Research workbench
Crystal structure of quorum-sensing transcriptional activator from yersinia enterocolitica in complex with 3-oxo-N-[(3S)-2- oxotetrahydrofuran-3-YL]HEXANAMIDE
Analyse Crystal structure of quorum-sensing transcriptional activator from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L09
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quorum-sensing transcriptional activator
- UniProt
- A1JMX7
- Ligands
- 482, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quorum-sensing transcriptional activator | protein | 161 | 50% helix, 19% strand | A1JMX7 |
| B | Quorum-sensing transcriptional activator | protein | 164 | 54% helix, 18% strand | A1JMX7 |
Ligands and binding sites
- 482 · 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- ACY · Acetic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.98 | 17 | 482 |
| 2 | 73 | 0.75 | 0.98 | 18 | 482 |
| 3 | 127 | 0.47 | 0.78 | 19 | ACY |
| 4 | 65 | 0.33 | 0.76 | 13 | empty |
| 5 | 59 | 0.31 | 0.76 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5L09 · Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia… · 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 A1JMX7
- Elsewhere: RCSB PDB 5L09 · PDBe 5L09 · UniProt A1JMX7
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