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Crystal structure of human wt-KRAS in complex with GDP (edta soaked)

Analyse Crystal structure of human wt-KRAS 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: 5VQ8
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, MG
Pockets: 6 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTPase KRAS	protein	156	37% 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

6 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	138	0.45	0.77	25	empty
2	82	0.37	0.76	19	GDP
3	93	0.33	0.74	21	empty
4	64	0.33	0.76	20	GDP
5	64	0.30	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1006 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5VQ8 · Crystal structure of human WT-KRAS 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 5VQ8 · PDBe 5VQ8 · UniProt P01116

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