MolNFT v1 · #108871 · protein
N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme pvdq
4WKT · Acyl-homoserine lactone acylase pvdq: “N-alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and…”. X-ray diffraction, 1 ligand (BUB), 9 pockets (best druggability 0.80). MolNFT v1 #108871…
- PDB
- 4WKT
- Type
- protein
- Length
- 713 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
- BUB
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 548 | 26% helix, 32% strand | Q9I194 |
| A | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 165 | 61% helix, 9% strand | Q9I194 |
Ligands and binding sites
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 | 127 | 0.80 | 0.97 | 22 | empty |
| 2 | 250 | 0.58 | 0.78 | 40 | GOL |
| 3 | 432 | 0.57 | 0.74 | 57 | BUB, GOL |
| 4 | 185 | 0.46 | 0.75 | 21 | GOL |
| 5 | 108 | 0.46 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- C–A · 3945 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4WKT · n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the… · the same entry in another collection · chain C against C, 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 4WKT · PDBe 4WKT · UniProt Q9I194
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