MolNFT v1 · #48369 · protein
Structural basis for light-dependent signaling in the dimeric lov photosensor ytva (dark structure)
2PR5 · Blue-light photoreceptor: “Structural basis for light-dependent signaling in the dimeric lov photosensor ytva (dark structure)”. X-ray diffraction, 2 ligands (FMN, NA), 3 pockets (best druggability 0.69). MolNFT v1 #48369 on…
- PDB
- 2PR5
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue-light photoreceptor
- UniProt
- O34627
- Ligands
- FMN, NA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light photoreceptor | protein | 127 | 37% helix, 31% strand | O34627 |
| B | Blue-light photoreceptor | protein | 126 | 37% helix, 32% strand | O34627 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.69 | 0.88 | 24 | FMN |
| 2 | 440 | 0.68 | 0.80 | 53 | ACY |
| 3 | 169 | 0.67 | 0.87 | 23 | FMN |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2PR5 · Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark… · the same entry in another collection · chain A against A, TM-score 1.00
- O34627 · AlphaFold monomer V2.0 prediction for blue-light photoreceptor (O34627) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O34627
- Elsewhere: RCSB PDB 2PR5 · PDBe 2PR5 · UniProt O34627
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