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9u8z

Crystal structure of KRAS-G12D/Q61H mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 50.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8z
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/Q61H 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	16.34 Å
rg_electron	14.96 Å
i0	7769390.00
molecular_weight	19527.0 kDa
excluded_volume	24091 Å³
envelope_volume	26767 Å³
shell_volume	14794 Å³
envelope_diameter	49.0 Å
shell_rg	21.25 Å
envelope_rg	15.29 Å
shape_rg	14.95 Å
total_rg	16.07 Å
total_atoms	1367
n_residues	167
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	50.1 Å
rg_real	16.19 Å
rg_real_error	0.19 Å
i0_real	7.7690e+06
i0_real_error	7.8590e+04
rg_reciprocal	16.20 Å
i0_reciprocal	7769000.0000
total_estimate	0.8975
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.8 Å
skewness	0.037
kurtosis	-0.477
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1577000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isoform 2B of GTPase KRas
formula_weight	21614.2 kDa
ec_number	3.6.5.2
mutation	G12D,Q61H
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1513

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGHEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	143

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6. Citations (1)

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length_a	41.224 Å
length_b	51.826 Å
length_c	68.266 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	29.170 Å
r_factor	0.1757
r_work	0.1746
r_free	0.1963

fit	/app/data/saxs_computation/u8/9u8z/9u8z.fit
pddf	/app/data/pr_computation/u8/9u8z/9u8z.pr.out
profile	/app/data/saxs_computation/u8/9u8z/9u8z.dat