Research workbench
Structure of a blue-light photoreceptor
Analyse Structure of a 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
- 4GCZ
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue-light photoreceptor, sensor protein fixl
- UniProt
- O34627, P23222
- Ligands
- FMN, ADP, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light photoreceptor, sensor protein fixl | protein | 366 | 46% helix, 23% strand | O34627, P23222 |
| B | Blue-light photoreceptor, sensor protein fixl | protein | 378 | 45% helix, 24% strand | O34627, P23222 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.76 | 0.82 | 72 | ADP, SO4 |
| 2 | 185 | 0.68 | 0.87 | 25 | FMN, SO4 |
| 3 | 189 | 0.68 | 0.86 | 25 | FMN |
| 4 | 173 | 0.53 | 0.79 | 27 | empty |
| 5 | 298 | 0.50 | 0.73 | 33 | SO4 |
Interfaces
1 interface between chains.
- A–B · 4702 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4GCZ · Structure of a blue-light photoreceptor · the same entry in another collection · chain A against A, TM-score 1.00
- P23222 · AlphaFold monomer V2.0 prediction for sensor protein fixl (P23222) · a predicted model of the same protein · chain B against A, TM-score 0.61
- O34627 · AlphaFold monomer V2.0 prediction for blue-light photoreceptor (O34627) · a predicted model of the same protein · chain B against A, TM-score 0.41
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
- Every structure of UniProt P23222
- Elsewhere: RCSB PDB 4GCZ · PDBe 4GCZ · UniProt O34627 · UniProt P23222
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