Research workbench
X-ray structure of human thioredoxin reductase 1
Analyse X-ray structure of human thioredoxin reductase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J3N
- Type
- protein
- Length
- 2,928 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase 1
- EC
- 1.8.1.9
- UniProt
- Q16881
- Ligands
- FAD, NAP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 486 | 32% helix, 26% strand | Q16881 |
| B | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 486 | 33% helix, 26% strand | Q16881 |
| C, E | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 490 | 33% helix, 25% strand | Q16881 |
| D | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 491 | 33% helix, 26% strand | Q16881 |
| F | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 485 | 32% helix, 25% strand | Q16881 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.85 | 0.88 | 92 | MPD |
| 2 | 896 | 0.84 | 0.86 | 95 | MPD |
| 3 | 861 | 0.84 | 0.86 | 93 | MPD |
| 4 | 968 | 0.82 | 0.83 | 64 | empty |
| 5 | 1003 | 0.81 | 0.82 | 109 | FAD, NAP |
Interfaces
9 interfaces between chains.
- C–D · 3867 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 3666 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3462 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 679 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 477 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2J3N · X-ray structure of human 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 Q16881
- Elsewhere: RCSB PDB 2J3N · PDBe 2J3N · UniProt Q16881
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