Research workbench
Crystal structures of a short blue light photoreceptor protein PPSB1- lov mutant (dark state) - R61H/R66I
Analyse Crystal structures of a short blue light photoreceptor protein PPSB1- lov… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GG9
- Type
- protein
- Length
- 538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensory box protein
- UniProt
- Q88E39
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory box protein | protein | 134 | 37% helix, 35% strand | Q88E39 |
| B, D | Sensory box protein | protein | 135 | 39% helix, 35% strand | Q88E39 |
| C | Sensory box protein | protein | 134 | 38% helix, 31% strand | Q88E39 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.84 | 0.85 | 97 | empty |
| 2 | 231 | 0.73 | 0.88 | 27 | FMN |
| 3 | 234 | 0.72 | 0.87 | 29 | FMN |
| 4 | 213 | 0.71 | 0.87 | 28 | FMN |
| 5 | 214 | 0.69 | 0.86 | 29 | FMN |
Interfaces
5 interfaces between chains.
- B–D · 1652 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1649 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 223 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 172 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6GG9 · Crystal structures of a short blue light photoreceptor protein PpSB1-LOV mutant (dark… · 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 Q88E39
- Elsewhere: RCSB PDB 6GG9 · PDBe 6GG9 · UniProt Q88E39
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