MolNFT v1 · #82739 · protein
Crystal strucuture of the berberine-bound form of ramr (transcriptional regurator of tetr family) from salmonella typhimurium
3VW2 · Putative regulatory protein: “Crystal strucuture of the berberine-bound form of ramr (transcriptional regurator of tetr family) from…”. X-ray diffraction, 2 ligands (BER, SO4), 8 pockets (best druggability 0.82). MolNFT v1 #82739 on…
- PDB
- 3VW2
- Type
- protein
- Length
- 736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative regulatory protein
- UniProt
- D0ZP76
- Ligands
- BER, SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative regulatory protein | protein | 184 | 79% helix, 1% strand | D0ZP76 |
| C | Putative regulatory protein | protein | 185 | 75% helix, 1% strand | D0ZP76 |
| D | Putative regulatory protein | protein | 183 | 76% helix, 1% strand | D0ZP76 |
Ligands and binding sites
- BER · Berberine · 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.82 | 0.88 | 54 | BER |
| 2 | 589 | 0.82 | 0.87 | 52 | BER |
| 3 | 915 | 0.82 | 0.83 | 74 | BER |
| 4 | 412 | 0.81 | 0.89 | 52 | BER |
| 5 | 502 | 0.62 | 0.75 | 46 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1302 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1287 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 401 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3VW2 · Crystal Strucuture of The Berberine-bound Form of RamR (Transcriptional Regurator 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 3VW2 · PDBe 3VW2 · UniProt D0ZP76
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