Research workbench
Crystal structure of wild type yellow fluorescent protein ZFP538 from zoanthus
Analyse Crystal structure of wild type yellow fluorescent protein ZFP538 from zoanthus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XAE
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein FP538
- UniProt
- Q9U6Y4
- Ligands
- CH7
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein FP538 | protein | 222 | 5% helix, 55% strand | Q9U6Y4 |
| B | Fluorescent protein FP538 | protein | 221 | 4% helix, 56% strand | Q9U6Y4 |
Ligands and binding sites
- CH7 · [(4Z)-4-(4-hydroxybenzylidene)-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.77 | 0.97 | 26 | CH7 |
| 2 | 108 | 0.76 | 0.96 | 29 | CH7 |
| 3 | 500 | 0.65 | 0.77 | 64 | empty |
Interfaces
1 interface between chains.
- A–B · 673 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent (oxidation, additive adduct, covalent ligand, nonstandard).
Compared structures
- 1XAE · Crystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y4 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein FP538 (Q9U6Y4) · 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 Q9U6Y4
- Elsewhere: RCSB PDB 1XAE · PDBe 1XAE · UniProt Q9U6Y4
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