Research workbench
The oxidized state of a redox sensitive variant of green fluorescent protein
Analyse The oxidized state of a redox sensitive variant of 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
- 1H6R
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- PIA, CL
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Green fluorescent protein | protein | 227 | 11% helix, 52% strand | P42212 |
Ligands and binding sites
- PIA · [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.99 | 20 | PIA |
| 2 | 58 | 0.71 | 0.98 | 21 | PIA |
| 3 | 56 | 0.70 | 0.97 | 20 | PIA |
| 4 | 228 | 0.64 | 0.83 | 33 | empty |
| 5 | 155 | 0.59 | 0.83 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 846 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 772 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 1H6R · The oxidized state of a redox sensitive variant of green fluorescent protein · 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 1H6R · PDBe 1H6R · UniProt P42212
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