MolNFT v1 · #170033 · protein
Crystal structure of human phosphoglucose isomerase in complex with inhibitor
6XUH · Glucose-6-phosphate isomerase: “Crystal structure of human phosphoglucose isomerase in complex with inhibitor”. X-ray diffraction, 2 ligands (PA5, O1B), 20 pockets (best druggability 0.79). MolNFT v1 #170033 on GenesisL1: 3D…
- PDB
- 6XUH
- 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, O1B
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 54% 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 | 54% helix, 13% strand | P06744 |
Ligands and binding sites
- PA5 · 5-phosphoarabinonic acid · ligand · 2 copies · chains A, B, C, D
- O1B · (2R,3R,4S)-5-((2-aminoethyl)amino)-2,3,4-trihydroxy-5-oxopentyl dihydrogen phosphate · ligand · 2 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.79 | 0.80 | 67 | empty |
| 2 | 1143 | 0.79 | 0.80 | 71 | empty |
| 3 | 152 | 0.73 | 0.92 | 35 | O1B |
| 4 | 149 | 0.71 | 0.90 | 34 | PA5 |
| 5 | 219 | 0.70 | 0.87 | 40 | PA5 |
Interfaces
5 interfaces between chains.
- A–B · 6591 Ų buried · 95 hydrogen bonds · protein-protein
- C–D · 6538 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 119 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XUH · 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 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 P06744
- Elsewhere: RCSB PDB 6XUH · PDBe 6XUH · UniProt P06744
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