MolNFT v1 · #23360 · protein

Crystal structure of the VPS9 domain of rabex-5

1TXU · RAB5 GDP/GTP exchange factor: “Crystal structure of the VPS9 domain of rabex-5”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.35). MolNFT v1 #23360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1TXU
Type: protein
Length: 254 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAB5 GDP/GTP exchange factor
UniProt: Q9UJ41
Ligands: MG
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAB5 GDP/GTP exchange factor	protein	254	74% helix, 0% strand	Q9UJ41

Ligands and binding sites

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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	59	0.35	0.78	15	empty

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

1TXU · Crystal Structure of the Vps9 Domain of Rabex-5 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UJ41 · AlphaFold monomer V2.0 prediction for RAB5 GDP/GTP exchange factor (Q9UJ41) · 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 Q9UJ41
Elsewhere: RCSB PDB 1TXU · PDBe 1TXU · UniProt Q9UJ41

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