Research workbench
Crystal structure of quorum-sensing transcriptional activator from yersinia enterocolitica
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
- 5L07
- 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
- A0A0T9SEJ2
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quorum-sensing transcriptional activator | protein | 162 | 51% helix, 19% strand | A0A0T9SEJ2 |
| B | Quorum-sensing transcriptional activator | protein | 163 | 53% helix, 19% strand | A0A0T9SEJ2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- ACY · Acetic acid · additive · 5 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 | 106 | 0.67 | 0.90 | 27 | ACY, EDO |
| 2 | 132 | 0.67 | 0.88 | 22 | ACY |
| 3 | 124 | 0.45 | 0.78 | 24 | EDO |
| 4 | 86 | 0.38 | 0.77 | 25 | empty |
| 5 | 89 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 870 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5L07 · Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica · 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 A0A0T9SEJ2
- Elsewhere: RCSB PDB 5L07 · PDBe 5L07 · UniProt A0A0T9SEJ2
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