9l6f

Crystal structure of KRas G12D (GDP) in complex with ASP3082

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

von Hippel-Lindau disease tumor suppressor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） ASP3082 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VHL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–163； UniProt 54–213 Author chain E； PDBConstruct 4–163； UniProt 54–213 Author chain I； PDBConstruct 4–163； UniProt 54–213 Author chain M； PDBConstruct 4–163； UniProt 54–213

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） ASP3082 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 17–112 Author chain F； PDBConstruct 1–96； UniProt 17–112 Author chain J； PDBConstruct 1–96； UniProt 17–112 Author chain N； PDBConstruct 1–96； UniProt 17–112

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） ASP3082 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–118； UniProt 1–118 Author chain G； PDBConstruct 1–118； UniProt 1–118 Author chain K； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

Isoform 2B of GTPase KRas

Homo sapiens

UniProt P01116

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ASP3082 × 1 GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ASP3082 × 1 GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ASP3082 × 1 GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASK_HUMAN
Isoform	P01116-2
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–170； UniProt 1–169 Author chain H； PDBConstruct 2–170； UniProt 1–169 Author chain L； PDBConstruct 2–170； UniProt 1–169 Author chain P； PDBConstruct 2–170； UniProt 1–169

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9l6f
Deposition date deposition_date	2024-12-24
Last revision last_revision	2025-09-03
Structure title title	Crystal structure of KRas G12D (GDP) in complex with ASP3082
Keywords keywords	GTPase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9l6f__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9l6f__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9l6f__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.71 Å
Rg (electron density)	23.74 Å
Total Rg	24.40 Å
Atom count	2707
Residues	340
Excluded volume	48324 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9l6f__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9l6f__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9l6f__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9l6f__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`9l6f__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`9l6f__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`9l6f__assembly_7__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`9l6f__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	18840.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	16509

GSHMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Elongin-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Elongin-B
Molecular weight formula_weight	13147.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Isoform 2B of GTPase KRas
Molecular weight formula_weight	19386.8 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	G12D
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P

GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ASP3082
Molecular weight formula_weight	1117.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	144.348 Å
Unit-cell length b length_b	58.905 Å
Unit-cell length c length_c	165.979 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	48.760 Å
R factor r_factor	0.2445
R_work r_work	0.2413
R_free r_free	0.3054

Crystal structure of KRas G12D (GDP) in complex with ASP3082

1. Protein Identity and Related Structures Protein Identity & Related Structures

von Hippel-Lindau disease tumor suppressor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Isoform 2B of GTPase KRas

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9l6f__assembly_3__model_1

9l6f__assembly_3__model_1 | I(q)

9l6f__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)