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9rkj

Crystal Structure of compound 3-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB

Method: X-RAY DIFFRACTION D_max: 105.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rkj
deposition_date	2025-06-13
title	Crystal Structure of compound 3-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	33.98 Å
rg_electron	33.29 Å
i0	360271000.00
molecular_weight	101660.0 kDa
excluded_volume	98143 Å³
envelope_volume	179370 Å³
shell_volume	44578 Å³
envelope_diameter	111.8 Å
shell_rg	40.36 Å
envelope_rg	32.85 Å
shape_rg	33.26 Å
total_rg	33.76 Å
total_atoms	7689
n_residues	982
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	105.4 Å
rg_real	33.87 Å
rg_real_error	0.88 Å
i0_real	3.6030e+08
i0_real_error	6.2650e+06
rg_reciprocal	33.94 Å
i0_reciprocal	360300000.0000
total_estimate	0.8963
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.8 Å
skewness	0.192
kurtosis	-0.396
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	26770000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.867

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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	7708

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	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	;(2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ;
formula_weight	1017.3 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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	13

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6. Citations (1)

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length_a	101.602 Å
length_b	110.612 Å
length_c	114.352 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.890 Å
resolution_low	79.500 Å
r_factor	0.2399
r_work	0.2374
r_free	0.2877

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

Crystal Structure of compound 3-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)