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Crystal structure of human KRAS G12A mutant in complex with GDP (edta soaked)

Analyse Crystal structure of human KRAS G12A mutant in complex with GDP (edta soaked) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VQ0
Type: protein
Length: 320 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, MG
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTPase KRAS	protein	160	36% helix, 26% strand	P01116

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	137	0.50	0.80	26	MG, GDP
2	131	0.48	0.79	24	MG, GDP
3	140	0.44	0.76	27	empty

Interfaces

1 interface between chains.

A–B · 1069 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5VQ0 · Crystal structure of human KRAS G12A mutant in complex with GDP (EDTA soaked) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01116
Elsewhere: RCSB PDB 5VQ0 · PDBe 5VQ0 · UniProt P01116

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