File:Response-of-a-simian-immunodeficiency-virus-(SIVmac251)-to-raltegravir-a-basis-for-a-new-treatment-1742-4690-7-21-S1.ogv

English: Structural alignment of the integrase catalytic core domains (IN CCDs) HIV-1 subtype B (PDB: 1BL3) and SIVmac251 (PDB: 1C6V). The alignment was conducted on structures deposited in the NCBI database using the VAST algorithm embedded in the website. The structures were then visualised using Cn 3D v. 4.1 (available freely from NCBI). The video was created using SnagIt (TechSmith Corporation Okemos, MI). The HIV-1 and SIVmac251 CCDs are shown in violet and blue, respectively. The active site is shown by the highly conserved catalytic residues D64, D116 and E152 (presented in yellow) and by the Mg2+ ion coordinated by D64 and D116 in the 1BL3 structure. The flexible loop (residues 140-151) is not present in the alignment, due to its variable conformation that may not correspond to that adopted in vivo when the IN CCD is complexed with proviral DNA. The corresponding sequence alignment is shown in Fig. 5.