MolNFT v1 · #157226 · protein

GDP-bound KRAS P34R mutant

6MS9 · GTPase KRAS: “GDP-bound KRAS P34R mutant”. X-ray diffraction, 2 ligands (GDP, MG), 3 pockets (best druggability 0.73). MolNFT v1 #157226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MS9
Type: protein
Length: 470 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GDP, MG
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	GTPase KRAS	protein	155	41% helix, 26% strand	P01116
B	GTPase KRAS	protein	156	40% helix, 27% strand	P01116
A	GTPase KRAS	protein	159	42% helix, 26% strand	P01116

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains C, B, A
MG · Magnesium ion · metal · 2 copies · chains C, 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	759	0.73	0.79	86	GDP
2	100	0.33	0.73	17	empty
3	50	0.28	0.75	13	empty

Interfaces

3 interfaces between chains.

B–A · 299 Å² buried · 4 hydrogen bonds · protein-protein
C–A · 299 Å² buried · 4 hydrogen bonds · protein-protein
C–B · 247 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6MS9 · GDP-bound KRAS P34R mutant · the same entry in another collection · chain C against C, 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 6MS9 · PDBe 6MS9 · UniProt P01116

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