{"id":256,"date":"2024-03-02T11:30:33","date_gmt":"2024-03-02T11:30:33","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/how-is-the-information-structured\/"},"modified":"2025-10-10T13:53:52","modified_gmt":"2025-10-10T13:53:52","slug":"how-is-the-information-structured","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/how-is-the-information-structured\/","title":{"rendered":"How is the information structured?"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">On PDBe webpages, information from a PDB entry is divided into different sections to make the data easier for you to browse (<strong>see below<\/strong>).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The image below shows you a snapshot of an individual PDB entry page, with the differnt sections separated into tabs named Model Quality, Assemblies, Macromolecules, Ligand and Envirnments, Domains, Text Annotations (AI) and Citations.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Not all entries contain information for all sections &#8211; if there is no data for a section a red N\/A will be shown on the tab title (as shown below).&nbsp;<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The scientists who generated this data gave the PDB entry (ID: <a href=\"https:\/\/www.ebi.ac.uk\/pdbe\/entry\/pdb\/4kgc\" target=\"_blank\" rel=\"noreferrer noopener\">4kgc<\/a>) the title:<br><strong>Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">DNA in eukaryotes, such as humans, is wrapped around protein units and this is known as a <a href=\"https:\/\/en.wikipedia.org\/wiki\/Nucleosome\" target=\"_blank\" rel=\"noreferrer noopener\">nucleosome<\/a>. This PDB entry is one of many examples of nucleosome structures in the PDB database.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">We will now go through each of these tabs in more detail.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<figure class=\"wp-block-image size-large\">\n\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-content\/uploads\/sites\/112\/2025\/10\/Screenshot-2025-10-02-at-10.13.19-1024x472.png\" alt=\"\" width=\"850\" height=\"550\">\n\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;\">A central feature of the PDB web interface is the top navigation bar, which provides access to various categories of information about the structural entry. These tabs include: Summary, providing a general overview; Model Quality, for assessing the crystallographic data and model fit; Complexes, Macromolecules, Ligands and Environments, and Domains, for detailed information on the different components of the structure; and Text Annotations (AI) and Citations for further contextual and bibliographic details. This tab-based system allows researchers to efficiently navigate and retrieve specific data related to the protein structure.<\/figcaption>\n\n<\/figure>\n","protected":false},"excerpt":{"rendered":"<p>On PDBe webpages, information from a PDB entry is divided into different sections to make the data easier for you to browse (see below). The image below shows you a snapshot of an individual PDB entry page, with the differnt sections separated into tabs named Model Quality, Assemblies, Macromolecules, Ligand and Envirnments, Domains, Text Annotations&#8230;<\/p>\n","protected":false},"author":187,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-256","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\/256","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=256"}],"version-history":[{"count":23,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages\/256\/revisions"}],"predecessor-version":[{"id":1837,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/pages\/256\/revisions\/1837"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/exploring-pdb-entry\/wp-json\/wp\/v2\/media?parent=256"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}