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11qe

Crystal structure of GDP-bound KRAS G12D/I55E: Suppressing G12D oncogenicity via second-site I55E mutation

Method: X-RAY DIFFRACTION D_max: 59.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11qe
deposition_date	2026-03-10
last_revision	2026-03-25
title	Crystal structure of GDP-bound KRAS G12D/I55E: Suppressing G12D oncogenicity via second-site I55E mutation
keywords	KRAS, RAS, nucleotide-binding protein, signaling protein, G12D, I55E, ONCOPROTEIN; ONCOPROTEIN
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	17.42 Å
rg_electron	16.27 Å
i0	7848560.00
molecular_weight	19530.0 kDa
excluded_volume	24029 Å³
envelope_volume	28087 Å³
shell_volume	14824 Å³
envelope_diameter	60.0 Å
shell_rg	21.98 Å
envelope_rg	16.74 Å
shape_rg	16.29 Å
total_rg	17.18 Å
total_atoms	1367
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

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3. P(r) Analysis (GNOM)

dmax	59.7 Å
rg_real	17.35 Å
rg_real_error	0.34 Å
i0_real	7.8490e+06
i0_real_error	9.3310e+04
rg_reciprocal	17.36 Å
i0_reciprocal	7849000.0000
total_estimate	0.8615
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.250
kurtosis	-0.136
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	1387000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.983

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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	19402.8 kDa
ec_number	3.6.5.2
mutation	G12D, I55E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1563

GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDELDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	148

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6. Citations (1)

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length_a	78.680 Å
length_b	78.680 Å
length_c	56.146 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	1.230 Å
resolution_low	43.330 Å
r_factor	0.1862
r_work	0.1853
r_free	0.2027

fit	/app/data/saxs_computation/1q/11qe/11qe.fit
pddf	/app/data/pr_computation/1q/11qe/11qe.pr.out
profile	/app/data/saxs_computation/1q/11qe/11qe.dat