MolNFT v1 · #135857 · protein
Inactive S1A/N269D-cppvdq mutant in complex with the pyoverdine precursor pvdiq reveals a specific binding pocket for the D-tyr of this substrate
5UBK · Acyl-homoserine lactone acylase pvdq: “Inactive S1A/N269D-cppvdq mutant in complex with the pyoverdine precursor pvdiq reveals a specific binding…”. X-ray diffraction, 1 ligand (83M), 6 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5UBK
- Type
- protein
- Length
- 709 residues
- Chains
- 1
- 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
- 83M
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97) | protein | 709 | 34% helix, 25% strand | Q9I194 |
Ligands and binding sites
- 83M · N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine · ligand · chains A
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 | 756 | 0.72 | 0.78 | 96 | 83M |
| 2 | 196 | 0.55 | 0.79 | 25 | empty |
| 3 | 188 | 0.43 | 0.73 | 31 | empty |
| 4 | 138 | 0.42 | 0.75 | 20 | empty |
| 5 | 51 | 0.36 | 0.80 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5UBK · Inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a… · 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 A against A, TM-score 0.77
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 5UBK · PDBe 5UBK · UniProt Q9I194
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