MolNFT v1 · #161966 · protein
Ghk tagged GFP variant
6QUJ · Green fluorescent protein: “Ghk tagged GFP variant”. X-ray diffraction, 3 ligands (CRO, CU, SO4), 6 pockets (best druggability 0.74). MolNFT v1 #161966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QUJ
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO, CU, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Green fluorescent protein | protein | 228 | 13% helix, 51% 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, D
- CU · Copper (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- GOL · Glycerol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.74 | 0.97 | 24 | CRO |
| 2 | 70 | 0.73 | 0.97 | 21 | CRO |
| 3 | 75 | 0.46 | 0.82 | 13 | empty |
| 4 | 124 | 0.46 | 0.78 | 21 | empty |
| 5 | 103 | 0.46 | 0.80 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–D · 728 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6QUJ · PDBe 6QUJ · UniProt P42212
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