MolNFT v1 · #109981 · protein

A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ångströms streptomyces rubiginosus structures with xylitol and D-xylose

4XIS: “A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ångströms streptomyces…”. X-ray diffraction, 3 ligands (XLS, XYS, MN), 3 pockets (best druggability 0.73). MolNFT v1 #109981 on GenesisL1: 3D structure…

PDB: 4XIS
Type: protein
Length: 386 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: XLS, XYS, MN
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylose isomerase (EC 5.3.1.5)	protein	386	51% helix, 10% strand	P24300

Ligands and binding sites

XLS · D-xylose · ligand · chains A
XYS · alpha-D-xylopyranose · sugar · chains A
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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.73	0.98	24	empty
2	471	0.64	0.77	51	XLS, XYS
3	93	0.50	0.82	13	empty

Compared structures

4XIS · A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ångströms… · the same entry in another collection · 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 4XIS · PDBe 4XIS · UniProt P24300

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