MolNFT v1 · #17959 · protein
Crystal structure analysis of methyl parathion hydrolase from pseudomonas sp wbc-3
1P9E: “Crystal structure analysis of methyl parathion hydrolase from pseudomonas sp wbc-3”. X-ray diffraction, 4 ligands (NA, K, ZN), 6 pockets (best druggability 0.85). MolNFT v1 #17959 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1P9E
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl parathion hydrolase
- EC
- 3.1.8.1
- Ligands
- NA, K, ZN, CD
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyl parathion hydrolase (EC 3.1.8.1) | protein | 294 | 27% helix, 29% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- CD · Cadmium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.85 | 0.86 | 102 | empty |
| 2 | 239 | 0.65 | 0.83 | 36 | empty |
| 3 | 156 | 0.63 | 0.85 | 23 | empty |
| 4 | 155 | 0.46 | 0.76 | 25 | empty |
| 5 | 99 | 0.41 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2366 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 1P9E · Crystal Structure Analysis of Methyl Parathion Hydrolase from Pseudomonas sp WBC-3 · 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
- Elsewhere: RCSB PDB 1P9E · PDBe 1P9E
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