MolNFT v1 · #140244 · protein

Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode

5Y4I · Xylose isomerase: “Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.73). MolNFT v1 #140244 on GenesisL1: 3D structure…

PDB: 5Y4I
Type: protein
Length: 384 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: MG
Pockets: 4 · 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	384	51% helix, 10% strand	P24300

Ligands and binding sites

MG · Magnesium ion · metal · chains A
ACT · Acetate ion · additive · chains A
GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.73	0.99	22	empty
2	516	0.66	0.77	52	GOL
3	68	0.45	0.82	13	empty
4	52	0.27	0.74	14	empty

Compared structures

5Y4I · Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode · 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 5Y4I · PDBe 5Y4I · UniProt P24300

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