Computational protocol: Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure

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Protocol publication

[…] The diffraction images were processed with HKL2000 []. The initial structures were determined by difference Fourier methods with the ligand-omitted structure of the human FPPS-YS0470 binary complex [PDB: 4DEM] as an input model. These structures were further improved through iterative rounds of manual and automated refinement with COOT [], PHENIX [], and REFMAC5 []. The final models of the ternary complexes have been deposited into the Protein Data Bank. Data collection and refinement statistics, as well as the PDB ID for each structure, is presented in Table . [...] Structure analysis and model representation were performed with the molecular modeling and visualization programs COOT [] and PyMOL (version 1.3 Schrödinger, LLC.). Information on the structure models used in this analysis, including the PDB IDs and bound ligands, is summarized in Table . […]

Pipeline specifications

Software tools Coot, PHENIX, REFMAC5, PyMOL
Application Protein structure analysis
Organisms Homo sapiens
Diseases Bone Diseases, Neoplasms