MolNFT v1 · #60599 · protein

D-xylose isomerase in complex with linear product, per-deuterated xylulose

3CWH: “D-xylose isomerase in complex with linear product, per-deuterated xylulose”. Neutron diffraction, 3 ligands (XUL, MG, OH), 3 pockets (best druggability 0.73). MolNFT v1 #60599 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3CWH
Type: protein
Length: 387 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: XUL, MG, OH
Pockets: 3 · best druggability 0.73

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	387	49% helix, 10% strand	P24300

Ligands and binding sites

XUL · D-xylulose · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
OH · Hydroxide ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.73	0.98	27	empty
2	484	0.64	0.77	50	XUL, OH
3	66	0.42	0.81	13	empty

Compared structures

3CWH · D-xylose Isomerase in complex with linear product, per-deuterated xylulose · 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 3CWH · PDBe 3CWH · UniProt P24300

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