MolNFT v1 · #157770 · protein
Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-ahl
6N9R · Putative hydrolase: “Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus bound to substrate…”. X-ray diffraction, 4 ligands (OHN, CO, FE), 6 pockets (best druggability 0.61). MolNFT v1 #157770 on…
- PDB
- 6N9R
- Type
- protein
- Length
- 828 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- UniProt
- A0A023DFE8
- Ligands
- OHN, CO, FE, SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P, X | Putative hydrolase | protein | 276 | 27% helix, 30% strand | A0A023DFE8 |
Ligands and binding sites
- OHN · N-3-oxo-dodecanoyl-L-homoserine lactone · ligand · 3 copies · chains A, P, X
- CO · Cobalt (II) ion · metal · 3 copies · chains A, P, X
- FE · Fe (III) ion · metal · 3 copies · chains A, P, X
- SO4 · Sulfate ion · ion · 7 copies · chains P, X
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, P, X
- ACT · Acetate ion · additive · 5 copies · chains A, P, X
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, P, X
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.61 | 0.81 | 26 | OHN |
| 2 | 249 | 0.60 | 0.80 | 30 | 1PE |
| 3 | 187 | 0.60 | 0.81 | 27 | OHN |
| 4 | 184 | 0.60 | 0.81 | 26 | OHN |
| 5 | 226 | 0.48 | 0.75 | 32 | empty |
Interfaces
2 interfaces between chains.
- P–X · 758 Ų buried · 9 hydrogen bonds · protein-protein
- A–P · 620 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6N9R · Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus 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 A0A023DFE8
- Elsewhere: RCSB PDB 6N9R · PDBe 6N9R · UniProt A0A023DFE8
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