Research workbench
Crystal structure of saccharomyces cerevisiae ndpph dependent thioredoxin reductase 1
Analyse Crystal structure of saccharomyces cerevisiae ndpph dependent thioredoxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D8X
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase 1
- EC
- 1.8.1.9
- UniProt
- P29509
- Ligands
- FAD, NDP
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 318 | 29% helix, 27% strand | P29509 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.83 | 0.88 | 96 | FAD |
| 2 | 438 | 0.82 | 0.90 | 72 | FAD |
| 3 | 356 | 0.70 | 0.83 | 45 | empty |
| 4 | 208 | 0.63 | 0.83 | 28 | empty |
| 5 | 180 | 0.45 | 0.74 | 32 | NDP |
Interfaces
1 interface between chains.
- A–B · 2337 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3D8X · Crystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thioredoxin Reductase 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P29509 · AlphaFold monomer V2.0 prediction for thioredoxin reductase 1 (P29509) · 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 P29509
- Elsewhere: RCSB PDB 3D8X · PDBe 3D8X · UniProt P29509
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