Computational protocol: Mechanism of Allosteric Activation of SAMHD1 by dGTP

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Protocol publication

[…] The structures were solved by molecular replacement using the previously published coordinates of SAMHD1c1 (PDB ID 3U1N) as a search model. The program PHASER was used for the molecular replacement search. Four molecules were identified in an asymmetric unit of the crystal. The initial model was auto-built by Buccaneer and refined by iterative rounds of TLS and non-crystallographic symmetry (NCS)-restrained refinement using Refmac5, followed by rebuilding manually using Coot. The high-resolution SAMHD1c2-RN structure was used as a reference model during the refinement of the wild type structure. Refinement statistics are summarized in . The final models were validated by MolProbity. The Φ, Ψ angels of 98.6% of residues of the RN structure and 98.8% of the wild type structure lie within favored regions of Ramachandran plot while those of all residues lie in the allowed regions. […]

Pipeline specifications

Software tools Buccaneer, REFMAC5, Coot, MolProbity
Application Protein structure analysis
Organisms Homo sapiens, Human immunodeficiency virus 2
Diseases Aicardi Syndrome