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9x54

Crystal structure of RhoGDI2 in complex with Compound 3054b

Method: X-RAY DIFFRACTION D_max: 57.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x54
deposition_date	2025-10-12
title	Crystal structure of RhoGDI2 in complex with Compound 3054b
keywords	Inhibitor, Complex, Rho GDP-dissociation inhibitor 2, SIGNALING PROTEIN; SIGNALING 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	16.44 Å
rg_electron	15.41 Å
i0	9016670.00
molecular_weight	15086.0 kDa
excluded_volume	14721 Å³
envelope_volume	23338 Å³
shell_volume	13160 Å³
envelope_diameter	56.3 Å
shell_rg	20.95 Å
envelope_rg	15.78 Å
shape_rg	15.36 Å
total_rg	16.31 Å
total_atoms	1145
n_residues	138
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	57.1 Å
rg_real	16.42 Å
rg_real_error	0.41 Å
i0_real	9.0170e+06
i0_real_error	1.2220e+05
rg_reciprocal	16.43 Å
i0_reciprocal	9017000.0000
total_estimate	0.6967
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	19.1 Å
skewness	0.367
kurtosis	-0.172
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1690000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 0.287; Positv: 1.000; Valcen: 0.985; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Rho GDP-dissociation inhibitor 2
formula_weight	16158.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1181

DPKAPNVVVTRLTLVCESAPGPITMDLTGDLEALKKETIVLKEGSEYRVKIHFKVNRDIVSGLKYVQHTYRTGVKVDKATFMVGSYGPRPEEYEFLTPVEEAPKGMLARGTYHNKSFFTDDDKQDHLSWEWNLSIKKEWTE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(3~{R})-~{N}-[2-oxidanylidene-2-[[(~{R})-(4-phenylphenyl)-thiophen-2-yl-methyl]amino]ethyl]pyrrolidine-3-carboxamide
formula_weight	419.5 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	55.313 Å
length_b	55.313 Å
length_c	95.148 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.130 Å
resolution_low	36.180 Å
r_factor	0.1946
r_work	0.1926
r_free	0.2337

fit	/app/data/saxs_computation/x5/9x54/9x54.fit
pddf	/app/data/pr_computation/x5/9x54/9x54.pr.out
profile	/app/data/saxs_computation/x5/9x54/9x54.dat

Crystal structure of RhoGDI2 in complex with Compound 3054b

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