Research workbench
The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus as isolated.
Analyse The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G50
- Type
- protein
- Length
- 1,868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- W0DP94
- Ligands
- CU, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein | protein | 467 | 10% helix, 43% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 13 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.82 | 0.83 | 118 | empty |
| 2 | 219 | 0.76 | 0.90 | 39 | CU, SO4 |
| 3 | 136 | 0.68 | 0.89 | 25 | CU, SO4 |
| 4 | 173 | 0.65 | 0.85 | 36 | SO4 |
| 5 | 180 | 0.49 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2677 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2665 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 312 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6G50 · The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated. · 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 W0DP94
- Elsewhere: RCSB PDB 6G50 · PDBe 6G50 · UniProt W0DP94
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