MolNFT v1 · #140263 · protein
Crystal structure of a novel pyrethroid hydrolase from sphingobium faniae jz-2
5Y57: “Crystal structure of a novel pyrethroid hydrolase from sphingobium faniae jz-2”. X-ray diffraction, 2 ligands (PMS, SO4), 18 pockets (best druggability 0.76). MolNFT v1 #140263 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5Y57
- Type
- protein
- Length
- 1,512 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrethroid hydrolase
- UniProt
- D0VUS3
- Ligands
- PMS, SO4
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Pyrethroid hydrolase | protein | 251 | 37% helix, 20% strand | D0VUS3 |
| B, D | Pyrethroid hydrolase | protein | 252 | 38% helix, 19% strand | D0VUS3 |
| C, F | Pyrethroid hydrolase | protein | 253 | 39% helix, 20% strand | D0VUS3 |
Ligands and binding sites
- PMS · phenylmethanesulfonic acid · ligand · 6 copies · chains A, B, C, D, E, F
- 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
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.76 | 0.88 | 46 | PMS |
| 2 | 1147 | 0.76 | 0.78 | 144 | PMS |
| 3 | 276 | 0.76 | 0.88 | 47 | PMS |
| 4 | 337 | 0.74 | 0.85 | 45 | PMS |
| 5 | 283 | 0.74 | 0.87 | 41 | PMS |
Interfaces
12 interfaces between chains.
- B–D · 334 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 318 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 316 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 6 covalent (engineered, covalent ligand).
Compared structures
- 5Y57 · Crystal structure of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2 · the same entry in another collection · chain D against D, 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 5Y57 · PDBe 5Y57 · UniProt D0VUS3
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