Research workbench
Crystal structure of thioesterase PA1618 from pseudomonas aeruginosa in complex with phenacyl-CoA
Analyse Crystal structure of thioesterase PA1618 from pseudomonas aeruginosa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QD8
- Type
- protein
- Length
- 834 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioesterase PA1618
- EC
- 3.1.2.-
- UniProt
- Q9I3A4
- Ligands
- 0FQ
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Thioesterase PA1618 (EC 3.1.2.-) | protein | 139 | 20% helix, 42% strand | Q9I3A4 |
Ligands and binding sites
- 0FQ · phenacyl coenzyme A · ligand · 4 copies · chains C, E, F, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.77 | 0.80 | 108 | 0FQ |
| 2 | 534 | 0.76 | 0.83 | 86 | 0FQ |
| 3 | 253 | 0.65 | 0.83 | 32 | empty |
| 4 | 73 | 0.37 | 0.78 | 24 | empty |
| 5 | 100 | 0.34 | 0.73 | 13 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1312 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1310 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 646 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 614 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 513 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4QD8 · Crystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I3A4 · AlphaFold monomer V2.0 prediction for putative esterase PA1618 (Q9I3A4) · a predicted model of the same protein · chain A 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 Q9I3A4
- Elsewhere: RCSB PDB 4QD8 · PDBe 4QD8 · UniProt Q9I3A4
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