Research workbench
Structure of the quorum quenching lactonase from alicyclobacillus acidoterrestris bound to C6-ahl
Analyse Structure of the quorum quenching lactonase from alicyclobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CGZ
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- T0BMH6
- Ligands
- HL6, CO
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase | protein | 275 | 27% helix, 30% strand | T0BMH6 |
Ligands and binding sites
- HL6 · N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide · ligand · 3 copies · chains A, B, C
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.78 | 0.80 | 99 | HL6, EDO |
| 2 | 198 | 0.60 | 0.81 | 28 | HL6 |
| 3 | 89 | 0.37 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1197 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 740 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CGZ · Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound… · 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 T0BMH6
- Elsewhere: RCSB PDB 6CGZ · PDBe 6CGZ · UniProt T0BMH6
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