Research workbench
Crystal structure of the ethidium bound ramr determined with xtalab synergy
Analyse Crystal structure of the ethidium bound ramr determined with xtalab synergy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KO7
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative regulatory protein
- UniProt
- A0A0F6AY66
- Ligands
- ET, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative regulatory protein | protein | 184 | 80% helix, 1% strand | A0A0F6AY66 |
| C | Putative regulatory protein | protein | 186 | 80% helix, 1% strand | A0A0F6AY66 |
| D | Putative regulatory protein | protein | 183 | 81% helix, 1% strand | A0A0F6AY66 |
Ligands and binding sites
- ET · Ethidium · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.83 | 0.90 | 48 | ET |
| 2 | 481 | 0.82 | 0.89 | 51 | ET |
| 3 | 479 | 0.81 | 0.88 | 54 | ET |
| 4 | 1178 | 0.80 | 0.82 | 87 | ET |
| 5 | 475 | 0.62 | 0.76 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1300 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1284 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KO7 · Crystal structure of the Ethidium bound RamR determined with XtaLAB Synergy · 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 A0A0F6AY66
- Elsewhere: RCSB PDB 6KO7 · PDBe 6KO7 · UniProt A0A0F6AY66
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