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Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free
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
- 6N9I
- Type
- protein
- Length
- 828 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Parageobacillus caldoxylosilyticus NBRC 107762
- Molecule
- Putative hydrolase
- UniProt
- A0A023DFE8
- Ligands
- CO, FE, SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative hydrolase | protein | 276 | 27% helix, 29% strand | A0A023DFE8 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C
- ACT · Acetate ion · additive · 6 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.51 | 0.79 | 27 | GOL, EDO |
| 2 | 121 | 0.51 | 0.80 | 27 | EDO |
| 3 | 217 | 0.47 | 0.74 | 32 | EDO, SO4 |
| 4 | 90 | 0.34 | 0.74 | 19 | EDO, PGE |
| 5 | 57 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6N9I · Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus - free · 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 A0A023DFE8
- Elsewhere: RCSB PDB 6N9I · PDBe 6N9I · UniProt A0A023DFE8
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