Research workbench
Crystal structure of a thermostable esterase complex with paraoxon
Analyse Crystal structure of a thermostable esterase complex with paraoxon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DOI
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- EC
- 3.1.1.1
- UniProt
- Q9WXP0
- Ligands
- DEP
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Esterase (EC 3.1.1.1) | protein | 375 | 25% helix, 33% strand | Q9WXP0 |
| B | Esterase (EC 3.1.1.1) | protein | 373 | 24% helix, 34% strand | Q9WXP0 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.59 | 0.79 | 32 | DEP |
| 2 | 205 | 0.55 | 0.78 | 29 | DEP |
| 3 | 54 | 0.43 | 0.83 | 16 | empty |
| 4 | 88 | 0.41 | 0.78 | 16 | empty |
| 5 | 122 | 0.38 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3DOI · Crystal Structure of a Thermostable Esterase complex with paraoxon · 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 Q9WXP0
- Elsewhere: RCSB PDB 3DOI · PDBe 3DOI · UniProt Q9WXP0
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