Research workbench
Crystal structure of green fluorescent protein (GFP); S65T, H148D; circular permutant ( 50-51)
Analyse Crystal structure of green fluorescent protein (GFP); S65T, H148D; circular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZF3
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 216 | 10% helix, 53% strand | P42212 |
| B | Green fluorescent protein | protein | 214 | 8% helix, 54% strand | P42212 |
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, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.98 | 24 | CRO |
| 2 | 93 | 0.76 | 0.97 | 24 | CRO |
| 3 | 209 | 0.51 | 0.77 | 28 | empty |
| 4 | 221 | 0.49 | 0.75 | 34 | empty |
| 5 | 72 | 0.36 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 797 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4ZF3 · Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D; circular permutant (… · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P42212
- Elsewhere: RCSB PDB 4ZF3 · PDBe 4ZF3 · UniProt P42212
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