Research workbench
Crystal structure of a monomeric cyan fluorescent protein in the photobleached state
Analyse Crystal structure of a monomeric cyan fluorescent protein in the photobleached… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OTE
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like fluorescent chromoprotein CFP484
- UniProt
- Q9U6Y3
- Ligands
- PIA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GFP-like fluorescent chromoprotein CFP484 | protein | 213 | 4% helix, 58% strand | Q9U6Y3 |
Ligands and binding sites
- PIA · [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.72 | 0.99 | 24 | PIA |
| 2 | 57 | 0.71 | 0.99 | 19 | PIA |
| 3 | 177 | 0.48 | 0.76 | 34 | empty |
| 4 | 146 | 0.45 | 0.76 | 28 | ACT |
Interfaces
1 interface between chains.
- A–B · 711 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2OTE · Crystal structure of a monomeric cyan fluorescent protein in the photobleached state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y3 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein CFP484 (Q9U6Y3) · 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 Q9U6Y3
- Elsewhere: RCSB PDB 2OTE · PDBe 2OTE · UniProt Q9U6Y3
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