Research workbench
Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme
Analyse Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZD
- Type
- protein
- Length
- 1,959 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate hydrolase subunit alpha; Thiocyanate hydrolase subunit beta; Thiocyanate…
- EC
- 3.5.5.8
- UniProt
- O66187, O66186, O66188
- Ligands
- FRU, BGC, 3CO
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 119 | 22% helix, 29% strand | O66187 |
| B | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 153 | 59% helix, 7% strand | O66186 |
| C, I | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 217 | 41% helix, 13% strand | O66188 |
| D, G, J | Thiocyanate hydrolase subunit alpha (EC 3.5.5.8) | protein | 120 | 21% helix, 28% strand | O66187 |
| E | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 151 | 60% helix, 6% strand | O66186 |
| F | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 218 | 39% helix, 12% strand | O66188 |
| H | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 156 | 59% helix, 6% strand | O66186 |
| K | Thiocyanate hydrolase subunit beta (EC 3.5.5.8) | protein | 152 | 59% helix, 6% strand | O66186 |
| L | Thiocyanate hydrolase subunit gamma (EC 3.5.5.8) | protein | 216 | 41% helix, 13% strand | O66188 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains B, E, F, J, L, H, K
- BGC · beta-D-glucopyranose · sugar · chains F
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.88 | 0.92 | 81 | empty |
| 2 | 842 | 0.87 | 0.90 | 99 | empty |
| 3 | 1158 | 0.82 | 0.83 | 157 | FRU |
| 4 | 941 | 0.81 | 0.83 | 124 | FRU |
| 5 | 53 | 0.68 | 0.97 | 25 | empty |
Interfaces
46 interfaces between chains.
- E–F · 3365 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 3364 Ų buried · 53 hydrogen bonds · protein-protein
- H–I · 3353 Ų buried · 50 hydrogen bonds · protein-protein
- K–L · 3341 Ų buried · 50 hydrogen bonds · protein-protein
- J–L · 1661 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 2ZZD · Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme · 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 2ZZD · PDBe 2ZZD · UniProt O66187 · UniProt O66186 · UniProt O66188
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