Research workbench
Crystal structure of saccharomyces cerevisiae thioredoxin reductase 1 (TRR1)
Analyse Crystal structure of saccharomyces cerevisiae thioredoxin reductase 1 (TRR1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ITJ
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- 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
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 317 | 27% helix, 30% strand | P29509 |
| B | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 319 | 29% helix, 29% strand | P29509 |
| C | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 314 | 25% helix, 28% strand | P29509 |
| D | Thioredoxin reductase 1 (EC 1.8.1.9) | protein | 307 | 24% helix, 27% strand | P29509 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.86 | 0.87 | 120 | FAD, CIT |
| 2 | 1145 | 0.83 | 0.84 | 129 | FAD, CIT |
| 3 | 458 | 0.79 | 0.87 | 73 | FAD |
| 4 | 688 | 0.77 | 0.82 | 80 | FAD |
| 5 | 295 | 0.69 | 0.84 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2241 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 3ITJ · Crystal structure of Saccharomyces cerevisiae thioredoxin reductase 1 (Trr1) · the same entry in another collection · chain D against D, 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 0.98
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 3ITJ · PDBe 3ITJ · UniProt P29509
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