MolNFT v1 · #112231 · protein
Crystal structure of green fluorescent protein (GFP); S65T, Y66(CL2Y), H148D; circular permutant ( 50-51)
4ZF5: “Crystal structure of green fluorescent protein (GFP); S65T, Y66(CL2Y), H148D; circular permutant ( 50-51)”. X-ray diffraction, 1 ligand (4NU), 8 pockets (best druggability 0.77). MolNFT v1 #112231 on GenesisL1: 3D structure, binding…
- PDB
- 4ZF5
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- 4NU
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 224 | 10% helix, 54% strand | P42212 |
| B | Green fluorescent protein | protein | 216 | 10% helix, 55% strand | P42212 |
Ligands and binding sites
- 4NU · {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-dichloro-4-oxocyclohexa-2,5-dien-1-yl)methylidene]-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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.77 | 0.97 | 27 | 4NU |
| 2 | 106 | 0.77 | 0.97 | 25 | 4NU |
| 3 | 82 | 0.58 | 0.88 | 21 | empty |
| 4 | 291 | 0.56 | 0.76 | 30 | empty |
| 5 | 262 | 0.53 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4ZF5 · Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(Cl2Y), 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 0.78
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 4ZF5 · PDBe 4ZF5 · UniProt P42212
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