Research workbench
Crystal structure of the multidrug binding transcriptional repressor qacr bound to the natural drug berberine
Analyse Crystal structure of the multidrug binding transcriptional repressor qacr bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JUM
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical transcriptional regulator in qaca 5'REGION
- UniProt
- P0A0N4
- Ligands
- BER, SO4
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, A, E | Hypothetical transcriptional regulator in qaca 5'REGION | protein | 186 | 74% helix, 0% strand | P0A0N4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.87 | 0.91 | 55 | BER |
| 2 | 1089 | 0.78 | 0.80 | 99 | SO4 |
| 3 | 175 | 0.67 | 0.87 | 26 | empty |
| 4 | 101 | 0.48 | 0.81 | 25 | empty |
| 5 | 60 | 0.34 | 0.77 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1617 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1541 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1JUM · Crystal structure of the multidrug binding transcriptional repressor QacR bound to the… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A0N4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator qacr (P0A0N4) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0A0N4
- Elsewhere: RCSB PDB 1JUM · PDBe 1JUM · UniProt P0A0N4
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