Research workbench
Crystal structure of bmrr bound to DNA at 2.4A resolution
Analyse Crystal structure of bmrr bound to DNA at 2.4A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R8E
- Type
- protein + DNA
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP *GP*GP*GP*TP*C)-3'…
- UniProt
- P39075
- Ligands
- P4P
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP *GP*GP*GP*TP*C)-3' | dna | 23 | — | — |
| A | Multidrug-efflux transporter regulator | protein | 275 | 41% helix, 24% strand | P39075 |
Ligands and binding sites
- P4P · Tetraphenylphosphonium · ligand · chains A
- IMD · Imidazole · additive · 11 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.63 | 0.85 | 27 | empty |
| 2 | 204 | 0.55 | 0.78 | 28 | IMD |
Interfaces
1 interface between chains.
- B–A · 353 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1R8E · Crystal Structure of BmrR Bound to DNA at 2.4A Resolution · 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 1R8E · PDBe 1R8E · UniProt P39075
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