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9u8v

Crystal structure of KRAS-G12D/Y96S mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 49.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8v
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/Y96S 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	16.31 Å
rg_electron	14.94 Å
i0	7558300.00
molecular_weight	19252.0 kDa
excluded_volume	23742 Å³
envelope_volume	26318 Å³
shell_volume	14626 Å³
envelope_diameter	49.5 Å
shell_rg	21.12 Å
envelope_rg	15.22 Å
shape_rg	14.94 Å
total_rg	16.01 Å
total_atoms	1347
n_residues	166
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	49.3 Å
rg_real	16.16 Å
rg_real_error	0.19 Å
i0_real	7.5580e+06
i0_real_error	7.4210e+04
rg_reciprocal	16.17 Å
i0_reciprocal	7558000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	21.5 Å
skewness	0.027
kurtosis	-0.493
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	1472000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.979

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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	21528.1 kDa
ec_number	3.6.5.2
mutation	G12D,Y96S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1482

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHSREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	135

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6. Citations (1)

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length_a	92.667 Å
length_b	92.667 Å
length_c	120.554 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	1.570 Å
resolution_low	28.210 Å
r_factor	0.1772
r_work	0.1763
r_free	0.1946

fit	/app/data/saxs_computation/u8/9u8v/9u8v.fit
pddf	/app/data/pr_computation/u8/9u8v/9u8v.pr.out
profile	/app/data/saxs_computation/u8/9u8v/9u8v.dat

Crystal structure of KRAS-G12D/Y96S 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