MolNFT v1 · #11474 · protein
Photoexcited structure of the plant photoreceptor domain, PHY3 LOV2
1JNU · PHY3 protein: “Photoexcited structure of the plant photoreceptor domain, PHY3 LOV2”. X-ray diffraction, 1 ligand (FMN), 6 pockets (best druggability 0.74). MolNFT v1 #11474 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1JNU
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHY3 protein
- UniProt
- Q9ZWQ6
- Ligands
- FMN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | PHY3 protein | protein | 104 | 27% helix, 35% strand | Q9ZWQ6 |
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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.74 | 0.89 | 24 | FMN |
| 2 | 215 | 0.72 | 0.88 | 25 | FMN |
| 3 | 278 | 0.71 | 0.85 | 34 | FMN |
| 4 | 217 | 0.71 | 0.87 | 24 | FMN |
| 5 | 268 | 0.60 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 444 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 1JNU · Photoexcited structure of the plant photoreceptor domain, phy3 LOV2 · 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 Q9ZWQ6
- Elsewhere: RCSB PDB 1JNU · PDBe 1JNU · UniProt Q9ZWQ6
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