Research workbench
Crystal structure of streptococcus thermophilus shp pheromone receptor RGG3 bound to DNA
Analyse Crystal structure of streptococcus thermophilus shp pheromone receptor RGG3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W1F
- Type
- protein + DNA
- Length
- 620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Positive transcriptional regulator mutr family; DNA (30-mer)
- UniProt
- Q5M4D0
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Positive transcriptional regulator mutr family | protein | 280 | 70% helix, 3% strand | Q5M4D0 |
| E | DNA (30-mer) | dna | 30 | — | — |
| F | DNA (30-mer) | dna | 30 | — | — |
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 | 959 | 0.81 | 0.82 | 86 | empty |
| 2 | 559 | 0.76 | 0.83 | 53 | empty |
| 3 | 447 | 0.75 | 0.84 | 42 | empty |
| 4 | 238 | 0.56 | 0.78 | 27 | empty |
| 5 | 82 | 0.44 | 0.80 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2746 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1242 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- B–F · 389 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–E · 368 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–E · 317 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6W1F · Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 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 Q5M4D0
- Elsewhere: RCSB PDB 6W1F · PDBe 6W1F · UniProt Q5M4D0
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