MolNFT v1 · #46443 · protein
Structure of phosphotriesterase mutant I106G/F132G/H257Y
2O4M · Parathion hydrolase: “Structure of phosphotriesterase mutant I106G/F132G/H257Y”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.74). MolNFT v1 #46443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2O4M
- Type
- protein
- Length
- 1,323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase (EC 3.1.8.1) | protein | 330 | 52% helix, 14% strand | P0A434 |
| B, C, P | Parathion hydrolase (EC 3.1.8.1) | protein | 331 | 51% helix, 15% strand | P0A434 |
Ligands and binding sites
- ZN · Zinc ion · metal · 23 copies · chains A, B, C, P
- GOL · Glycerol · additive · 5 copies · chains B, C, P
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, P
- ACY · Acetic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.74 | 0.80 | 87 | empty |
| 2 | 109 | 0.68 | 0.91 | 28 | empty |
| 3 | 307 | 0.68 | 0.82 | 41 | empty |
| 4 | 250 | 0.60 | 0.80 | 37 | ZN, CAC, ACY |
| 5 | 281 | 0.59 | 0.78 | 39 | ZN, CAC, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1381 Ų buried · 35 hydrogen bonds · protein-protein
- C–P · 1361 Ų buried · 34 hydrogen bonds · protein-protein
- A–P · 629 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
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 P0A434
- Elsewhere: RCSB PDB 2O4M · PDBe 2O4M · UniProt P0A434
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