Research workbench
Crystal structure of Thiocyanate hydrolase mutant R136W
Analyse Crystal structure of Thiocyanate hydrolase mutant R136W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VYG
- Type
- protein
- Length
- 1,952 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.72
- Source
- Thiobacillus thioparus
- Molecule
- Thiocyanate hydrolase subunit alpha; Thiocyanate hydrolase subunit beta; Thiocyanate…
- EC
- 3.5.5.8
- UniProt
- O66187, O66186, O66188
- Ligands
- 3CO
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 1.72 · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 120 | 22% helix, 28% strand | O66187 |
| B | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 152 | 61% helix, 7% strand | O66186 |
| C, F, I, L | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 217 | 41% helix, 12% strand | O66188 |
| D | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 119 | 22% helix, 29% strand | O66187 |
| E, H, K | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 151 | 60% helix, 7% strand | O66186 |
Ligands and binding sites
- 3CO · Cobalt (III) ion · metal · 4 copies · chains C, F, I, L
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, C, D, F, G, I, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.88 | 0.93 | 89 | empty |
| 2 | 669 | 0.88 | 0.93 | 84 | empty |
| 3 | 1126 | 0.84 | 0.84 | 143 | empty |
| 4 | 978 | 0.83 | 0.84 | 126 | empty |
| 5 | 141 | 0.62 | 0.86 | 35 | empty |
Interfaces
46 interfaces between chains.
- H–I · 3425 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 3414 Ų buried · 54 hydrogen bonds · protein-protein
- K–L · 3403 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 3397 Ų buried · 53 hydrogen bonds · protein-protein
- G–I · 1657 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 3VYG · Crystal structure of thiocyanate hydrolase mutant R136W · the same entry in another collection · chain L against L, 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 O66187
- Every structure of UniProt O66186
- Every structure of UniProt O66188
- Elsewhere: RCSB PDB 3VYG · PDBe 3VYG · UniProt O66187 · UniProt O66186 · UniProt O66188
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