MolNFT v1 · #160888 · protein

N-terminal SH2 domain of the P120RASGAP

6PXB · RAS GTPase-activating protein 1: “N-terminal SH2 domain of the P120RASGAP”. X-ray diffraction, 6 pockets (best druggability 0.61). MolNFT v1 #160888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PXB
Type: protein
Length: 611 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS GTPase-activating protein 1
UniProt: P20936
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	RAS GTPase-activating protein 1	protein	101	24% helix, 35% strand	P20936
C, A	RAS GTPase-activating protein 1	protein	103	20% helix, 35% strand	P20936
D, B	RAS GTPase-activating protein 1	protein	101	24% helix, 36% strand	P20936
E	RAS GTPase-activating protein 1	protein	102	21% helix, 36% strand	P20936

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	357	0.61	0.77	45	empty
2	373	0.59	0.76	33	empty
3	324	0.57	0.76	34	empty
4	166	0.44	0.74	21	empty
5	52	0.29	0.76	14	empty

Interfaces

8 interfaces between chains.

F–E · 816 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 795 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 770 Å² buried · 10 hydrogen bonds · protein-protein
F–A · 316 Å² buried · 0 hydrogen bonds · protein-protein
F–C · 285 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6PXB · N-Terminal SH2 domain of the p120RasGAP · the same entry in another collection · chain B against B, TM-score 1.00
P20936 · AlphaFold monomer V2.0 prediction for RAS GTPase-activating protein 1 (P20936) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 P20936
Elsewhere: RCSB PDB 6PXB · PDBe 6PXB · UniProt P20936

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