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9u8w

Crystal structure of KRAS-G12D/Q99L mutant in complex with GDP

Method: X-RAY DIFFRACTION D_max: 75.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8w
deposition_date	2025-03-26
last_revision	2026-03-25
title	Crystal structure of KRAS-G12D/Q99L 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	23.15 Å
rg_electron	22.27 Å
i0	28886000.00
molecular_weight	39613.0 kDa
excluded_volume	48916 Å³
envelope_volume	59950 Å³
shell_volume	22798 Å³
envelope_diameter	81.3 Å
shell_rg	28.61 Å
envelope_rg	22.37 Å
shape_rg	22.26 Å
total_rg	23.06 Å
total_atoms	2774
n_residues	340
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	75.9 Å
rg_real	23.15 Å
rg_real_error	0.61 Å
i0_real	2.8890e+07
i0_real_error	3.8390e+05
rg_reciprocal	23.15 Å
i0_reciprocal	28890000.0000
total_estimate	0.8031
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.9 Å
skewness	0.361
kurtosis	-0.383
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	7316000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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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	21589.2 kDa
ec_number	3.6.5.2
mutation	G12D,Q99L
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3039

MGSSHHHHHHSSGENLYFQGMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYRELIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

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	2

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	251

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6. Citations (1)

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length_a	63.553 Å
length_b	37.396 Å
length_c	66.214 Å
angle_alpha	90.00 °
angle_beta	117.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.500 Å
resolution_low	31.760 Å
r_factor	0.1850
r_work	0.1836
r_free	0.2102

fit	/app/data/saxs_computation/u8/9u8w/9u8w.fit
pddf	/app/data/pr_computation/u8/9u8w/9u8w.pr.out
profile	/app/data/saxs_computation/u8/9u8w/9u8w.dat

Crystal structure of KRAS-G12D/Q99L 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