Research workbench
Crystal structure of human thioredoxin reductase I and terpyridine PLATINUM(II)
Analyse Crystal structure of human thioredoxin reductase I and terpyridine PLATINUM(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZB
- Type
- protein
- Length
- 1,952 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
- Q16881
- Ligands
- FAD, TPT, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 490 | 29% helix, 26% strand | Q16881 |
| B | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 485 | 31% helix, 23% strand | Q16881 |
| C | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 493 | 30% helix, 25% strand | Q16881 |
| D | Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) | protein | 484 | 31% helix, 25% strand | Q16881 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- TPT · 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride · ligand · 2 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.87 | 0.91 | 84 | empty |
| 2 | 613 | 0.86 | 0.91 | 71 | empty |
| 3 | 905 | 0.82 | 0.84 | 105 | FAD, SO4 |
| 4 | 1070 | 0.81 | 0.82 | 112 | FAD, SO4 |
| 5 | 1058 | 0.81 | 0.82 | 110 | FAD, SO4 |
Interfaces
6 interfaces between chains.
- C–D · 3611 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3519 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 640 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 165 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2ZZB · Crystal structure of human thioredoxin reductase I and terpyridine platinum(II) · 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 2ZZB · PDBe 2ZZB · UniProt Q16881
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