MolNFT v1 · #29152 · protein

Gppnhp-bound RAB6 GTPase

1YZQ · Small GTP binding protein RAB6 isoform: “Gppnhp-bound RAB6 GTPase”. X-ray diffraction, 2 ligands (GNP, MG), 1 pocket (best druggability 0.58). MolNFT v1 #29152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YZQ
Type: protein
Length: 164 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small GTP binding protein RAB6 isoform
UniProt: P20340
Ligands: GNP, MG
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Small GTP binding protein RAB6 isoform	protein	164	38% helix, 26% strand	P20340

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · 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

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	154	0.58	0.82	28	MG, GNP

Compared structures

1YZQ · GppNHp-Bound Rab6 GTPase · the same entry in another collection · chain A against A, TM-score 1.00
P20340 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6A (P20340) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P20340
Elsewhere: RCSB PDB 1YZQ · PDBe 1YZQ · UniProt P20340

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