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9u8y

Crystal structure of KRAS-G12D/G13D mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 48.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8y
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/G13D 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	16.33 Å
rg_electron	14.98 Å
i0	7649480.00
molecular_weight	19387.0 kDa
excluded_volume	23875 Å³
envelope_volume	26603 Å³
shell_volume	14734 Å³
envelope_diameter	47.6 Å
shell_rg	21.18 Å
envelope_rg	15.26 Å
shape_rg	14.98 Å
total_rg	16.02 Å
total_atoms	1358
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	48.6 Å
rg_real	16.18 Å
rg_real_error	0.19 Å
i0_real	7.6490e+06
i0_real_error	8.6350e+04
rg_reciprocal	16.19 Å
i0_reciprocal	7650000.0000
total_estimate	0.9038
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.0 Å
skewness	0.014
kurtosis	-0.512
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1448000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; 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	21662.2 kDa
ec_number	3.6.5.2
mutation	G12D,G13D
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1423

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADDVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	65

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6. Citations (1)

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length_a	61.054 Å
length_b	34.412 Å
length_c	59.875 Å
angle_alpha	90.00 °
angle_beta	103.28 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.730 Å
resolution_low	29.780 Å
r_factor	0.2181
r_work	0.2157
r_free	0.2657

fit	/app/data/saxs_computation/u8/9u8y/9u8y.fit
pddf	/app/data/pr_computation/u8/9u8y/9u8y.pr.out
profile	/app/data/saxs_computation/u8/9u8y/9u8y.dat

Crystal structure of KRAS-G12D/G13D 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