Research workbench
Dark-state structure of sfgfp containing the unnatural amino acid P- azido-phenylalanine at residue 66
Analyse Dark-state structure of sfgfp containing the unnatural amino acid P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J88
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CQ1, 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 | 227 | 11% helix, 52% strand | P42212 |
| B | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
Ligands and binding sites
- CQ1 · [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-azidobenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · 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 | 110 | 0.77 | 0.97 | 25 | CQ1 |
| 2 | 84 | 0.76 | 0.98 | 26 | CQ1 |
| 3 | 94 | 0.40 | 0.77 | 22 | empty |
| 4 | 54 | 0.36 | 0.80 | 21 | EDO |
| 5 | 81 | 0.33 | 0.74 | 17 | EDO, SO4 |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4J88 · Dark-state structure of sfGFP containing the unnatural amino acid p-azido-phenylalanine… · 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 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 P42212
- Elsewhere: RCSB PDB 4J88 · PDBe 4J88 · UniProt P42212
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