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Crystal structure of RAB5-GDP complex

Analyse Crystal structure of RAB5-GDP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TU4
Type: protein
Length: 664 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-5A
UniProt: P20339
Ligands: GDP, CO, SO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RAS-related protein rab-5A	protein	169	36% helix, 27% strand	P20339
B	RAS-related protein rab-5A	protein	162	38% helix, 28% strand	P20339
D	RAS-related protein rab-5A	protein	164	38% helix, 31% strand	P20339

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
CO · Cobalt (II) ion · metal · 6 copies · chains A, D, B, C
SO4 · Sulfate ion · ion · 6 copies · chains B, D, A, C

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

Pockets

4 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	1007	0.77	0.79	87	empty
2	185	0.46	0.75	32	CO
3	135	0.40	0.74	23	empty
4	104	0.38	0.75	25	CO

Interfaces

5 interfaces between chains.

A–B · 713 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 660 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 437 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 397 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 241 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

1TU4 · Crystal Structure of Rab5-GDP Complex · the same entry in another collection · chain A against A, TM-score 1.00
P20339 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-5A (P20339) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P20339
Elsewhere: RCSB PDB 1TU4 · PDBe 1TU4 · UniProt P20339

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