{"id":2707,"date":"2021-03-27T13:11:29","date_gmt":"2021-03-27T20:11:29","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/psquared\/?page_id=2707"},"modified":"2021-03-27T16:57:16","modified_gmt":"2021-03-27T23:57:16","slug":"zero-in-on-a-pdb-structure","status":"publish","type":"page","link":"https:\/\/blogs.oregonstate.edu\/psquared\/zero-in-on-a-pdb-structure\/","title":{"rendered":"Zero in on a PDB structure"},"content":{"rendered":"<h2>Lots of proteins to choose from!<\/h2>\n<p>Let&#8217;s look up one of the\u00a0enzyme molecules that many people are interested in these days, \u00a0HMG CoA reductase. \u00a0This is the enzyme that is inhibited by the statin drugs, the drugs that block cholesterol synthesis. \u00a0One of the most informative examples of the structure of HMG CoA reductase is listed under the code name <a href=\"http:\/\/www.rcsb.org\/pdb\/explore\/explore.do?structureId=1hwk\">1hwk<\/a> in the PDB. \u00a0How did I discover this enzyme molecule in the PDB? \u00a0I used the dynamic duo of online resources that every protein artist will use often:<\/p>\n<ul>\n<li>Good ol&#8217; Wikipedia (I looked up the term &#8220;<a href=\"http:\/\/en.wikipedia.org\/wiki\/Statin\">statin drug<\/a>&#8221; and discovered an image of HMG CoA reductase which referred to the codename\u00a01hwk), and then I used the amazing &#8230;<\/li>\n<li>Protein Data Bank (I searched for &#8220;1hwk&#8221;, or I could haves searched directly for &#8220;HMG CoA reductase&#8221;).<\/li>\n<\/ul>\n<div id=\"attachment_1736\" style=\"width: 411px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.rcsb.org\/pdb\/explore\/images.do?structureId=1HWK\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1736\" class=\"wp-image-1736\" src=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2015\/04\/1HWK_bio_r_250.jpg\" alt=\"1HWK_bio_r_250\" width=\"401\" height=\"401\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2015\/04\/1HWK_bio_r_250.jpg 250w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2015\/04\/1HWK_bio_r_250-150x150.jpg 150w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2015\/04\/1HWK_bio_r_250-120x120.jpg 120w\" sizes=\"auto, (max-width: 401px) 100vw, 401px\" \/><\/a><p id=\"caption-attachment-1736\" class=\"wp-caption-text\">HMG CoA reductase 1HWK, shown as a ribbon depicting the polypeptide chains.<\/p><\/div>\n<p>Once you arrive at the PDB entry for 1hwk, you can use sidebar commands to view the structure in 3D. \u00a0You can change the appearance of the molecule. \u00a0Change from view the proteins chains as ribbons to viewing space filling versions with every atom depicted by color schemes of your choice. \u00a0There are a few varieties of 3D viewers to choose among. \u00a0A lot depend on which platform and operating system you are using, be it a phone, laptop or console computer. \u00a0Invest some time to explore.<\/p>\n<div id=\"attachment_2706\" style=\"width: 274px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2706\" class=\" wp-image-2706\" src=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-ball-and-stick-by-chain-coloration.png\" alt=\"\" width=\"264\" height=\"350\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-ball-and-stick-by-chain-coloration.png 910w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-ball-and-stick-by-chain-coloration-226x300.png 226w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-ball-and-stick-by-chain-coloration-773x1024.png 773w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-ball-and-stick-by-chain-coloration-768x1018.png 768w\" sizes=\"auto, (max-width: 264px) 100vw, 264px\" \/><p id=\"caption-attachment-2706\" class=\"wp-caption-text\">HMG CoA reductase. PDB ID 1HWK. Rotated about the long axis; color coded to show the several chains that are assembled together to make the complete molecule.<\/p><\/div>\n<div id=\"attachment_2705\" style=\"width: 307px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2705\" class=\"wp-image-2705 \" src=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-space-filling-839x1024.png\" alt=\"\" width=\"297\" height=\"363\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-space-filling-839x1024.png 839w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-space-filling-246x300.png 246w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-space-filling-768x937.png 768w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2021\/03\/HMG-CoA-reductase-space-filling.png 918w\" sizes=\"auto, (max-width: 297px) 100vw, 297px\" \/><p id=\"caption-attachment-2705\" class=\"wp-caption-text\">HMG CoA reductase. PDB ID 1HWK. Ball-and-stick model of the atoms, color-coded to highlight in yellow the relatively uncommon sulfur atoms.<\/p><\/div>\n<h2><\/h2>\n","protected":false},"excerpt":{"rendered":"<p>Lots of proteins to choose from! Let&#8217;s look up one of the\u00a0enzyme molecules that many people are interested in these days, \u00a0HMG CoA reductase. \u00a0This is the enzyme that is inhibited by the statin drugs, the drugs that block cholesterol &hellip; <a href=\"https:\/\/blogs.oregonstate.edu\/psquared\/zero-in-on-a-pdb-structure\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":196,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2707","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2707","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/users\/196"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/comments?post=2707"}],"version-history":[{"count":2,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2707\/revisions"}],"predecessor-version":[{"id":2743,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2707\/revisions\/2743"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/media?parent=2707"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}