Research workbench
Application of the superfolder YFP bimolecular fluorescence complementation for studying protein-protein interactions in vitro
Analyse Application of the superfolder YFP bimolecular fluorescence complementation for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ED8
- Type
- protein
- Length
- 1,134 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yellow fluorescence protein
- Ligands
- CRO
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yellow fluorescence protein | protein | 228 | 10% helix, 51% strand | — |
| B | Yellow fluorescence protein | protein | 227 | 8% helix, 51% strand | — |
| C | Yellow fluorescence protein | protein | 230 | 9% helix, 51% strand | — |
| D | Yellow fluorescence protein | protein | 228 | 9% helix, 51% strand | — |
| E | Yellow fluorescence protein | protein | 221 | 7% helix, 49% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.97 | 25 | empty |
| 2 | 70 | 0.73 | 0.97 | 27 | CRO |
| 3 | 948 | 0.72 | 0.76 | 99 | empty |
| 4 | 53 | 0.71 | 0.98 | 20 | CRO |
| 5 | 90 | 0.69 | 0.94 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 722 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 173 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 165 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3ED8 · Application of the superfolder YFP bimolecular fluorescence complementation for studying… · 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
- Elsewhere: RCSB PDB 3ED8 · PDBe 3ED8
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