Research workbench
Crystal structure of E253Q bmrr bound to 22 base pair promoter site
Analyse Crystal structure of E253Q bmrr bound to 22 base pair promoter site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D71
- Type
- protein + DNA
- Length
- 300 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
- ZN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Bmr promoter DNA | dna | 23 | — | — |
| A | Multidrug-efflux transporter 1 regulator | protein | 277 | 40% helix, 23% strand | P39075 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- IMD · Imidazole · additive · 5 copies · chains A
- PGO · S-1,2-propanediol · additive · 3 copies · chains A
- FLC · Citrate anion · additive · chains A
- ETF · Trifluoroethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.58 | 0.85 | 26 | empty |
| 2 | 76 | 0.53 | 0.86 | 19 | IMD |
| 3 | 162 | 0.53 | 0.79 | 20 | FLC, IMD |
Interfaces
1 interface between chains.
- M–A · 374 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3D71 · Crystal structure of E253Q BMRR bound to 22 base pair promoter site · 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 0.98
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 3D71 · PDBe 3D71 · UniProt P39075
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