MolNFT v1 · #38062 · protein

High-resolution study of D-xylose isomerase, 0.94A resolution.

2GLK: “High-resolution study of D-xylose isomerase, 0.94A resolution.”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.64). MolNFT v1 #38062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GLK
Type: protein
Length: 388 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: MN
Pockets: 4 · best druggability 0.64

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	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
GOL · Glycerol · additive · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.64	0.77	48	GOL
2	62	0.39	0.80	13	empty
3	51	0.32	0.77	11	empty
4	69	0.28	0.72	19	GOL

Compared structures

2GLK · High-resolution study of D-Xylose isomerase, 0.94A resolution. · 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 2GLK · PDBe 2GLK · UniProt P24300

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