Research workbench
Crystal structure of human phosphoglucose isomerase in complex with inhibitor
Analyse Crystal structure of human phosphoglucose isomerase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XUI
- Type
- protein
- Length
- 2,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- P06744
- Ligands
- PA5
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 556 | 56% helix, 13% strand | P06744 |
Ligands and binding sites
- PA5 · 5-phosphoarabinonic acid · ligand · 4 copies · chains A, D, B, C
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.85 | 0.85 | 74 | empty |
| 2 | 1097 | 0.78 | 0.80 | 61 | empty |
| 3 | 1091 | 0.78 | 0.80 | 62 | empty |
| 4 | 157 | 0.73 | 0.91 | 36 | PA5 |
| 5 | 167 | 0.73 | 0.91 | 38 | PA5 |
Interfaces
5 interfaces between chains.
- A–D · 6567 Ų buried · 88 hydrogen bonds · protein-protein
- B–C · 6468 Ų buried · 88 hydrogen bonds · protein-protein
- A–B · 506 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 102 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XUI · Crystal structure of human phosphoglucose isomerase in complex with inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P06744 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase (P06744) · 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 P06744
- Elsewhere: RCSB PDB 6XUI · PDBe 6XUI · UniProt P06744
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