Research workbench
Crystal structure of split GFP complexed with engineered sfcherry with an insertion of GFP fragment
Analyse Crystal structure of split GFP complexed with engineered sfcherry with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KF5
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein GFP1-9; Fluorescent protein SFCHERRY+GFP10-11
- Ligands
- CRO, CH6
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fluorescent protein GFP1-9 | protein | 189 | 11% helix, 50% strand | — |
| C, D | Fluorescent protein SFCHERRY+GFP10-11 | protein | 257 | 4% helix, 57% 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 · 2 copies · chains A, C, B, D
- CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.79 | 0.98 | 27 | CRO |
| 2 | 108 | 0.79 | 0.98 | 26 | CRO |
| 3 | 101 | 0.78 | 0.98 | 28 | CH6 |
| 4 | 87 | 0.75 | 0.97 | 27 | CH6 |
| 5 | 244 | 0.52 | 0.75 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1865 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1800 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 348 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4KF5 · Crystal Structure of Split GFP complexed with engineered sfCherry with an insertion of… · 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 4KF5 · PDBe 4KF5
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