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Crystal structure of human RAB4B in complex with GDP

Analyse Crystal structure of human RAB4B in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O52
Type: protein
Length: 325 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-4B
UniProt: P61018
Ligands: GDP, MG, UNX
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-4B	protein	167	41% helix, 26% strand	P61018
B	RAS-related protein rab-4B	protein	158	40% helix, 27% strand	P61018

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · chains A
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.52	0.78	29	empty

Interfaces

1 interface between chains.

A–B · 532 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

2O52 · Crystal structure of human RAB4B in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
P61018 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-4B (P61018) · a predicted model of the same protein · chain B 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 P61018
Elsewhere: RCSB PDB 2O52 · PDBe 2O52 · UniProt P61018

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