Research workbench
Thiocyanate hydrolase (scnase) from thiobacillus thioparus recombinant apo-enzyme
Analyse Thiocyanate hydrolase (scnase) from thiobacillus thioparus recombinant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DD4
- Type
- protein
- Length
- 1,954 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiocyanate hydrolase alpha subunit; Thiocyanate hydrolase beta subunit; Thiocyanate…
- EC
- 3.5.5.8
- UniProt
- O66187, O66186, O66188
- Ligands
- FRU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiocyanate hydrolase alpha subunit (EC 3.5.5.8) | protein | 118 | 21% helix, 29% strand | O66187 |
| B, K | Thiocyanate hydrolase beta subunit (EC 3.5.5.8) | protein | 152 | 59% helix, 7% strand | O66186 |
| C, I | Thiocyanate hydrolase gamma subunit (EC 3.5.5.8) | protein | 217 | 40% helix, 12% strand | O66188 |
| D | Thiocyanate hydrolase alpha subunit (EC 3.5.5.8) | protein | 119 | 21% helix, 29% strand | O66187 |
| E | Thiocyanate hydrolase beta subunit (EC 3.5.5.8) | protein | 151 | 59% helix, 6% strand | O66186 |
| F, L | Thiocyanate hydrolase gamma subunit (EC 3.5.5.8) | protein | 216 | 40% helix, 13% strand | O66188 |
| G, J | Thiocyanate hydrolase alpha subunit (EC 3.5.5.8) | protein | 120 | 22% helix, 28% strand | O66187 |
| H | Thiocyanate hydrolase beta subunit (EC 3.5.5.8) | protein | 156 | 59% helix, 6% strand | O66186 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 8 copies · chains B, D, E, F, J, K, C, H, L, G, I, A
- TLA · L(+)-tartaric acid · additive · 8 copies · chains B, C, A, E, F, D, H, I, G, K, L, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.87 | 0.92 | 82 | FRU |
| 2 | 818 | 0.87 | 0.90 | 94 | FRU |
| 3 | 1049 | 0.82 | 0.83 | 143 | FRU |
| 4 | 1024 | 0.82 | 0.83 | 129 | FRU |
| 5 | 52 | 0.69 | 0.97 | 22 | empty |
Interfaces
46 interfaces between chains.
- B–C · 3391 Ų buried · 50 hydrogen bonds · protein-protein
- H–I · 3359 Ų buried · 48 hydrogen bonds · protein-protein
- K–L · 3327 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3278 Ų buried · 50 hydrogen bonds · protein-protein
- J–L · 1631 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2DD4 · Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-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 2DD4 · PDBe 2DD4 · UniProt O66187 · UniProt O66186 · UniProt O66188
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