Computational protocol: Insights into the Conformational Variability and Regulation of Human Nek2 Kinase

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Protocol publication

[…] X-ray diffraction data were integrated using Mosflm and scaled using SCALA. The structure of Nek2-T175AATPγS was solved by PHASER using the Nek2-T175ASU model. Nek2ADP and Nek2-T175AApo were solved using Nek2ATPγS as the model. Structures were refined using Phenix and built using Coot. TLS refinement used a single group for Nek2-T175AATPγS and Nek2-T175AApo, and eight groups were defined using TLSMD for Nek2ADP. The final models comprised residues 3–131, 138–166, 171–191 and 193–271 (+ 8-residue tag) for Nek2ADP, residues 3–131 and 138–271 (+ 8-residue tag) for Nek2-T175AATPγS and residues 3–131, 139–164, 168–189 and 192–271 (+ 8-residue tag) for Nek2-T175AApo. Least-squares fitting used LSQKAB. Structure figures were produced using PyMOL (Warren L. DeLano, “The PyMOL Molecular Graphics System,” DeLano Scientific, San Carlos, CA, USA). An active Cdk2 model shown is 1QMZ; inactive, 1B39; and Aurora-A/TPX2, 1OL5. Crystal structures of Nek2-T175AATPγS, Nek2ADP and Nek2-T175AApo were used. […]

Pipeline specifications

Software tools iMosflm, CCP4, PHENIX, Coot, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens
Diseases Neoplasms
Chemicals Adenosine Diphosphate, Adenosine Triphosphate, Nucleotides