{"id":258,"date":"2024-03-02T11:30:51","date_gmt":"2024-03-02T11:30:51","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/pdb-entry-overview\/"},"modified":"2025-10-10T13:52:39","modified_gmt":"2025-10-10T13:52:39","slug":"pdb-entry-overview","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/pdb-entry-overview\/","title":{"rendered":"PDB entry overview"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">The <strong>Summary tab<\/strong> gives you a quick snapshot of the key information for a specific PDB entry. Here you\u2019ll find:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The <strong>source organism<\/strong> of the structure<\/li>\n\n\n\n<li>A link to the <strong>primary publication<\/strong><\/li>\n\n\n\n<li>A <strong>model quality summary<\/strong><\/li>\n\n\n\n<li>An <strong>interactive 3D viewer<\/strong> powered by Mol*<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Page Layout<\/strong><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">At the top of every entry page you\u2019ll see a row of tabs:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Model Quality<\/li>\n\n\n\n<li>Assembly<\/li>\n\n\n\n<li>Macromolecules<\/li>\n\n\n\n<li>Ligands and Environment<\/li>\n\n\n\n<li>Domains<\/li>\n\n\n\n<li>Text annotations<\/li>\n\n\n\n<li>Citations<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">You\u2019ll also find the <strong>Download Files<\/strong> menu, which lets you save the structure in several formats.<\/p>\n\n\n<div class=\"h5p-iframe-wrapper\"><iframe id=\"h5p-iframe-1\" class=\"h5p-iframe\" data-content-id=\"1\" style=\"height:1px\" src=\"about:blank\" frameBorder=\"0\" scrolling=\"no\" title=\"PDB entry overview\"><\/iframe><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">The Summary Accordion<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">The collapsible <strong>accordion<\/strong> to the right of the graphical viewer in the Summary tab <strong>(see below)<\/strong> highlights the most important features of the entry:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Preferred assembly<\/strong> (the biologically relevant form of the structure)<\/li>\n\n\n\n<li><strong>Number of macromolecules<\/strong> (proteins, nucleic acids, etc.)<\/li>\n\n\n\n<li><strong>Domains, ligands, and modifications<\/strong> present in the entry<br><\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Expanding each section provides more detail and links the feature directly to the Mol* viewer. For example, clicking on \u201cLigands\u201d will highlight the ligands in the 3D view. Clicking on one ligand will highlight and then focus the viewer on it. In this way, you can explore the entry in 3D.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<!DOCTYPE html>\n<html lang=\"en\">\n<head>\n<style>\n.image-grid-container {\n  display: grid;\n  \/* Creates 2 columns of equal width *\/\n  grid-template-columns: 1fr 1fr; \n  \/* Adds a 10px gap between the images, you can change this value *\/\n  gap: 10px; \n  \/* Adds some space between the grid and the caption below it *\/\n  margin-bottom: 1em; \n}\n\n.image-grid-container img {\n  \/* Ensures the image fills its grid cell without distortion *\/\n  width: 100%; \n  height: auto;\n  \/* Removes any extra space below the image if it's treated as inline *\/\n  display: block; \n}\n\n    <\/style>\n<\/head>\n<figure class=\"wp-block-image\">\n    <div class=\"image-grid-container\">\n        <img loading=\"lazy\" decoding=\"async\" width=\"765\" height=\"467\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.22.42.png\" alt=\"PDB entry summary tab\" class=\"wp-image-1529\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.22.42.png 765w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.22.42-300x183.png 300w\" sizes=\"auto, (max-width: 765px) 100vw, 765px\" \/>\n        <img loading=\"lazy\" decoding=\"async\" width=\"767\" height=\"487\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.23.43.png\" alt=\"PDB entry model quality tab\" class=\"wp-image-1531\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.23.43.png 767w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.23.43-300x190.png 300w\" sizes=\"auto, (max-width: 767px) 100vw, 767px\" \/>\n        <img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"494\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.19.png\" alt=\"PDB entry macromolecules tab\" class=\"wp-image-1533\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.19.png 768w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.19-300x193.png 300w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/>\n        <img loading=\"lazy\" decoding=\"async\" width=\"766\" height=\"459\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.54.png\" alt=\"PDB entry ligands and environments tab\" class=\"wp-image-1535\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.54.png 766w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.24.54-300x180.png 300w\" sizes=\"auto, (max-width: 766px) 100vw, 766px\" \/>\n    <\/div>\n\n    <figcaption style=\"text-align: center; color: #54585a; margin-top: 0px; margin-left:20px; margin-right:20px; font-size: 16px; margin-block-start: 0.5em !important; margin-block-end: 1.5em !important;\">Interactive exploration of the nucleosome core particle structure (PDB ID: <a href=\"http:\/\/pdbe.org\/4KGC\" target=\"_blank\">4KGC<\/a>) using the Mol viewer. This composite image demonstrates the functionality of the expandable selection menus for detailed structural analysis. <b>(Top left)<\/b> The complete nucleosome complex is shown. <b>(Top right)<\/b> The &#8220;Macromolecules&#8221; menu is expanded, and Histone H3.2 is selected, highlighting the corresponding in the structural view. <b>(Bottom left)<\/b> The &#8220;Ligands&#8221; menu is used to select and zoom in on the ruthenium-containing compound (HRU), shown in a stick representation at its binding site. <b>(Bottom right)<\/b> The &#8220;Domains&#8221; menu is expanded to select a specific CATH domain, which is then highlighted in the viewer (orange).<\/figcaption>\n<\/figure>\n<\/html>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>The 3D Viewer and Set Views<\/strong><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">In the centre of the page is the <strong>Mol*<\/strong> 3D viewer. Here, you can:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Switch between pre-set views<\/strong> (e.g. whole assembly, ligand binding site, or specific domain) via the accordion panel<\/li>\n\n\n\n<li><strong>Manually explore the structure<\/strong> by zooming, rotating, or changing display styles<\/li>\n\n\n\n<li><strong>Using the toggle menu:&nbsp;<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>Take a snapshot<\/strong> of the current view<\/li>\n\n\n\n<li><strong>Expand to full screen<\/strong> for detailed exploration<\/li>\n\n\n\n<li>P<strong>lay animations<\/strong> (e.g. rotating the structure automatically)<br><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">For a deeper dive into Mol* functionality, see the Mol* course\/tutorial. <a href=\"https:\/\/molstar.org\/viewer-docs\/\">https:\/\/molstar.org\/viewer-docs\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Summary tab gives you a quick snapshot of the key information for a specific PDB entry. Here you\u2019ll find: Page Layout At the top of every entry page you\u2019ll see a row of tabs: You\u2019ll also find the Download Files menu, which lets you save the structure in several formats. The Summary Accordion The&#8230;<\/p>\n","protected":false},"author":187,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-258","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages\/258","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/users\/187"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/comments?post=258"}],"version-history":[{"count":12,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages\/258\/revisions"}],"predecessor-version":[{"id":1835,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages\/258\/revisions\/1835"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/media?parent=258"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}