Research workbench
Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers
Analyse Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DXB
- Type
- protein
- Length
- 3,908 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Thiobacillus thioparus
- Molecule
- Thiocyanate hydrolase subunit alpha; Thiocyanate hydrolase subunit beta; Thiocyanate…
- EC
- 3.5.5.8
- UniProt
- O66187, O66186, O66188
- Ligands
- 3CO, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.25 · 8 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 118 | 21% helix, 29% strand | O66187 |
| B, K, N, W | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 152 | 57% helix, 7% strand | O66186 |
| C, I, O, U | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 217 | 41% helix, 13% strand | O66188 |
| D, P | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 119 | 22% helix, 29% strand | O66187 |
| E, Q | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 151 | 60% helix, 7% strand | O66186 |
| F, L, R, X | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 216 | 41% helix, 14% strand | O66188 |
| G, J, S, V | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 120 | 22% helix, 28% strand | O66187 |
| H, T | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 156 | 58% helix, 6% strand | O66186 |
Ligands and binding sites
- 3CO · Cobalt (III) ion · metal · 8 copies · chains C, F, I, L, O, R, U, X
- PO4 · Phosphate ion · ion · 8 copies · chains B, C, E, F, H, I, K, L, N, O, Q, R, T, U, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.88 | 0.92 | 80 | empty |
| 2 | 682 | 0.88 | 0.92 | 83 | empty |
| 3 | 865 | 0.87 | 0.90 | 106 | empty |
| 4 | 658 | 0.87 | 0.91 | 79 | empty |
| 5 | 1040 | 0.83 | 0.84 | 141 | empty |
Interfaces
97 interfaces between chains.
- K–L · 3381 Ų buried · 52 hydrogen bonds · protein-protein
- H–I · 3377 Ų buried · 53 hydrogen bonds · protein-protein
- N–O · 3377 Ų buried · 51 hydrogen bonds · protein-protein
- W–X · 3369 Ų buried · 48 hydrogen bonds · protein-protein
- T–U · 3364 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (oxidation).
Compared structures
- 2DXB · Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers · the same entry in another collection · chain I against I, 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 2DXB · PDBe 2DXB · UniProt O66187 · UniProt O66186 · UniProt O66188
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