MolNFT v1 · #89278 · protein
Crystal structure of amphioxus green fluorescent protein, GFPA1
4DKN: “Crystal structure of amphioxus green fluorescent protein, GFPA1”. X-ray diffraction, 1 ligand (CR2), 5 pockets (best druggability 0.72). MolNFT v1 #89278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DKN
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amphioxus green fluorescent protein, GFPA1
- UniProt
- C3YKQ3
- Ligands
- CR2
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amphioxus green fluorescent protein, GFPA1 | protein | 209 | 7% helix, 59% strand | C3YKQ3 |
| B | Amphioxus green fluorescent protein, GFPA1 | protein | 214 | 8% helix, 57% strand | C3YKQ3 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 20 | CR2 |
| 2 | 55 | 0.71 | 0.98 | 23 | CR2 |
| 3 | 113 | 0.46 | 0.79 | 19 | empty |
| 4 | 106 | 0.42 | 0.77 | 21 | empty |
| 5 | 69 | 0.40 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4DKN · Crystal structure of amphioxus green fluorescent protein, GFPA1 · 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 C3YKQ3
- Elsewhere: RCSB PDB 4DKN · PDBe 4DKN · UniProt C3YKQ3
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