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

Analyse Crystal structure of glucose isomerase in complex with glycerol in one metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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