Research workbench
Ghk tagged GFP variant at 17KEV
Analyse Ghk tagged GFP variant at 17KEV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QUI
- 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
- 5 · best druggability 0.75
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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.75 | 0.97 | 26 | CRO |
| 2 | 81 | 0.74 | 0.97 | 27 | CRO |
| 3 | 177 | 0.50 | 0.78 | 35 | empty |
| 4 | 115 | 0.46 | 0.79 | 20 | SO4 |
| 5 | 153 | 0.39 | 0.73 | 29 | empty |
Interfaces
1 interface between chains.
- A–D · 820 Ų buried · 16 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 6QUI · PDBe 6QUI · UniProt P42212
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