A Structural View of Biology

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Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states.

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Celebrate 200 Molecule of the Month articles

September Molecule of the Month

RCSB PDB Molecule of the Month
Isoprene Synthase

Deposition Preparation Tools

Data Extraction

  • pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs
  • SF-Tool: Convert structure factor files among various formats

Small Molecules

  • Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands

Data Format Conversion

  • PDBML2CIF: Convert PDBML-format data into PDBx/mmCIF-format
  • PointSuite: Generate symmetry records for macromolecular assemblies with point and helical symmetries
  • MAXIT: Translate data between file formats and more

Explore the PDB Archive

Jsmol and Jmol

JSmol, the JavaScript version of Jmol offers several options for display and analysis. Launch the viewer from any entry's Structure Summary page or by entering an ID below.  The Jmol Applet remains available from the 3D View page, and will continue to work in most browsers.  Learn more about Jsmol/Jmol.

  • Hemoglobin
    Jmol Thumbnail for Hemoglobin 4HHB

    PDB ID: 4HHB

  • Streptavidin
    Jmol Thumbnail for Streptavidin 1STP

    PDB ID: 1STP

  • Purine Nucleoside Phosphorylase
    Jmol Thumbnail for Purine Nucleoside Phosphorylase 4EAR

    PDB ID: 4EAR

Sequence & Structure Alignment

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, Mammoth, TM-Align, TopMatch).

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments and detection of circular permutations.


Download: Coordinates & Experimental Data

Enter PDB IDs separated by comma or white space. Note: The Download Tool is launched as a stand-alone application using the Java Web Start protocol. More Download Help


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PDB-101 is an online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

Browse all PDB-101 resources by biological theme or start exploring:

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  • Geis Digital Archive

    View iconic illustrations by the gifted artist Irving Geis (1908-1997) in context with PDB structures and educational information.

Search by Unreleased & Access New Entries

The PDB archive is updated weekly in two phases

Phase I: Every Saturday by 3:00 UTC, for every new entry, wwPDB website provides sequence(s) (amino acid or nucleotide) for each distinct polymer and, where appropriate, the InChI string(s) for each distinct ligand and the crystallization pH value(s).

Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.

As of Tuesday Sep 20, 2016 at 5 PM PDT there are 122799 structures.

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Structural Biology Knowledgebase

Collection of Research Highlights

Collection of Research Highlights

The Structural Biology Knowledgebase (SBKB) is a free resource supported by the Protein Structure Initiative that gathers the latest protein structures, models, targets, and annotations from over 100 data sources. Research highlights by SBKB and the Nature Publishing Group provide insights into biology and medicine, spanning from basic molecular biology to infectious diseases and pathogenesis to drug discovery. Reviews of novel bench methods as well as improvements to tried-and-tested techniques also help researchers with their lab work. There are more than 450 articles to learn from in this collection.Read More

Molecule of the Month

Isoprene Synthase

Isoprene Synthase

Plants release a billion metric tons of isoprene and other organic gases every year.Read More

Quarterly News (see archive)

Summer 2016 Issue

Meet our summer interns, watch the Video Challenge award winners, explore protein modifications in the PDB, and more. In the Education Corner, Krystle J. McLaughlin describes Lysozyme, Models and the PDB: Helping Undergraduates Explore Structure. Summer 2016 Newsletter

Annual Reports

2014 Annual Report

Download the 2014 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

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