Research workbench
The quorum quenching N-acyl homoserine lactone acylase pvdq in complex with dodecanoic acid
Analyse The quorum quenching N-acyl homoserine lactone acylase pvdq in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WYD
- Type
- protein
- Length
- 710 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-homoserine lactone acylase pvdq subunit alpha; Acyl-homoserine lactone acylase pvdq…
- EC
- 3.5.1.97
- UniProt
- Q9I194
- Ligands
- DAO
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-homoserine lactone acylase pvdq subunit alpha (EC 3.5.1.97) | protein | 164 | 60% helix, 9% strand | Q9I194 |
| B | Acyl-homoserine lactone acylase pvdq subunit beta (EC 3.5.1.97) | protein | 546 | 25% helix, 32% strand | Q9I194 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.76 | 0.96 | 21 | DAO |
| 2 | 883 | 0.70 | 0.75 | 114 | GOL, DAO |
| 3 | 112 | 0.46 | 0.79 | 24 | empty |
| 4 | 127 | 0.40 | 0.75 | 19 | GOL |
| 5 | 60 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3957 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2WYD · The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with dodecanoic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I194 · AlphaFold monomer V2.0 prediction for acyl-homoserine lactone acylase pvdq (Q9I194) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9I194
- Elsewhere: RCSB PDB 2WYD · PDBe 2WYD · UniProt Q9I194
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