Research workbench
Crystal structure of the light-state dimer of fungal blue-light photoreceptor vivid
Analyse Crystal structure of the light-state dimer of fungal 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
- 3RH8
- Type
- protein
- Length
- 296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vivid pas protein vvd
- UniProt
- Q9C3Y6
- Ligands
- FAD
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Vivid pas protein vvd | protein | 148 | 25% helix, 24% strand | Q9C3Y6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.69 | 0.86 | 34 | FAD |
| 2 | 229 | 0.69 | 0.86 | 30 | FAD |
| 3 | 157 | 0.45 | 0.75 | 39 | empty |
| 4 | 84 | 0.34 | 0.75 | 22 | empty |
| 5 | 69 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- B–D · 1415 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3RH8 · Crystal Structure of the Light-state Dimer of Fungal Blue-Light Photoreceptor Vivid · the same entry in another collection · chain B against B, 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 Q9C3Y6
- Elsewhere: RCSB PDB 3RH8 · PDBe 3RH8 · UniProt Q9C3Y6
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