MolNFT v1 · #151979 · protein
The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus complex with acetate ions.
6I3Q · Uncharacterized protein: “The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus complex with acetate ions.”. X-ray diffraction, 1 ligand (CU), 10 pockets (best druggability 0.79). MolNFT v1 #151979 on GenesisL1…
- PDB
- 6I3Q
- Type
- protein
- Length
- 1,867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- W0DP94
- Ligands
- CU
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Uncharacterized protein | protein | 467 | 10% helix, 43% strand | W0DP94 |
| C | Uncharacterized protein | protein | 466 | 9% helix, 43% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.79 | 0.85 | 74 | empty |
| 2 | 181 | 0.76 | 0.92 | 29 | CU, ACT, GOL |
| 3 | 174 | 0.72 | 0.90 | 34 | CU, ACT |
| 4 | 148 | 0.71 | 0.91 | 27 | ACT |
| 5 | 399 | 0.69 | 0.81 | 44 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2699 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2646 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 288 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6I3Q · The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus complex with… · the same entry in another collection · chain B against B, 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 6I3Q · PDBe 6I3Q · UniProt W0DP94
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