MolNFT v1 · #46368 · protein
Crystal structure of phosphoglucose isomerase from trypanosoma brucei complexed with citrate
2O2D · Glucose-6-phosphate isomerase, glycosomal: “Crystal structure of phosphoglucose isomerase from trypanosoma brucei complexed with citrate”. X-ray diffraction, 14 pockets (best druggability 0.79). MolNFT v1 #46368 on GenesisL1: 3D…
- PDB
- 2O2D
- Type
- protein
- Length
- 1,698 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase, glycosomal
- EC
- 5.3.1.9
- UniProt
- P13377
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-6-phosphate isomerase, glycosomal (EC 5.3.1.9) | protein | 568 | 53% helix, 13% strand | P13377 |
| B | Glucose-6-phosphate isomerase, glycosomal (EC 5.3.1.9) | protein | 569 | 52% helix, 14% strand | P13377 |
| C | Glucose-6-phosphate isomerase, glycosomal (EC 5.3.1.9) | protein | 561 | 53% helix, 14% strand | P13377 |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.79 | 0.80 | 69 | empty |
| 2 | 308 | 0.66 | 0.82 | 42 | CIT |
| 3 | 288 | 0.65 | 0.82 | 37 | CIT |
| 4 | 246 | 0.58 | 0.79 | 37 | CIT |
| 5 | 246 | 0.58 | 0.79 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–C · 6452 Ų buried · 82 hydrogen bonds · protein-protein
- A–B · 421 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2O2D · Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P13377 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase, glycosomal (P13377) · a predicted model of the same protein · chain C 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 P13377
- Elsewhere: RCSB PDB 2O2D · PDBe 2O2D · UniProt P13377
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