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- What information does a PDB entry contain?
- How is the information structured?
- PDB entry overview
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- Is the protein an enzyme?
- What specific biological processes are associated with the proteins?
- Which sequence family does the protein belong to?
- What protein signatures can be found in the structure?
- What are the structural folds/domains present in the proteins from this entry?
- The SCOP classification of protein folds
- Structure analysis
- Detailed structure analysis
- How can I interactively explore the protein and DNA molecules present in the entry?
- Which amino acids from the protein chain participate in binding interactions with ligands?
- What is the build quality of the protein chain?
- What are the signature domains/folds – Pfam
- What are the signature domains/folds – CATH
- What are the signature domains/folds – SCOP
- What are the probable quaternary structures and biological assemblies?
- Unravelling the symmetry of a virus capsid using assembly information
- Ligands and Environments
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Summary
- A typical PDB entry contains 3D coordinates of the macromolecular structures that are experimentally derived using X-ray/NMR/electron microscopy
- It also contains information about secondary structure, biological assemblies, sequence mapping information (UniProt for protein and GenBank for RNA) for the proteins and nucleic acids that are present in the entry
- The PDB entry can be further explored for binding environment of ligands and other small molecules
- The information from a PDB entry is structured into five major sections on the PDBe website to make the data easier to browse
- Every PDB entry page comes with a portfolio of images – displaying the contents of the entry from various structural, functional and chemical perspectives
- The citation page not only provides information about primary and associated publications related to the entry, it also displays figures and figure legends for open access publications
- The ‘Structure analysis’ section enables you to interactively explore proteins in 1D/2D/3D layout
- The ‘Ligands and Environments’ section lists all the chemically distinct ligands that are present in a particular PDB entry and shows their binding sites
- There are several different download options and file formats present from a PDB entry page
- In addition to the PDB archive files, every entry page provides download options for biological assembly files (which can be instantly viewed using any visualisation tool like Chimera, pymol etc.), sequence files and SIFTS information