Research workbench

A dehydrated form of glucose isomerase collected at 100K.

Analyse A dehydrated form of glucose isomerase collected at 100K. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZBC
Type: protein
Length: 774 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Streptomyces rubiginosus
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: GLC, FRU, MN
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · resolution 2 · 1 distinct chain · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xylose isomerase (EC 5.3.1.5)	protein	387	49% helix, 11% strand	P24300

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B
MN · Manganese (II) ion · metal · 11 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.72	0.99	24	MN
2	545	0.69	0.78	48	GLC, FRU
3	545	0.67	0.78	48	GLC, FRU
4	227	0.58	0.80	36	MN
5	226	0.58	0.80	39	empty

Interfaces

1 interface between chains.

A–B · 4825 Å² buried · 82 hydrogen bonds · protein-protein

Compared structures

4ZBC · A dehydrated form of glucose isomerase collected at 100K. · 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 4ZBC · PDBe 4ZBC · UniProt P24300

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.