MolNFT v1 · #29156 · protein

Gppnhp-bound RAB21 GTPase at 2.50 a resolution

1YZU · RAS-related protein rab-21: “Gppnhp-bound RAB21 GTPase at 2.50 a resolution”. X-ray diffraction, 2 ligands (GNP, MG), 2 pockets (best druggability 0.54). MolNFT v1 #29156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YZU
Type: protein
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-21
UniProt: Q9UL25
Ligands: GNP, MG
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RAS-related protein rab-21	protein	165	40% helix, 29% strand	Q9UL25

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.54	0.79	31	MG, GNP
2	170	0.53	0.79	30	MG, GNP

Compared structures

1YZU · GppNHp-Bound Rab21 GTPase at 2.50 A Resolution · the same entry in another collection · chain A against A, TM-score 1.00
Q9UL25 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-21 (Q9UL25) · a predicted model of the same protein · chain A 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 Q9UL25
Elsewhere: RCSB PDB 1YZU · PDBe 1YZU · UniProt Q9UL25

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