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Crystal structure of human small GTPase RAB7(GTP)

Analyse Crystal structure of human small GTPase RAB7(GTP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T91
Type: protein
Length: 704 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-7
UniProt: P51149
Ligands: GTP, MG
Pockets: 9 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RAS-related protein rab-7	protein	176	36% helix, 24% strand	P51149

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · 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

9 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	187	0.57	0.81	31	MG, GTP
2	178	0.56	0.80	31	MG, GTP
3	176	0.55	0.80	31	MG, GTP
4	168	0.55	0.80	30	MG, GTP
5	255	0.55	0.77	27	empty

Interfaces

3 interfaces between chains.

A–D · 466 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 335 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 152 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1T91 · crystal structure of human small GTPase Rab7(GTP) · the same entry in another collection · chain C against C, TM-score 1.00
P51149 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51149) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P51149
Elsewhere: RCSB PDB 1T91 · PDBe 1T91 · UniProt P51149

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