Research workbench
Crystal structures reveal signaling states of a short blue light photoreceptor protein PPSB1-lov (dark state)
Analyse Crystal structures reveal signaling states of a short blue light photoreceptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J3W
- Type
- protein
- Length
- 535 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 · 2 distinct chains · 38% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory box protein | protein | 133 | 38% helix, 35% strand | Q88E39 |
| B, C, D | Sensory box protein | protein | 134 | 37% helix, 35% 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 | 1071 | 0.84 | 0.85 | 102 | empty |
| 2 | 231 | 0.77 | 0.90 | 29 | FMN |
| 3 | 348 | 0.75 | 0.86 | 40 | FMN |
| 4 | 205 | 0.74 | 0.90 | 30 | FMN |
| 5 | 255 | 0.68 | 0.84 | 37 | FMN |
Interfaces
5 interfaces between chains.
- B–D · 1588 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1476 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 454 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 251 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J3W · Crystal structures reveal signaling states of a short blue light photoreceptor protein… · 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 5J3W · PDBe 5J3W · UniProt Q88E39
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