Research workbench

Modes of binding substrates and their analogues to the enzyme D-xylose isomerase

Analyse Modes of binding substrates and their analogues to the enzyme D-xylose isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XIB
Type: protein
Length: 388 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: MN
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-xylose isomerase (EC 5.3.1.5)	protein	388	50% helix, 10% strand	P24300

Ligands and binding sites

MN · Manganese (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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.71	0.98	23	empty
2	463	0.65	0.77	48	empty
3	93	0.49	0.82	14	empty

Compared structures

1XIB · Modes of binding substrates and their analogues to the enzyme 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 1XIB · PDBe 1XIB · UniProt P24300

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