MolNFT v1 · #108291 · protein
Crystal structure of the thiosulfate dehydrogenase tsda in complex with thiosulfate
4V2K: “Crystal structure of the thiosulfate dehydrogenase tsda in complex with thiosulfate”. X-ray diffraction, 2 ligands (HEC, THJ), 2 pockets (best druggability 0.72). MolNFT v1 #108291 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4V2K
- Type
- protein
- Length
- 235 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
- 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 | 235 | 40% helix, 6% strand | D3RVD4 |
Ligands and binding sites
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 | 263 | 0.72 | 0.86 | 39 | HEC |
| 2 | 404 | 0.72 | 0.82 | 46 | HEC, THJ |
Modifications
Observed in the structure: 4 cofactor, 1 modified (heme c attachment, oxidation).
Compared structures
- 4V2K · Crystal structure of the thiosulfate dehydrogenase TsdA in complex with thiosulfate · 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 4V2K · PDBe 4V2K · UniProt D3RVD4
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