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9u90

Crystal structure of KRAS-G12D/E62K mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 51.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u90
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/E62K mutant in complex with GDP
keywords	Complex structure, 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	16.44 Å
rg_electron	15.07 Å
i0	7908410.00
molecular_weight	19773.0 kDa
excluded_volume	24421 Å³
envelope_volume	27220 Å³
shell_volume	14942 Å³
envelope_diameter	51.9 Å
shell_rg	21.36 Å
envelope_rg	15.42 Å
shape_rg	15.07 Å
total_rg	16.19 Å
total_atoms	1384
n_residues	169
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	51.4 Å
rg_real	16.29 Å
rg_real_error	0.21 Å
i0_real	7.9080e+06
i0_real_error	9.4060e+04
rg_reciprocal	16.30 Å
i0_reciprocal	7908000.0000
total_estimate	0.8923
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.7 Å
skewness	0.041
kurtosis	-0.473
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1618000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Isoform 2B of GTPase KRas
formula_weight	21604.3 kDa
ec_number	3.6.5.2
mutation	G12D,E62K
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1532

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQKEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

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

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	140

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6. Citations (1)

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length_a	41.226 Å
length_b	51.682 Å
length_c	67.627 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	1.200 Å
resolution_low	33.810 Å
r_factor	0.1730
r_work	0.1715
r_free	0.2024

fit	/app/data/saxs_computation/u9/9u90/9u90.fit
pddf	/app/data/pr_computation/u9/9u90/9u90.pr.out
profile	/app/data/saxs_computation/u9/9u90/9u90.dat

Crystal structure of KRAS-G12D/E62K mutant in complex with GDP

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