MolNFT v1 · #157761 · protein
Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus - free
6N9I · Putative hydrolase: “Structure of the quorum quenching lactonase from parageobacillus caldoxylosilyticus - free”. X-ray diffraction, 3 ligands (CO, FE, SO4), 5 pockets (best druggability 0.51). MolNFT v1 #157761 on GenesisL1: 3D…
- PDB
- 6N9I
- 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
- CO, FE, SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 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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