Research workbench
Structure of N-acylhomoserine lactone acylase macq in complex with phenylacetic acid
Analyse Structure of N-acylhomoserine lactone acylase macq in complex with phenylacetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YFB
- Type
- protein
- Length
- 3,033 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein related to penicillin acylase
- UniProt
- A0A0A1VBK6
- Ligands
- PAC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein related to penicillin acylase | protein | 168 | 60% helix, 9% strand | A0A0A1VBK6 |
| B, H | Protein related to penicillin acylase | protein | 15 | 20% helix, 0% strand | A0A0A1VBK6 |
| C, F, I | Protein related to penicillin acylase | protein | 575 | 28% helix, 30% strand | A0A0A1VBK6 |
| E | Protein related to penicillin acylase | protein | 14 | 21% helix, 0% strand | A0A0A1VBK6 |
| G | Protein related to penicillin acylase | protein | 171 | 60% helix, 9% strand | A0A0A1VBK6 |
| J | Protein related to penicillin acylase | protein | 167 | 60% helix, 8% strand | A0A0A1VBK6 |
| K | Protein related to penicillin acylase | protein | 16 | 19% helix, 0% strand | A0A0A1VBK6 |
| L | Protein related to penicillin acylase | protein | 574 | 27% helix, 30% strand | A0A0A1VBK6 |
Ligands and binding sites
- PAC · 2-phenylacetic acid · ligand · 4 copies · chains C, F, I, L
- GOL · Glycerol · additive · 4 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.83 | 0.84 | 127 | empty |
| 2 | 1146 | 0.75 | 0.78 | 113 | empty |
| 3 | 69 | 0.75 | 0.98 | 22 | PAC |
| 4 | 70 | 0.74 | 0.98 | 21 | PAC |
| 5 | 60 | 0.72 | 0.98 | 16 | PAC |
Interfaces
28 interfaces between chains.
- G–I · 4411 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 4391 Ų buried · 83 hydrogen bonds · protein-protein
- D–F · 4372 Ų buried · 88 hydrogen bonds · protein-protein
- J–L · 4293 Ų buried · 85 hydrogen bonds · protein-protein
- C–I · 789 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4YFB · Structure of N-acylhomoserine lactone acylase MacQ in complex with phenylacetic acid · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0A1VBK6
- Elsewhere: RCSB PDB 4YFB · PDBe 4YFB · UniProt A0A0A1VBK6
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