MolNFT v1 · #113793 · protein
Trypanosoma cruzi glucose-6-phosphate dehydrogenase in complex with G6P and NADPH
5AQ1: “Trypanosoma cruzi glucose-6-phosphate dehydrogenase in complex with G6P and NADPH”. X-ray diffraction, 2 ligands (NDP, BG6), 12 pockets (best druggability 0.76). MolNFT v1 #113793 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5AQ1
- Type
- protein
- Length
- 1,452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate dehydrogenase
- EC
- 1.1.1.49
- UniProt
- Q4E0B2
- Ligands
- NDP, BG6
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glucose-6-phosphate dehydrogenase (EC 1.1.1.49) | protein | 484 | 38% helix, 20% strand | Q4E0B2 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.76 | 0.79 | 82 | empty |
| 2 | 622 | 0.71 | 0.79 | 65 | BG6, NDP |
| 3 | 679 | 0.70 | 0.77 | 70 | BG6, NDP |
| 4 | 691 | 0.69 | 0.77 | 66 | BG6, NDP |
| 5 | 116 | 0.57 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2634 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5AQ1 · Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH · 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 Q4E0B2
- Elsewhere: RCSB PDB 5AQ1 · PDBe 5AQ1 · UniProt Q4E0B2
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