Research workbench
Crystal structure of multidrug binding protein EbrR complexed with proflavin
Analyse Crystal structure of multidrug binding protein EbrR complexed with proflavin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HTH
- Type
- protein
- Length
- 514 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Streptomyces lividans
- Molecule
- EbrA repressor
- UniProt
- Q79SH7
- Ligands
- PRL, NI
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EbrA repressor | protein | 171 | 75% helix, 0% strand | Q79SH7 |
| B | EbrA repressor | protein | 173 | 80% helix, 0% strand | Q79SH7 |
| C | EbrA repressor | protein | 170 | 74% helix, 0% strand | Q79SH7 |
Ligands and binding sites
- PRL · Proflavin · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.66 | 0.79 | 51 | PRL |
| 2 | 102 | 0.65 | 0.89 | 17 | PRL |
| 3 | 266 | 0.61 | 0.80 | 23 | empty |
| 4 | 92 | 0.40 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1793 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3HTH · Crystal structure of multidrug binding protein ebrr complexed with proflavin · the same entry in another collection · chain A against A, TM-score 1.00
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 Q79SH7
- Elsewhere: RCSB PDB 3HTH · PDBe 3HTH · UniProt Q79SH7
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