Research workbench
Thiosulfate dehydrogenase (tsdba) from marichromatium purpuratum - "as isolated" form
Analyse Thiosulfate dehydrogenase (tsdba) from marichromatium purpuratum - "as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LO9
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- W0DW89
- Ligands
- HEC, THJ, CL
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C | protein | 471 | 44% helix, 5% strand | W0DW89 |
| B | Cytochrome C | protein | 469 | 43% helix, 5% strand | W0DW89 |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B
- THJ · Thiosulfate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.88 | 0.88 | 128 | HEC, CL, EDO |
| 2 | 1085 | 0.87 | 0.88 | 135 | HEC, CL |
| 3 | 540 | 0.73 | 0.81 | 54 | HEC, THJ |
| 4 | 65 | 0.72 | 0.98 | 19 | EDO |
| 5 | 554 | 0.72 | 0.80 | 52 | HEC, THJ, EDO |
Interfaces
1 interface between chains.
- A–B · 1145 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor, 2 covalent (heme c attachment, covalent ligand).
Compared structures
- 5LO9 · Thiosulfate dehydrogenase (TsdBA) from Marichromatium purpuratum - "as isolated" form · 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 W0DW89
- Elsewhere: RCSB PDB 5LO9 · PDBe 5LO9 · UniProt W0DW89
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