MolNFT v1 · #117099 · protein
Enhanced superfolder GFP with dbco at 148
5DY6 · Green fluorescent protein: “Enhanced superfolder GFP with dbco at 148”. X-ray diffraction, 2 ligands (CRO, SO4), 4 pockets (best druggability 0.80). MolNFT v1 #117099 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DY6
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- CRO, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 225 | 9% helix, 52% strand | A0A059PIQ0 |
| B | Green fluorescent protein | protein | 224 | 9% helix, 52% 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
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.97 | 30 | CRO |
| 2 | 120 | 0.77 | 0.96 | 27 | CRO |
| 3 | 104 | 0.37 | 0.74 | 16 | empty |
| 4 | 66 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 modified (chromophore, nonstandard).
Compared structures
- 5DY6 · Enhanced superfolder GFP with DBCO at 148 · 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 5DY6 · PDBe 5DY6 · UniProt A0A059PIQ0
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