MolNFT v1 · #108872 · protein
N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme pvdq
4WKU · Acyl-homoserine lactone acylase pvdq: “N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and…”. X-ray diffraction, 1 ligand (3QJ), 8 pockets (best druggability 0.70). MolNFT v1 #108872…
- PDB
- 4WKU
- 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
- 3QJ
- Pockets
- 8 · best druggability 0.70
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 (EC 3.5.1.97) | protein | 164 | 61% helix, 8% strand | Q9I194 |
| B | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 548 | 24% helix, 31% strand | Q9I194 |
Ligands and binding sites
- 3QJ · hexyl(trihydroxy)borate(1-) · ligand · chains B
- GOL · Glycerol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.70 | 0.96 | 16 | 3QJ |
| 2 | 523 | 0.64 | 0.76 | 73 | GOL |
| 3 | 135 | 0.49 | 0.79 | 25 | empty |
| 4 | 78 | 0.44 | 0.80 | 18 | empty |
| 5 | 178 | 0.43 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 3971 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4WKU · 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 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 4WKU · PDBe 4WKU · UniProt Q9I194
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