MolNFT v1 · #109042 · protein
Thiosulfate dehydrogenase (tsda) from allochromatium vinosum - dithionite soak
4WQ9: “Thiosulfate dehydrogenase (tsda) from allochromatium vinosum - dithionite soak”. X-ray diffraction, 5 ligands (HEC, THJ, IOD), 2 pockets (best druggability 0.73). MolNFT v1 #109042 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4WQ9
- Type
- protein
- Length
- 230 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiosulfate dehydrogenase
- EC
- 1.8.2.2
- UniProt
- D3RVD4
- Ligands
- HEC, THJ, IOD, SO4, H2S
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiosulfate dehydrogenase (EC 1.8.2.2) | protein | 230 | 40% helix, 6% strand | D3RVD4 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A
- THJ · Thiosulfate · ligand · chains A
- IOD · Iodide ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- H2S · Hydrosulfuric acid · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.73 | 0.87 | 32 | HEC |
| 2 | 403 | 0.71 | 0.82 | 43 | HEC, H2S, THJ |
Modifications
Observed in the structure: 4 cofactor, 1 covalent, 1 modified (heme c attachment, covalent ligand, oxidation).
Compared structures
- 4WQ9 · Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - dithionite soak · the same entry in another collection · chain A against A, TM-score 1.00
- D3RVD4 · AlphaFold monomer V2.0 prediction for thiosulfate dehydrogenase (D3RVD4) · a predicted model of the same protein · 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 D3RVD4
- Elsewhere: RCSB PDB 4WQ9 · PDBe 4WQ9 · UniProt D3RVD4
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