MolNFT v1 · #34345 · protein
Thiocyanate hydrolase (scnase) from thiobacillus thioparus native holo-enzyme
2DD5 · Thiocyanate hydrolase alpha subunit: “Thiocyanate hydrolase (scnase) from thiobacillus thioparus native holo-enzyme”. X-ray diffraction, 2 ligands (3CO, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #34345 on GenesisL1: 3D…
- PDB
- 2DD5
- Type
- protein
- Length
- 1,955 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
- 3CO, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Thiocyanate hydrolase alpha subunit (EC 3.5.5.8) | protein | 119 | 22% helix, 29% strand | O66187 |
| B, K | Thiocyanate hydrolase beta subunit (EC 3.5.5.8) | protein | 152 | 61% helix, 7% strand | O66186 |
| C, I | Thiocyanate hydrolase gamma subunit (EC 3.5.5.8) | protein | 217 | 40% helix, 13% strand | O66188 |
| E | Thiocyanate hydrolase beta subunit (EC 3.5.5.8) | protein | 151 | 61% helix, 7% strand | O66186 |
| F, L | Thiocyanate hydrolase gamma subunit (EC 3.5.5.8) | protein | 216 | 40% helix, 12% 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 | 61% helix, 6% strand | O66186 |
Ligands and binding sites
- 3CO · Cobalt (III) ion · metal · 4 copies · chains C, F, I, L
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, K, C, D, E, H, F, G, I, 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 | 496 | 0.88 | 0.95 | 64 | empty |
| 2 | 914 | 0.87 | 0.89 | 109 | empty |
| 3 | 1140 | 0.83 | 0.84 | 159 | empty |
| 4 | 992 | 0.82 | 0.83 | 137 | empty |
| 5 | 50 | 0.68 | 0.98 | 24 | empty |
Interfaces
46 interfaces between chains.
- K–L · 3390 Ų buried · 57 hydrogen bonds · protein-protein
- H–I · 3385 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 3377 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3333 Ų buried · 51 hydrogen bonds · protein-protein
- G–I · 1626 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 2DD5 · Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus native 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 2DD5 · PDBe 2DD5 · UniProt O66187 · UniProt O66186 · UniProt O66188
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