MolNFT v2 · #226717 · protein
Structure of the quorum quenching lactonase GcL D122N mutant - monometal center
9B2N · quorum-quenching N-acyl-homoserine lactonase: “Structure of the quorum quenching lactonase GcL D122N mutant - monometal center”. X-ray diffraction at 1.9, 2 ligands (CO, SO4), 4 pockets (best druggability 0.50). MolNFT v2 #226717 on…
- PDB
- 9B2N
- Type
- protein
- Length
- 827 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Parageobacillus caldoxylosilyticus
- Molecule
- quorum-quenching N-acyl-homoserine lactonase
- EC
- 3.1.1.81
- UniProt
- A0A023DFE8
- Ligands
- CO, SO4
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | quorum-quenching N-acyl-homoserine lactonase (EC 3.1.1.81) | protein | 275 | 27% helix, 29% strand | A0A023DFE8 |
| B, C | quorum-quenching N-acyl-homoserine lactonase (EC 3.1.1.81) | protein | 276 | 27% helix, 29% strand | A0A023DFE8 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.50 | 0.75 | 31 | SO4 |
| 2 | 114 | 0.50 | 0.80 | 26 | empty |
| 3 | 81 | 0.33 | 0.74 | 19 | GOL |
| 4 | 70 | 0.31 | 0.74 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 104 Ų buried · 1 hydrogen bond · protein-protein
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 9B2N · PDBe 9B2N · UniProt A0A023DFE8
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