Research workbench
Crystal structure of R275E mutant of bmrr bound to DNA and berberine
Analyse Crystal structure of R275E mutant of bmrr bound to DNA and berberine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D6Y
- Type
- protein + DNA
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bmr promoter DNA; Multidrug-efflux transporter 1 regulator
- UniProt
- P39075
- Ligands
- BER
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Bmr promoter DNA | dna | 24 | — | — |
| A | Multidrug-efflux transporter 1 regulator | protein | 277 | 41% helix, 22% strand | P39075 |
Ligands and binding sites
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 | 206 | 0.64 | 0.83 | 28 | empty |
| 2 | 203 | 0.56 | 0.79 | 26 | BER |
| 3 | 61 | 0.27 | 0.73 | 9 | empty |
Interfaces
1 interface between chains.
- B–A · 356 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3D6Y · Crystal structure of R275E mutant of BMRR bound to DNA and berberine · the same entry in another collection · chain B against B, TM-score 1.00
- P39075 · AlphaFold monomer V2.0 prediction for multidrug-efflux transporter 1 regulator (P39075) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P39075
- Elsewhere: RCSB PDB 3D6Y · PDBe 3D6Y · UniProt P39075
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