MolNFT v1 · #102087 · protein

Crystal structure of GDP-bound human KRAS

4OBE · GTPase KRAS: “Crystal structure of GDP-bound human KRAS”. X-ray diffraction, 2 ligands (GDP, MG), 6 pockets (best druggability 0.60). MolNFT v1 #102087 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OBE
Type: protein
Length: 339 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
EC: 3.6.5.2
UniProt: P01116
Ligands: GDP, MG
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase KRAS (EC 3.6.5.2)	protein	169	38% helix, 25% strand	P01116
B	GTPase KRAS (EC 3.6.5.2)	protein	170	38% 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

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

Pockets

6 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	387	0.60	0.76	46	empty
2	127	0.46	0.78	28	GDP, MG
3	137	0.45	0.77	28	GDP, MG
4	112	0.43	0.78	23	empty
5	67	0.34	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 405 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4OBE · Crystal Structure of GDP-bound Human KRas · 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 4OBE · PDBe 4OBE · UniProt P01116

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