Research workbench
X-ray crystal structure of streptococcus dysgalactiae shp pheromone receptor RGG2
Analyse X-ray crystal structure of streptococcus dysgalactiae shp pheromone receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YV6
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 260 | 72% helix, 1% strand | — |
| B | Transcriptional regulator | protein | 271 | 71% helix, 1% strand | — |
| C | Transcriptional regulator | protein | 267 | 69% helix, 1% strand | — |
| D | Transcriptional regulator | protein | 266 | 70% helix, 2% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.78 | 0.80 | 64 | empty |
| 2 | 925 | 0.78 | 0.80 | 72 | empty |
| 3 | 244 | 0.68 | 0.84 | 47 | empty |
| 4 | 172 | 0.63 | 0.84 | 38 | empty |
| 5 | 210 | 0.58 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2752 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2745 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YV6 · X-ray crystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2 · 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
- Elsewhere: RCSB PDB 4YV6 · PDBe 4YV6
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