Research workbench
Crystal structure of transcription activator bmrr, from B. subtilis, bound to 21 base pair bmr operator and tpsb
Analyse Crystal structure of transcription activator bmrr, from B. subtilis, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EXI
- Type
- protein + DNA
- Length
- 296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)- 3')…
- UniProt
- P39075
- Ligands
- 118, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'- D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)- 3') | dna | 21 | — | — |
| A | Multidrug-efflux transporter regulator | protein | 275 | 38% helix, 19% 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 | 459 | 0.67 | 0.78 | 43 | empty |
| 2 | 219 | 0.54 | 0.77 | 25 | 118 |
| 3 | 79 | 0.46 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- M–A · 312 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1EXI · Crystal structure of transcription activator bmrr, from B. subtilis, bound to 21 base… · the same entry in another collection · chain M against M, 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 0.95
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 1EXI · PDBe 1EXI · UniProt P39075
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