Research workbench
Structural basis for recognition and ring-cleavage of the pseudomonas quinolone signal (pqs) by aqdc variant in complex with its substrate
Analyse Structural basis for recognition and ring-cleavage of the pseudomonas quinolone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RB3
- Type
- protein
- Length
- 801 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4- dioxygenase)
- UniProt
- B1MFK2
- Ligands
- JWW
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, B | Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4- dioxygenase) | protein | 267 | 47% helix, 16% strand | B1MFK2 |
Ligands and binding sites
- JWW · 2-heptylquinoline-3,4-diol · ligand · 3 copies · chains E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 83 | JWW |
| 2 | 772 | 0.74 | 0.79 | 86 | JWW |
| 3 | 272 | 0.70 | 0.84 | 40 | JWW |
| 4 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- E–A · 541 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6RB3 · Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal… · the same entry in another collection · chain E against E, TM-score 1.00
- B1MFK2 · AlphaFold monomer V2.0 prediction for 2-heptyl-3-hydroxy-4(1H)-quinolone dioxygenase… · a predicted model of the same protein · 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 B1MFK2
- Elsewhere: RCSB PDB 6RB3 · PDBe 6RB3 · UniProt B1MFK2
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