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Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bind to substrate C4-AHL
Analyse Structure of the Quorum Quenching lactonase from Parageobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N9Q
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Parageobacillus caldoxylosilyticus NBRC 107762
- Molecule
- Lactonase GcL
- UniProt
- A0A023DFE8
- Ligands
- HL4, CO, FE, SO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.35 · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, D | Lactonase GcL | protein | 277 | 27% helix, 29% strand | A0A023DFE8 |
Ligands and binding sites
- HL4 · N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide · ligand · 2 copies · chains P, D
- CO · Cobalt (II) ion · metal · 2 copies · chains P, D
- FE · Fe (III) ion · metal · 2 copies · chains P, D
- SO4 · Sulfate ion · ion · 5 copies · chains P, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains P, D
- 1PE · Pentaethylene glycol · additive · 4 copies · chains P, D
- PGE · Triethylene glycol · additive · 4 copies · chains P, D
- ACT · Acetate ion · additive · 3 copies · chains P, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.65 | 0.78 | 52 | HL4, EDO |
| 2 | 207 | 0.62 | 0.82 | 28 | HL4, EDO |
Interfaces
1 interface between chains.
- P–D · 749 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6N9Q · Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus bind… · the same entry in another collection · chain D against D, 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 A0A023DFE8
- Elsewhere: RCSB PDB 6N9Q · PDBe 6N9Q · UniProt A0A023DFE8
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