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A Structural View of Biology

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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December Molecule of the Month

RCSB PDB Molecule of the Month
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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

3D Structure Viewers

View PDB structures in 3D using NGL from any entry's Structure Summary page.


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.

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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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Experimental Data:

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Molecular explorations
through biology and medicine

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:

  • Molecule of the Month

    Presents short accounts on selected molecules from the Protein Data Bank.

  • News and Events

    Upcoming meetings and events RCSB will hold

  • Educational Resources

    Access materials that promote exploration in the world of proteins and nucleic acids.

  • Guide to PDB Data

    Understanding PDB Data is a reference to help explore and interpret individual PDB entries.

  • Curricula

    Authentic, hands-on teaching materials, individual and group activities.

  • Geis Digital Archive

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

Features & Highlights

Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

A new FTP repository, ftp-versioned.wwpdb.org, now hosts versioned structural model files in PDBx/mmCIF and PDBML formats.
Improved Text Searching

Improved Text Searching

Simple text searches at rcsb.org are now easier and more accurate. Text searching from the top query bar has been redesigned and is now powered by the open source Apache Solr platform. Results are based on an indexing of PDBx/mmCIF data.
HTTPS @ www.rcsb.org

HTTPS @ www.rcsb.org

Access RCSB.org data and resources over HTTPS.
Structural variation in clusters from PDBFlex

Structural variation in clusters from PDBFlex

Explore variations in structures with similar sequences through the integration of PDBFlex data.
View Validation in 3D

View Validation in 3D

Visualizing structure quality metrics in three dimensions

See new feature archive