MolNFT v1 · #149614 · protein
The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus complex with CU(I) ions.
6G5M: “The structure of thiocyanate dehydrogenase from thioalkalivibrio paradoxus complex with CU(I) ions.”. X-ray diffraction, 1 ligand (CU), 12 pockets (best druggability 0.73). MolNFT v1 #149614 on GenesisL1: 3D structure, binding sites…
- PDB
- 6G5M
- Type
- protein
- Length
- 1,863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate dehydrogenase
- UniProt
- W0DP94
- Ligands
- CU
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiocyanate dehydrogenase | protein | 464 | 9% helix, 44% strand | W0DP94 |
| B | Thiocyanate dehydrogenase | protein | 466 | 9% helix, 44% strand | W0DP94 |
| C | Thiocyanate dehydrogenase | protein | 467 | 9% helix, 42% strand | W0DP94 |
| D | Thiocyanate dehydrogenase | protein | 466 | 8% helix, 44% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 29 copies · chains A, B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.73 | 0.87 | 46 | empty |
| 2 | 726 | 0.69 | 0.76 | 72 | empty |
| 3 | 130 | 0.66 | 0.88 | 26 | CU |
| 4 | 129 | 0.63 | 0.87 | 26 | CU |
| 5 | 466 | 0.63 | 0.76 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2671 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2668 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 310 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6G5M · The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus complex 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 6G5M · PDBe 6G5M · UniProt W0DP94
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