MolNFT v1 · #112230 · protein
Crystal structure of green fluorescent protein (GFP); S65T, Y66(CL1Y), H148D; circular permutant (50-51)
4ZF4: “Crystal structure of green fluorescent protein (GFP); S65T, Y66(CL1Y), H148D; circular permutant (50-51)”. X-ray diffraction, 1 ligand (4NT), 4 pockets (best druggability 0.76). MolNFT v1 #112230 on GenesisL1: 3D structure, binding…
- PDB
- 4ZF4
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- 4NT
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
| B | Green fluorescent protein | protein | 223 | 9% helix, 52% strand | P42212 |
Ligands and binding sites
- 4NT · [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(3-chloro-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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.76 | 0.97 | 23 | 4NT |
| 2 | 82 | 0.75 | 0.97 | 23 | 4NT |
| 3 | 641 | 0.66 | 0.76 | 92 | empty |
| 4 | 67 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4ZF4 · Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(Cl1Y), H148D; circular… · 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 B against A, TM-score 0.79
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 4ZF4 · PDBe 4ZF4 · UniProt P42212
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