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This resource is powered by the Protein Data Bank archive - information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

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Deposition Preparation Tools

Data Extraction

  • pdb_extract : Extract and harvest data in PDBx/mmCIF format from structure determination programs
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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

3D Structure: Jmol

The Jmol molecular viewer offers several options for display and analysis. Launch the viewer using the 3D View feature from any entry's Structure Summary or by entering an ID below. Learn more about Jmol and JSmol.

  • 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

Comparison Tool

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.

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Download: Structures

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Molecule of the Month

Articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.

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The PDB is updated weekly on Wednesdays around 00:00 UTC (Coordinated Universal Time)

As of Tuesday Sep 02, 2014 at 5 PM PDT there are 103015 Structures.

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Protein Structure Initiative Featured System

Peptidyl-carrier Proteins

Peptidyl-carrier Proteins

Bacteria are creative chemists, constantly discovering new ways to build unusualmolecules for exploiting natural resources and fighting competitors. Many of these molecules look like short proteins, but they are not built the same way as traditional proteins. Instead of using the information in DNA, they are built using a dedicated assembly line of enzymes, each... Read More

Molecule of the Month

Apoptosomes

Apoptosomes

"To be, or not to be"--that question is continually being asked by each of your cells. Your cells are preprogrammed to die on command. This is essential during development of large organisms like ourselves, where cells work together, growing and dying to shape our complicated bodies. It is also essential throughout our adult lives, to remove damaged or infected... Read More

Quarterly News ( see archive )

Summer 2014 Issue

PDB Reaches a New Milestone of 100,000+ Entries; the new wwPDB Deposition & Annotation System; RCSB PDB Mobile; a new Molecular Machinery poster; and more. The Education Corner highlights the results of our High School Video Challenge. » 07/08/14

Annual Reports

2013 Annual Report

Download the 2013 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

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