Research workbench
Molecular insight into the regulatory mechanism of the quorum-sensing repressor rsal in pseudomonas aeruginosa
Analyse Molecular insight into the regulatory mechanism of the quorum-sensing repressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J2Y
- Type
- protein + DNA
- Length
- 238 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein; DNA (26-mer)
- UniProt
- Q9X7H4
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein | protein | 70 | 67% helix, 0% strand | Q9X7H4 |
| B | Regulatory protein | protein | 68 | 65% helix, 0% strand | Q9X7H4 |
| F, f | DNA (26-mer) | dna | 25 | — | — |
| R, r | DNA (26-mer) | dna | 25 | — | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.33 | 0.75 | 20 | empty |
| 2 | 60 | 0.31 | 0.76 | 12 | empty |
| 3 | 54 | 0.27 | 0.74 | 9 | empty |
Interfaces
7 interfaces between chains.
- F–r · 1136 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- R–f · 1089 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- B–R · 340 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 333 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–r · 297 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 5J2Y · Molecular insight into the regulatory mechanism of the quorum-sensing repressor RsaL in… · 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 Q9X7H4
- Elsewhere: RCSB PDB 5J2Y · PDBe 5J2Y · UniProt Q9X7H4
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