MolNFT v1 · #138434 · protein
Crystal structure of the green fluorescent protein clover
5WJ2: “Crystal structure of the green fluorescent protein clover”. X-ray diffraction, 1 ligand (CR2), 5 pockets (best druggability 0.77). MolNFT v1 #138434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WJ2
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CR2
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 234 | 12% helix, 50% strand | P42212 |
| B | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.77 | 0.98 | 31 | CR2 |
| 2 | 92 | 0.76 | 0.97 | 27 | CR2 |
| 3 | 236 | 0.52 | 0.76 | 38 | empty |
| 4 | 175 | 0.51 | 0.78 | 38 | empty |
| 5 | 86 | 0.35 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
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 5WJ2 · PDBe 5WJ2 · UniProt P42212
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