Research workbench
Oxidized thioredoxin reductase from helicobacter pylori in complex with NADP+
Analyse Oxidized thioredoxin reductase from helicobacter pylori in complex with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q0K
- Type
- protein
- Length
- 620 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
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase (EC 1.8.1.9) | protein | 310 | 26% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.79 | 0.80 | 114 | FAD, NAP |
| 2 | 1098 | 0.77 | 0.79 | 111 | FAD, NAP |
| 3 | 58 | 0.43 | 0.82 | 13 | empty |
| 4 | 53 | 0.37 | 0.80 | 13 | empty |
| 5 | 58 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2254 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2Q0K · Oxidized thioredoxin reductase from Helicobacter pylori in complex with NADP+ · 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 2Q0K · PDBe 2Q0K · UniProt P56431
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