Research workbench
Complex with iodine ion for thiocyanate dehydrogenase from thioalkalivibrio paradoxus
Analyse Complex with iodine ion for thiocyanate dehydrogenase from thioalkalivibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OEX
- 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
- P4G, CU, IOD
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thiocyanate dehydrogenase | protein | 467 | 9% helix, 43% strand | W0DP94 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A
- CU · Copper (II) ion · metal · 15 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 8 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.79 | 0.85 | 70 | IOD |
| 2 | 152 | 0.69 | 0.89 | 30 | CU, IOD |
| 3 | 171 | 0.69 | 0.88 | 27 | CU |
| 4 | 394 | 0.69 | 0.81 | 46 | empty |
| 5 | 165 | 0.66 | 0.86 | 29 | CU, IOD |
Interfaces
5 interfaces between chains.
- C–D · 2710 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2684 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 297 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5OEX · Complex with iodine ion for 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 5OEX · PDBe 5OEX · UniProt W0DP94
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