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9vng

Small GTPase RhoA Y42C mutant in complex with covalent inhibitor

Method: X-RAY DIFFRACTION D_max: 57.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vng
deposition_date	2025-06-30
title	Small GTPase RhoA Y42C mutant in complex with covalent inhibitor
keywords	Small GTPase, RhoA, Y42C mutant, covalent inhibitor, CELL INVASION; CELL INVASION
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	16.68 Å
rg_electron	15.77 Å
i0	13997600.00
molecular_weight	18542.0 kDa
excluded_volume	17761 Å³
envelope_volume	28386 Å³
shell_volume	15087 Å³
envelope_diameter	58.6 Å
shell_rg	21.81 Å
envelope_rg	16.30 Å
shape_rg	15.78 Å
total_rg	16.52 Å
total_atoms	1393
n_residues	172
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	57.2 Å
rg_real	16.62 Å
rg_real_error	0.36 Å
i0_real	1.4000e+07
i0_real_error	1.9220e+05
rg_reciprocal	16.63 Å
i0_reciprocal	14000000.0000
total_estimate	0.7848
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	20.8 Å
skewness	0.307
kurtosis	-0.134
angular_range	— – 0.4750 Å⁻¹
current_alpha	0.0000
highest_alpha	3556000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Transforming protein RhoA
formula_weight	20464.5 kDa
ec_number	3.6.5.2
mutation	Y42C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1519

GMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENCVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	4-(2-nitroethyl)-1~{H}-indole
formula_weight	190.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	120

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6. Citations (1)

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length_a	32.040 Å
length_b	63.500 Å
length_c	82.720 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.430 Å
resolution_low	34.660 Å
r_factor	0.1907
r_work	0.1892
r_free	0.2206

fit	/app/data/saxs_computation/vn/9vng/9vng.fit
pddf	/app/data/pr_computation/vn/9vng/9vng.pr.out
profile	/app/data/saxs_computation/vn/9vng/9vng.dat