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Crystal structure of pgi glucosephosphate isomerase

Analyse Crystal structure of pgi glucosephosphate isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NBU
Type: protein
Length: 3,290 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-6-phosphate isomerase
EC: 5.3.1.9
UniProt: P0A6T1
Ligands: CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucose-6-phosphate isomerase (EC 5.3.1.9)	protein	545	53% helix, 13% strand	P0A6T1
B, C, D, E, F	Glucose-6-phosphate isomerase (EC 5.3.1.9)	protein	549	53% helix, 11% strand	P0A6T1

Ligands and binding sites

CL · Chloride ion · ion · chains D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.81	0.82	72	empty
2	956	0.81	0.82	74	empty
3	944	0.80	0.82	68	empty
4	497	0.72	0.81	49	empty
5	450	0.71	0.81	49	empty

Interfaces

7 interfaces between chains.

A–B · 6524 Å² buried · 87 hydrogen bonds · protein-protein
C–D · 6518 Å² buried · 88 hydrogen bonds · protein-protein
E–F · 6511 Å² buried · 87 hydrogen bonds · protein-protein
A–E · 285 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 202 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3NBU · Crystal structure of pGI glucosephosphate isomerase · the same entry in another collection · chain F against F, TM-score 1.00
P0A6T1 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase (P0A6T1) · a predicted model of the same protein · chain D 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 P0A6T1
Elsewhere: RCSB PDB 3NBU · PDBe 3NBU · UniProt P0A6T1

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