MolNFT v1 · #48675 · protein
Helicobacter pylori thioredoxin reductase reduced by sodium dithionite in complex with NADP+
2Q0L: “Helicobacter pylori thioredoxin reductase reduced by sodium dithionite in complex with NADP+”. X-ray diffraction, 2 ligands (FAD, NAP), 4 pockets (best druggability 0.80). MolNFT v1 #48675 on GenesisL1: 3D structure, binding sites…
- PDB
- 2Q0L
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- P56431
- Ligands
- FAD, NAP
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase (EC 1.8.1.9) | protein | 311 | 27% helix, 31% strand | P56431 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.80 | 0.82 | 107 | FAD, NAP |
| 2 | 1035 | 0.80 | 0.81 | 110 | FAD |
| 3 | 70 | 0.36 | 0.77 | 16 | empty |
| 4 | 101 | 0.34 | 0.73 | 20 | NAP |
Interfaces
1 interface between chains.
- A–B · 2288 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2Q0L · Helicobacter pylori thioredoxin reductase reduced by sodium dithionite in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P56431 · AlphaFold monomer V2.0 prediction for thioredoxin reductase (P56431) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P56431
- Elsewhere: RCSB PDB 2Q0L · PDBe 2Q0L · UniProt P56431
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