MolNFT v1 · #109046 · protein
Thiosulfate dehydrogenase (tsda) from allochromatium vinosum - K208G mutant
4WQD: “Thiosulfate dehydrogenase (tsda) from allochromatium vinosum - K208G mutant”. X-ray diffraction, 4 ligands (HEC, GAI, IOD), 2 pockets (best druggability 0.72). MolNFT v1 #109046 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4WQD
- Type
- protein
- Length
- 227 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, GAI, IOD, SO4
- Pockets
- 2 · best druggability 0.72
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 | 227 | 40% helix, 6% strand | D3RVD4 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A
- GAI · Guanidine · ligand · chains A
- IOD · Iodide ion · ion · chains A
- SO4 · Sulfate ion · 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 | 392 | 0.72 | 0.82 | 44 | HEC, GAI |
| 2 | 202 | 0.68 | 0.86 | 35 | HEC |
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 4WQD · Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208G mutant · 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 4WQD · PDBe 4WQD · UniProt D3RVD4
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