Research workbench
Crystal structure analysis of a rate-enhanced variant of redox- sensitive green fluorescent protein in the reduced form, ROGFP1-R8.
Analyse Crystal structure analysis of a rate-enhanced variant of redox- sensitive green… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AHA
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- GYS, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green fluorescent protein | protein | 225 | 9% helix, 52% strand | P42212 |
Ligands and binding sites
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.79 | 0.98 | 26 | GYS |
| 2 | 127 | 0.79 | 0.97 | 29 | GYS |
| 3 | 57 | 0.72 | 0.99 | 17 | empty |
| 4 | 126 | 0.39 | 0.74 | 23 | empty |
| 5 | 71 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 2AHA · Crystal structure analysis of a rate-enhanced variant of redox-sensitive green… · 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 B 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 2AHA · PDBe 2AHA · UniProt P42212
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.