MolNFT v1 · #25122 · protein

Gppnhp-bound RAB7

1VG8 · RAS-related protein rab-7: “Gppnhp-bound RAB7”. X-ray diffraction, 2 ligands (GNP, MG), 17 pockets (best druggability 0.59). MolNFT v1 #25122 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VG8
Type: protein
Length: 725 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-7
UniProt: P09527
Ligands: GNP, MG
Pockets: 17 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	RAS-related protein rab-7	protein	184	38% helix, 23% strand	P09527
B	RAS-related protein rab-7	protein	179	38% helix, 24% strand	P09527
C	RAS-related protein rab-7	protein	178	38% helix, 25% strand	P09527

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.59	0.77	44	MG, GNP
2	152	0.54	0.81	31	MG, GNP
3	160	0.54	0.80	31	MG, GNP
4	187	0.53	0.79	37	MG, GNP
5	212	0.51	0.76	28	empty

Interfaces

4 interfaces between chains.

A–D · 666 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 490 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 257 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 199 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1VG8 · GPPNHP-Bound Rab7 · the same entry in another collection · chain A against A, TM-score 1.00
P09527 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P09527) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P09527
Elsewhere: RCSB PDB 1VG8 · PDBe 1VG8 · UniProt P09527

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