MolNFT v1 · #82738 · protein
Crystal strucuture of the crystal violet-bound form of ramr (transcriptional regurator of tetr family) from salmonella typhimurium
3VW1 · Putative regulatory protein: “Crystal strucuture of the crystal violet-bound form of ramr (transcriptional regurator of tetr family) from…”. X-ray diffraction, 3 ligands (CVI, SO4, CL), 6 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 3VW1
- Type
- protein
- Length
- 735 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative regulatory protein
- UniProt
- D0ZP76
- Ligands
- CVI, SO4, CL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative regulatory protein | protein | 184 | 78% helix, 1% strand | D0ZP76 |
| D | Putative regulatory protein | protein | 183 | 80% helix, 1% strand | D0ZP76 |
Ligands and binding sites
- CVI · Crystal violet · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.84 | 0.85 | 98 | CVI |
| 2 | 585 | 0.83 | 0.88 | 48 | empty |
| 3 | 549 | 0.83 | 0.88 | 54 | empty |
| 4 | 1028 | 0.81 | 0.82 | 94 | CVI |
| 5 | 74 | 0.35 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1291 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1278 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 370 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3VW1 · Crystal Strucuture of the Crystal Violet-Bound Form of RamR (Transcriptional Regurator of… · 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 3VW1 · PDBe 3VW1 · UniProt D0ZP76
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