Research workbench
Phosphotriesterase PTE_A53_5
Analyse Phosphotriesterase PTE_A53_5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FFW
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- D6K, ZN
- Pockets
- 6 · best druggability 0.66
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 | 51% helix, 14% strand | P0A434 |
| B | Parathion hydrolase (EC 3.1.8.1) | protein | 331 | 51% helix, 14% strand | P0A434 |
Ligands and binding sites
- D6K · (4~{S},6~{R})-2,2,6-trimethyl-1,3-dioxan-4-ol · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 294 | 0.66 | 0.82 | 36 | FMT, ZN |
| 2 | 305 | 0.65 | 0.81 | 38 | FMT, ZN, D6K, TRS |
| 3 | 198 | 0.61 | 0.82 | 37 | empty |
| 4 | 71 | 0.37 | 0.77 | 15 | empty |
| 5 | 50 | 0.32 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1449 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6FFW · Phosphotriesterase PTE_A53_5 · 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 P0A434
- Elsewhere: RCSB PDB 6FFW · PDBe 6FFW · UniProt P0A434
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