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
- 4YV9
- Type
- protein
- Length
- 1,107 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator; Cyclosporin a
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 261 | 72% helix, 1% strand | — |
| B | Transcriptional regulator | protein | 270 | 71% helix, 1% strand | — |
| C | Transcriptional regulator | protein | 268 | 73% helix, 1% strand | — |
| D | Transcriptional regulator | protein | 264 | 73% helix, 2% strand | — |
| E, F, G, H | Cyclosporin a | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.83 | 0.89 | 50 | empty |
| 2 | 575 | 0.82 | 0.88 | 65 | empty |
| 3 | 230 | 0.67 | 0.85 | 40 | empty |
| 4 | 179 | 0.61 | 0.83 | 35 | empty |
| 5 | 221 | 0.58 | 0.79 | 23 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2883 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2879 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 758 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 748 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 729 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified, 4 d-amino, 2 disulfide (nonstandard, engineered, methylation, D-amino acid, disulfide).
Compared structures
- 4YV9 · 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 4YV9 · PDBe 4YV9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.