Research workbench
Crystal structure of PYTH_H230A
Analyse Crystal structure of PYTH_H230A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y51
- Type
- protein
- Length
- 1,497 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrethroid hydrolase
- UniProt
- D0VUS3
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Pyrethroid hydrolase | protein | 248 | 41% helix, 20% strand | D0VUS3 |
| B | Pyrethroid hydrolase | protein | 249 | 39% helix, 20% strand | D0VUS3 |
| C, D | Pyrethroid hydrolase | protein | 251 | 39% helix, 20% strand | D0VUS3 |
| E | Pyrethroid hydrolase | protein | 250 | 38% helix, 20% 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
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.78 | 0.88 | 43 | empty |
| 2 | 359 | 0.78 | 0.88 | 47 | empty |
| 3 | 388 | 0.78 | 0.87 | 46 | empty |
| 4 | 362 | 0.78 | 0.88 | 48 | empty |
| 5 | 332 | 0.78 | 0.88 | 45 | empty |
Interfaces
11 interfaces between chains.
- B–D · 331 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 286 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y51 · Crystal structure of PytH_H230A · 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 5Y51 · PDBe 5Y51 · UniProt D0VUS3
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