MolNFT v1 · #5938 · protein + DNA
Crystal structure of transcription activator bmrr, from B. subtilis, bound to 21 base pair bmr operator and tpp
1EXJ · DNA (5'- D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*…: “Crystal structure of transcription activator bmrr, from B. subtilis, bound to 21 base pair bmr operator and…”. X-ray diffraction, 3 ligands (P4P, NA, ZN), 2 pockets…
- PDB
- 1EXJ
- 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
- P4P, NA, ZN
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% 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 | 40% helix, 21% strand | P39075 |
Ligands and binding sites
- P4P · Tetraphenylphosphonium · ligand · chains A
- NA · Sodium ion · metal · chains M
- ZN · Zinc ion · metal · chains 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 | 478 | 0.67 | 0.78 | 44 | empty |
| 2 | 202 | 0.54 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- M–A · 315 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1EXJ · 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 0.96
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 P39075
- Elsewhere: RCSB PDB 1EXJ · PDBe 1EXJ · UniProt P39075
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