Research workbench
Crystal structure analysis of a redox-sensitive green fluorescent protein variant in a reduced form
Analyse Crystal structure analysis of a redox-sensitive green fluorescent protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JC0
- Type
- protein
- Length
- 675 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green fluorescent protein | protein | 225 | 10% helix, 52% strand | P42212 |
| C | Green fluorescent protein | protein | 225 | 10% helix, 50% 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 · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.79 | 0.97 | 31 | CRO |
| 2 | 102 | 0.78 | 0.98 | 25 | CRO |
| 3 | 100 | 0.77 | 0.97 | 26 | CRO |
| 4 | 170 | 0.60 | 0.83 | 33 | empty |
| 5 | 242 | 0.46 | 0.73 | 39 | empty |
Interfaces
3 interfaces between chains.
- B–C · 634 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 82 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 cofactor (chromophore).
Compared structures
- 1JC0 · Crystal structure analysis of a redox-sensitive green fluorescent protein variant in a… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 1JC0 · PDBe 1JC0 · UniProt P42212
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