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9rkc

Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP with pVHL:ElonginC:ElonginB

Method: X-RAY DIFFRACTION D_max: 111.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rkc
deposition_date	2025-06-13
title	Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP 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	34.57 Å
rg_electron	34.02 Å
i0	387105000.00
molecular_weight	105350.0 kDa
excluded_volume	101580 Å³
envelope_volume	184310 Å³
shell_volume	45401 Å³
envelope_diameter	111.4 Å
shell_rg	40.52 Å
envelope_rg	33.47 Å
shape_rg	33.98 Å
total_rg	34.45 Å
total_atoms	7974
n_residues	995
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	111.7 Å
rg_real	34.49 Å
rg_real_error	0.74 Å
i0_real	3.8710e+08
i0_real_error	6.1350e+06
rg_reciprocal	34.54 Å
i0_reciprocal	387100000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.7 Å
skewness	0.240
kurtosis	-0.396
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	28860000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.909

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	8044

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	GTPase KRas
formula_weight	19370.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	;(2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(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]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ;
formula_weight	970.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

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6. Citations (1)

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length_a	71.915 Å
length_b	106.467 Å
length_c	82.742 Å
angle_alpha	90.00 °
angle_beta	108.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.190 Å
resolution_low	44.810 Å
r_factor	0.2336
r_work	0.2323
r_free	0.2745

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

Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP 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 (8)

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)