MolNFT v1 · #145922 · protein
Trypanosoma cruzi glucose-6-P dehydrogenase in complex with G6P
6D24 · Glucose-6-phosphate 1-dehydrogenase: “Trypanosoma cruzi glucose-6-P dehydrogenase in complex with G6P”. X-ray diffraction, 3 ligands (BG6, CL, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #145922 on GenesisL1: 3D structure…
- PDB
- 6D24
- Type
- protein
- Length
- 1,992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 1.1.1.49
- UniProt
- Q1WBU6
- Ligands
- BG6, CL, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 502 | 36% helix, 21% strand | Q1WBU6 |
| C, D | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 494 | 37% helix, 21% strand | Q1WBU6 |
Ligands and binding sites
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 23 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.82 | 0.89 | 49 | GOL, CL |
| 2 | 429 | 0.80 | 0.88 | 52 | GOL |
| 3 | 738 | 0.73 | 0.79 | 65 | BG6, SO4 |
| 4 | 536 | 0.69 | 0.79 | 63 | BG6, GOL |
| 5 | 506 | 0.68 | 0.78 | 47 | BG6, GOL |
Interfaces
6 interfaces between chains.
- A–D · 2593 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2559 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 580 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 6D24 · Trypanosoma cruzi Glucose-6-P Dehydrogenase in complex with G6P · the same entry in another collection · 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 Q1WBU6
- Elsewhere: RCSB PDB 6D24 · PDBe 6D24 · UniProt Q1WBU6
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