2.1 | Homology modeling of rice AGPase sub-unitsĀ
The amino acid sequences of OsAGPase-L1 (OsL1; XP_015640472/
Os05g0580000 LOC_Os05g50380) and OsAGPase-S1 (OsS1; XP_015612224/
LOC_Os09g12660/ Os09g0298200) were retrieved from NCBI-protein
database. Using MODELLER 9.17,28 we generated
three-dimensional models of the domain regions of OsL1 and OsS1. These
models were created by employing the crystal structure of the potato
AGPase SS (1YP3)29 as a template. In total, fifty 3D
models were generated, and the representative models for each subunit
were selected based on the lowest DOPE score. The random loop regions
were subsequently remodeled using GalaxyLoop,30 and
final refinement of the models was carried out using the GalaxyRefine
server.31 Following the model refinement, the
stereochemical properties and overall quality of the OsAGPase-L1 and
OsS1 models were evaluated using PROCHECK,32ProSA,33 ProQ,34 and
Verify3D.35