MolNFT v1 · #38378 · protein

Time-of-flight neutron diffraction structure of D-xylose isomerase

2GVE: “Time-of-flight neutron diffraction structure of D-xylose isomerase”. Neutron diffraction, 1 ligand (CO), 3 pockets (best druggability 0.71). MolNFT v1 #38378 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GVE
Type: protein
Length: 388 residues
Chains: 1
Method: neutron diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: CO
Pockets: 3 · best druggability 0.71

Structure

neutron diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylose isomerase (EC 5.3.1.5)	protein	388	49% helix, 10% strand	P24300

Ligands and binding sites

CO · Cobalt (II) ion · metal · 2 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.71	0.99	21	empty
2	455	0.66	0.78	45	empty
3	89	0.51	0.83	13	empty

Compared structures

2GVE · Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase · the same entry in another collection · chain A against A, TM-score 1.00
P24300 · AlphaFold monomer V2.0 prediction for xylose isomerase (P24300) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P24300
Elsewhere: RCSB PDB 2GVE · PDBe 2GVE · UniProt P24300

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