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The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus mutant with his 482 replaced by gln
Analyse The structure of 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
- 6SJI
- Type
- protein
- Length
- 1,871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate dehydrogenase
- UniProt
- W0DP94
- Ligands
- CU, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiocyanate dehydrogenase | protein | 470 | 9% helix, 44% strand | W0DP94 |
| B, J, K | Thiocyanate dehydrogenase | protein | 467 | 9% helix, 44% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 9 copies · chains A, B, J, K
- SO4 · Sulfate ion · ion · 3 copies · chains A, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.81 | 0.83 | 103 | empty |
| 2 | 167 | 0.68 | 0.88 | 25 | empty |
| 3 | 168 | 0.65 | 0.86 | 27 | empty |
| 4 | 166 | 0.65 | 0.86 | 28 | empty |
| 5 | 151 | 0.64 | 0.86 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2709 Ų buried · 44 hydrogen bonds · protein-protein
- J–K · 2706 Ų buried · 40 hydrogen bonds · protein-protein
- B–J · 501 Ų buried · 3 hydrogen bonds · protein-protein
- B–K · 303 Ų buried · 4 hydrogen bonds · protein-protein
- A–J · 299 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6SJI · The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with… · 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 6SJI · PDBe 6SJI · UniProt W0DP94
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