MolNFT v1 · #166639 · protein
Crystal structure of recombinant thiocyanate dehydrogenase from thioalkalivibrio paradoxus saturated with copper
6UWE: “Crystal structure of recombinant thiocyanate dehydrogenase from thioalkalivibrio paradoxus saturated with…”. X-ray diffraction, 2 ligands (CU, UNX), 11 pockets (best druggability 0.76). MolNFT v1 #166639 on GenesisL1: 3D structure…
- PDB
- 6UWE
- Type
- protein
- Length
- 1,868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate dehydrogenase
- UniProt
- W0DP94
- Ligands
- CU, UNX
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thiocyanate dehydrogenase | protein | 467 | 10% helix, 45% strand | W0DP94 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.76 | 0.91 | 50 | empty |
| 2 | 277 | 0.68 | 0.83 | 41 | empty |
| 3 | 212 | 0.65 | 0.84 | 28 | empty |
| 4 | 207 | 0.49 | 0.76 | 25 | empty |
| 5 | 168 | 0.47 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2699 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2676 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 310 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UWE · Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio… · 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 6UWE · PDBe 6UWE · UniProt W0DP94
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