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Crystal structure of human RAB5A GTPase domain at 1.05 a resolution

Analyse Crystal structure of human RAB5A GTPase domain at 1.05 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R2Q
Type: protein
Length: 170 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-5A
UniProt: P20339
Ligands: GNP, MG
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-5A	protein	170	38% helix, 28% strand	P20339

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 6 copies · chains A

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	118	0.50	0.81	28	MG, GNP

Compared structures

1R2Q · Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution · 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 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 P20339
Elsewhere: RCSB PDB 1R2Q · PDBe 1R2Q · UniProt P20339

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