSAITQGKREEETPVE

Source

organism	Zika virus
ncbi_taxonomy_id	64320
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	(3,5-dimethylfuran-2-yl)-[(2~{S})-2-(methylaminomethyl)pyrrolidin-1-yl]methanone
formula_weight	236.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	222

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6. Citations (1)

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length_a	59.820 Å
length_b	59.820 Å
length_c	214.120 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.380 Å
resolution_low	41.500 Å
r_factor	0.1782
r_work	0.1779
r_free	0.1901

fit	/app/data/saxs_computation/rg/9rga/9rga.fit
pddf	/app/data/pr_computation/rg/9rga/9rga.pr.out
profile	/app/data/saxs_computation/rg/9rga/9rga.dat

Crystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS87208 from ECBL

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)