← Back to search

9u8x

Crystal structure of KRAS-G12D/R68M mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 49.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9u8x
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/R68M mutant in complex with GDP
keywords	Complex structure, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	16.28 Å
rg_electron	14.93 Å
i0	7722950.00
molecular_weight	19592.0 kDa
excluded_volume	24160 Å³
envelope_volume	26476 Å³
shell_volume	14719 Å³
envelope_diameter	49.2 Å
shell_rg	21.16 Å
envelope_rg	15.17 Å
shape_rg	14.92 Å
total_rg	15.98 Å
total_atoms	1371
n_residues	168
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

▼

3. P(r) Analysis (GNOM)

dmax	49.2 Å
rg_real	16.12 Å
rg_real_error	0.21 Å
i0_real	7.7230e+06
i0_real_error	7.9010e+04
rg_reciprocal	16.14 Å
i0_reciprocal	7723000.0000
total_estimate	0.8993
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.5 Å
skewness	0.007
kurtosis	-0.512
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	1661000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Isoform 2B of GTPase KRas
formula_weight	21578.2 kDa
ec_number	3.6.5.2
mutation	G12D,R68M
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1482

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMMDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	111

▶

6. Citations (1)

▶

length_a	90.553 Å
length_b	90.553 Å
length_c	36.844 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	1.650 Å
resolution_low	33.350 Å
r_factor	0.2230
r_work	0.2211
r_free	0.2563

fit	/app/data/saxs_computation/u8/9u8x/9u8x.fit
pddf	/app/data/pr_computation/u8/9u8x/9u8x.pr.out
profile	/app/data/saxs_computation/u8/9u8x/9u8x.dat

Crystal structure of KRAS-G12D/R68M 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