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Crystal structure of human KRAS Q61A mutant in complex with GDP

Analyse Crystal structure of human KRAS Q61A mutant in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VQ1
Type: protein
Length: 334 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, MG
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTPase KRAS	protein	167	37% helix, 25% 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
PG4 · Tetraethylene glycol · additive · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.47	0.78	27	GDP, MG
2	158	0.45	0.76	31	PG4
3	124	0.44	0.77	27	GDP, MG
4	90	0.38	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 1067 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5VQ1 · Crystal structure of human KRAS Q61A mutant in complex with GDP · 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 5VQ1 · PDBe 5VQ1 · UniProt P01116

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