Research workbench
Structure of SFYFP66BPA
Analyse Structure of SFYFP66BPA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YR3
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yellow fluorescent protein
- UniProt
- A0A059PIR9
- Ligands
- BF6
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yellow fluorescent protein | protein | 224 | 9% helix, 52% strand | A0A059PIR9 |
Ligands and binding sites
- BF6 · [(4Z)-2-(aminomethyl)-4-{[4-(benzenecarbonyl) phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic 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 | 109 | 0.72 | 0.93 | 28 | BF6 |
| 2 | 60 | 0.39 | 0.80 | 14 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5YR3 · Structure of sfYFP66BPA · 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 A0A059PIR9
- Elsewhere: RCSB PDB 5YR3 · PDBe 5YR3 · UniProt A0A059PIR9
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