Research workbench
Different photochemical events of a genetically encoded aryl azide define and modulate GFP fluorescence
Analyse Different photochemical events of a genetically encoded aryl azide define and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J89
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CQ2, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 228 | 11% helix, 51% strand | P42212 |
| B | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
Ligands and binding sites
- CQ2 · {(4Z)-4-(4-aminobenzylidene)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 30 | CQ2 |
| 2 | 110 | 0.77 | 0.96 | 25 | CQ2 |
| 3 | 153 | 0.45 | 0.76 | 28 | TRS, SO4 |
| 4 | 130 | 0.41 | 0.75 | 23 | EDO |
| 5 | 53 | 0.31 | 0.77 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 890 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4J89 · Different photochemical events of a genetically encoded aryl azide define and modulate… · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P42212
- Elsewhere: RCSB PDB 4J89 · PDBe 4J89 · UniProt P42212
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.