MolNFT v1 · #167972 · protein + DNA
Crystal structure of streptococcus dysgalactiae shp pheromone receptor RGG2 bound to DNA
6W1A · Transcriptional regulator: “Crystal structure of streptococcus dysgalactiae shp pheromone receptor RGG2 bound to DNA”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.76). MolNFT v1 #167972 on GenesisL1: 3D…
- PDB
- 6W1A
- Type
- protein + DNA
- Length
- 607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator; DNA (30-mer)
- UniProt
- A0A0J9X288
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 274 | 69% helix, 2% strand | A0A0J9X288 |
| B | Transcriptional regulator | protein | 273 | 67% helix, 1% strand | A0A0J9X288 |
| E | DNA (30-mer) | dna | 30 | — | — |
| F | DNA (30-mer) | dna | 30 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.76 | 0.80 | 72 | GOL |
| 2 | 191 | 0.76 | 0.91 | 31 | empty |
| 3 | 253 | 0.71 | 0.86 | 42 | empty |
| 4 | 175 | 0.50 | 0.78 | 25 | empty |
| 5 | 121 | 0.39 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2790 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1302 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- A–F · 353 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 352 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 324 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6W1A · Crystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2 bound to DNA · 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 A0A0J9X288
- Elsewhere: RCSB PDB 6W1A · PDBe 6W1A · UniProt A0A0J9X288
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