Research workbench
Crystal structure of the dequalinum-bound form of ramr (transcriptional regulator of tetr family) from salmonella typhimurium
Analyse Crystal structure of the dequalinum-bound form of ramr (transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VW0
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative regulatory protein
- UniProt
- D0ZP76
- Ligands
- DEQ, SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative regulatory protein | protein | 184 | 76% helix, 0% strand | D0ZP76 |
| B | Putative regulatory protein | protein | 185 | 77% helix, 1% strand | D0ZP76 |
| D | Putative regulatory protein | protein | 184 | 80% helix, 1% strand | D0ZP76 |
Ligands and binding sites
- DEQ · Dequalinium · ligand · 2 copies · chains B, 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.84 | 0.89 | 55 | empty |
| 2 | 614 | 0.81 | 0.86 | 57 | empty |
| 3 | 979 | 0.80 | 0.81 | 73 | DEQ |
| 4 | 1053 | 0.80 | 0.81 | 83 | DEQ |
| 5 | 366 | 0.59 | 0.76 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1229 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1191 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 571 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 73 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VW0 · Crystal Structure of The Dequalinum-bound Form of RamR (Transcriptional Regulator of TetR… · 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 D0ZP76
- Elsewhere: RCSB PDB 3VW0 · PDBe 3VW0 · UniProt D0ZP76
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