MolNFT v1 · #97796 · protein
Tetrameric form of rat selenoprotein thioredoxin reductase 1
4KPR · Thioredoxin reductase 1, cytoplasmic: “Tetrameric form of rat selenoprotein thioredoxin reductase 1”. X-ray diffraction, 2 ligands (FAD, SO3), 20 pockets (best druggability 0.85). MolNFT v1 #97796 on GenesisL1: 3D structure, binding…
- PDB
- 4KPR
- Type
- protein
- Length
- 1,937 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase 1, cytoplasmic
- EC
- 1.8.1.9
- UniProt
- O89049
- Ligands
- FAD, SO3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, B | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 484 | 33% helix, 26% strand | O89049 |
| F | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 485 | 33% helix, 26% strand | O89049 |
| A | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 484 | 33% helix, 26% strand | O89049 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains E, F, A, B
- SO3 · Sulfite ion · ion · 3 copies · chains E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains E, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.85 | 0.86 | 108 | MPD |
| 2 | 1106 | 0.84 | 0.85 | 121 | MPD |
| 3 | 987 | 0.81 | 0.82 | 114 | FAD |
| 4 | 971 | 0.81 | 0.82 | 109 | FAD |
| 5 | 948 | 0.81 | 0.83 | 111 | FAD |
Interfaces
5 interfaces between chains.
- E–F · 3511 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3485 Ų buried · 32 hydrogen bonds · protein-protein
- E–B · 498 Ų buried · 7 hydrogen bonds · protein-protein
- F–A · 497 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 213 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KPR · Tetrameric form of rat selenoprotein thioredoxin reductase 1 · 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 O89049
- Elsewhere: RCSB PDB 4KPR · PDBe 4KPR · UniProt O89049
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