MolNFT v1 · #108873 · protein
N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme pvdq
4WKV · Acyl-homoserine lactone acylase pvdq: “N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and…”. X-ray diffraction, 1 ligand (3QK), 9 pockets (best druggability 0.75). MolNFT v1 #108873…
- PDB
- 4WKV
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-homoserine lactone acylase pvdq
- EC
- 3.5.1.97
- UniProt
- Q9I194
- Ligands
- 3QK
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 548 | 25% helix, 32% strand | Q9I194 |
| A | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 164 | 61% helix, 9% strand | Q9I194 |
Ligands and binding sites
- 3QK · trihydroxy(octyl)borate(1-) · ligand · chains C, A
- GOL · Glycerol · additive · 15 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.75 | 0.96 | 21 | 3QK |
| 2 | 187 | 0.54 | 0.79 | 26 | GOL |
| 3 | 106 | 0.50 | 0.81 | 30 | GOL |
| 4 | 115 | 0.49 | 0.80 | 26 | empty |
| 5 | 222 | 0.48 | 0.74 | 31 | GOL |
Interfaces
1 interface between chains.
- C–A · 3973 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4WKV · n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the… · 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 C 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 4WKV · PDBe 4WKV · UniProt Q9I194
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