MolNFT v1 · #123920 · protein
The structure of ultra stable green fluorescent protein
5JZK: “The structure of ultra stable green fluorescent protein”. X-ray diffraction, 3 ligands (CRO, NO3, CL), 5 pockets (best druggability 0.76). MolNFT v1 #123920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JZK
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- CRO, NO3, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 235 | 14% helix, 50% strand | A0A059PIQ0 |
| B | Green fluorescent protein | protein | 233 | 13% helix, 50% strand | A0A059PIQ0 |
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
- NO3 · Nitrate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
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 | 74 | 0.76 | 0.99 | 22 | CRO |
| 2 | 69 | 0.74 | 0.98 | 22 | CRO |
| 3 | 379 | 0.63 | 0.78 | 65 | empty |
| 4 | 101 | 0.39 | 0.76 | 22 | empty |
| 5 | 89 | 0.31 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 5JZK · The Structure of Ultra Stable Green Fluorescent Protein · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A059PIQ0
- Elsewhere: RCSB PDB 5JZK · PDBe 5JZK · UniProt A0A059PIQ0
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