Research workbench

GDP-bound RAB7

Analyse GDP-bound RAB7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VG1
Type: protein
Length: 166 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-7
UniProt: P09527
Ligands: GDP, MG
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-7	protein	166	37% helix, 27% strand	P09527

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

2 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	89	0.38	0.77	20	empty
2	57	0.31	0.76	16	empty

Compared structures

1VG1 · GDP-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 A against A, TM-score 0.93

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 1VG1 · PDBe 1VG1 · UniProt P09527

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