Research workbench
Thiocyanate dehydrogenase from thioalkalivibrio paradoxus
Analyse Thiocyanate dehydrogenase from thioalkalivibrio paradoxus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F75
- Type
- protein
- Length
- 1,881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate dehydrogenase
- UniProt
- W0DP94
- Ligands
- CU
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiocyanate dehydrogenase | protein | 474 | 9% helix, 43% strand | W0DP94 |
| B, D | Thiocyanate dehydrogenase | protein | 466 | 11% helix, 44% strand | W0DP94 |
| C | Thiocyanate dehydrogenase | protein | 475 | 9% helix, 44% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.77 | 0.83 | 75 | empty |
| 2 | 140 | 0.66 | 0.88 | 26 | empty |
| 3 | 419 | 0.65 | 0.79 | 42 | empty |
| 4 | 133 | 0.64 | 0.87 | 35 | CU |
| 5 | 125 | 0.61 | 0.86 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2826 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2663 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 477 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 294 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5F75 · Thiocyanate dehydrogenase from Thioalkalivibrio paradoxus · 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 5F75 · PDBe 5F75 · UniProt W0DP94
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.