Research workbench
Crystal structure of pseudomonas aeruginosa pvdq in complex with a transition state analogue
Analyse Crystal structure of pseudomonas aeruginosa pvdq in complex with a transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M1J
- 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 subunit beta; Acyl-homoserine lactone acylase pvdq…
- EC
- 3.5.1.97
- UniProt
- Q9I194
- Ligands
- B0S
- Pockets
- 8 · 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 subunit beta (EC 3.5.1.97) | protein | 548 | 25% helix, 32% strand | Q9I194 |
| A | Acyl-homoserine lactone acylase pvdq subunit alpha (EC 3.5.1.97) | protein | 165 | 61% helix, 8% strand | Q9I194 |
Ligands and binding sites
- B0S · tridecylboronic acid · ligand · chains C, A
- GOL · Glycerol · additive · 20 copies · chains C, A
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 | 122 | 0.80 | 0.97 | 23 | B0S |
| 2 | 383 | 0.57 | 0.75 | 56 | GOL |
| 3 | 185 | 0.47 | 0.76 | 26 | GOL |
| 4 | 106 | 0.44 | 0.78 | 19 | GOL |
| 5 | 154 | 0.44 | 0.75 | 24 | GOL |
Interfaces
1 interface between chains.
- C–A · 4022 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, additive adduct, covalent ligand).
Compared structures
- 4M1J · Crystal structure of Pseudomonas aeruginosa PvdQ in complex with a transition state… · 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 4M1J · PDBe 4M1J · UniProt Q9I194
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.