Research workbench
Crystal structure of a novel pyrethroid hydrolase pyth (S78A)
Analyse Crystal structure of a novel pyrethroid hydrolase pyth (S78A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y5V
- Type
- protein
- Length
- 1,505 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrethroid hydrolase
- UniProt
- D0VUS3
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Pyrethroid hydrolase | protein | 251 | 39% helix, 20% strand | D0VUS3 |
| B | Pyrethroid hydrolase | protein | 252 | 37% helix, 22% strand | D0VUS3 |
| F | Pyrethroid hydrolase | protein | 249 | 36% helix, 18% strand | D0VUS3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.78 | 0.88 | 38 | empty |
| 2 | 305 | 0.77 | 0.88 | 49 | empty |
| 3 | 319 | 0.77 | 0.87 | 41 | empty |
| 4 | 1116 | 0.76 | 0.79 | 134 | empty |
| 5 | 366 | 0.76 | 0.86 | 46 | empty |
Interfaces
10 interfaces between chains.
- B–D · 361 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 259 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 249 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y5V · Crystal structure of a novel Pyrethroid Hydrolase PytH (S78A) · the same entry in another collection · chain A against A, 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 D0VUS3
- Elsewhere: RCSB PDB 5Y5V · PDBe 5Y5V · UniProt D0VUS3
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