Research workbench
Ligand binding domain of the P. putida receptor PCAY_PP in complex with protocatechuate
Analyse Ligand binding domain of the P. putida receptor PCAY_PP in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S33
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic acid chemoreceptor
- UniProt
- Q88JK6
- Ligands
- DHB
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic acid chemoreceptor | protein | 142 | 92% helix, 0% strand | Q88JK6 |
| B | Aromatic acid chemoreceptor | protein | 133 | 91% helix, 0% strand | Q88JK6 |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.66 | 0.79 | 30 | empty |
| 2 | 120 | 0.58 | 0.85 | 21 | DHB |
| 3 | 57 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6S33 · Ligand binding domain of the P. putida receptor PcaY_PP in complex with Protocatechuate · 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 Q88JK6
- Elsewhere: RCSB PDB 6S33 · PDBe 6S33 · UniProt Q88JK6
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