MolNFT v1 · #122932 · protein
Crystal structures reveal signaling states of a short blue light photoreceptor protein PPSB1-lov (photoexcited state)
5J4E · Sensory box protein: “Crystal structures reveal signaling states of a short blue light photoreceptor protein PPSB1-lov…”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.82). MolNFT v1 #122932 on GenesisL1: 3D…
- PDB
- 5J4E
- 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
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory box protein | protein | 133 | 37% helix, 34% strand | Q88E39 |
| B, C, D | Sensory box protein | protein | 134 | 37% helix, 34% 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.82 | 0.87 | 74 | FMN |
| 2 | 298 | 0.78 | 0.90 | 45 | empty |
| 3 | 225 | 0.74 | 0.89 | 28 | FMN |
| 4 | 203 | 0.72 | 0.88 | 29 | FMN |
| 5 | 331 | 0.71 | 0.84 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1585 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1482 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 305 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J4E · 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 5J4E · PDBe 5J4E · UniProt Q88E39
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