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9rke

Crystal Structure of compound 1-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB

Method: X-RAY DIFFRACTION D_max: 103.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rke
deposition_date	2025-06-13
title	Crystal Structure of compound 1-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB
keywords	KRAS, TPD, PROTAC, VHL, ternary complex, 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	33.69 Å
rg_electron	32.80 Å
i0	194521000.00
molecular_weight	110200.0 kDa
excluded_volume	137290 Å³
envelope_volume	178230 Å³
shell_volume	44966 Å³
envelope_diameter	110.7 Å
shell_rg	39.92 Å
envelope_rg	32.36 Å
shape_rg	32.76 Å
total_rg	33.49 Å
total_atoms	7754
n_residues	994
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	103.5 Å
rg_real	33.57 Å
rg_real_error	0.83 Å
i0_real	1.9450e+08
i0_real_error	3.0620e+06
rg_reciprocal	33.65 Å
i0_reciprocal	194500000.0000
total_estimate	0.8951
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.0 Å
skewness	0.194
kurtosis	-0.393
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	25440000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.846

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Elongin-B
formula_weight	11748.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	7771

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Elongin-C
formula_weight	10974.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	von Hippel-Lindau disease tumor suppressor
formula_weight	18702.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Isoform 2B of GTPase KRas
formula_weight	19429.0 kDa
ec_number	3.6.5.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

GMTEYKLVVVGARGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	;(2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ;
formula_weight	989.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
formula_weight	521.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	2

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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6. Citations (1)

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length_a	101.934 Å
length_b	101.934 Å
length_c	275.675 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	2.830 Å
resolution_low	91.890 Å
r_factor	0.2363
r_work	0.2338
r_free	0.2858

fit	/app/data/saxs_computation/rk/9rke/9rke.fit
pddf	/app/data/pr_computation/rk/9rke/9rke.pr.out
profile	/app/data/saxs_computation/rk/9rke/9rke.dat

Crystal Structure of compound 1-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB

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

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)