Research workbench
Xfel structure of the on state of a reversibly photoswitching fluorescent protein determined using the droplet injection method
Analyse Xfel structure of the on state of a reversibly photoswitching fluorescent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OQE
- Type
- protein
- Length
- 216 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green to red photoconvertible GFP-like protein eosfp
- UniProt
- Q5S6Z9
- Ligands
- VYA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green to red photoconvertible GFP-like protein eosfp | protein | 216 | 6% helix, 58% strand | Q5S6Z9 |
Ligands and binding sites
- VYA · 2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.76 | 0.97 | 27 | VYA |
| 2 | 72 | 0.41 | 0.79 | 20 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5OQE · XFEL structure of the on state of a reversibly photoswitching fluorescent protein… · the same entry in another collection · 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 Q5S6Z9
- Elsewhere: RCSB PDB 5OQE · PDBe 5OQE · UniProt Q5S6Z9
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