MolNFT v1 · #53250 · protein
Trypanosoma brucei trypanothione reductase with bound NADP.
2WOV: “Trypanosoma brucei trypanothione reductase with bound NADP.”. X-ray diffraction, 3 ligands (NDP, FAD, NA), 16 pockets (best druggability 0.86). MolNFT v1 #53250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WOV
- Type
- protein
- Length
- 1,953 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- Q389T8
- Ligands
- NDP, FAD, NA
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Trypanothione reductase (EC 1.8.1.12) | protein | 490 | 33% helix, 27% strand | Q389T8 |
| B | Trypanothione reductase (EC 1.8.1.12) | protein | 486 | 32% helix, 28% strand | Q389T8 |
| D | Trypanothione reductase (EC 1.8.1.12) | protein | 487 | 33% helix, 27% strand | Q389T8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.86 | 0.88 | 78 | empty |
| 2 | 1136 | 0.85 | 0.86 | 101 | NA |
| 3 | 909 | 0.81 | 0.83 | 98 | NDP, FAD |
| 4 | 840 | 0.80 | 0.83 | 95 | NDP, FAD |
| 5 | 846 | 0.80 | 0.83 | 102 | NDP, FAD |
Interfaces
3 interfaces between chains.
- A–B · 3473 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3472 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2WOV · Trypanosoma brucei trypanothione reductase with bound NADP. · 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 Q389T8
- Elsewhere: RCSB PDB 2WOV · PDBe 2WOV · UniProt Q389T8
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