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.

July Molecule of the Month

RCSB PDB Molecule of the Month
Non-Homologous End Joining Supercomplexes

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

Validation Services

Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. These reports are developed using the recommendations of thewwPDB Validation Task Forces.

Reports for released entries are available from Structure Summary pages.

Validation reports for manuscript reviewers are created during annotation of deposited structures.

Information and example Validation Reports (at wwpdb.org).

Check your X-ray, NMR, or EM structures before depositing (standalone server).

Deposit 3D macromolecular structure data to the PDB

Have non-atomic coordinates, multi-scale structures obtained through integrative/hybrid (I/H) methods? Deposit at PDB-Dev which is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods.

Basic Search

From any page on the site, a Basic Search can be run by entering a search term in the top Search Bar.

Use the dropdown to the left of the search bar to define the search scope, which can be either “PDB Archive” or “Documentation”.

As you enter a term, you will see a list suggestions in the dropdown menu that appears below the search bar. You can click on an item in the menu, or, if no menu appears for the term or terms you have entered, click the
Search icon. If “PDB Archive“ is selected, suggestions are grouped by field or attribute name, indicating in which specific field or fields the search term was found. Clicking on an item in the menu will return only those results that match the search term in the specified field. Clicking the
Search icon will return results matching multiple fields.

Advanced Search

The Advanced Search Query Builder tool allows you to construct complex boolean queries by specifying values for a wide range of structure attributes.

Text-based queries can be combined with sequence and structure similarity searches.

Search results can be returned at the structure, entity, or assembly level, and viewed in a variety of formats, for example, as a summary view, an images only gallery view, or in a Tabular Report format.

Any query and its results can be further refined by selecting additional criteria from the 'Refinements' panel.

Go to Advanced Search

Search by Sequences

Search protein and nucleic acid sequences using the mmseqs2 method to find similar protein or nucleic acid chains in the PDB.

The new Advanced Search Query Builder tool can be used to run sequence searches, and to combine the results with the other search criteria that are available.

Read Tutorial

Advanced Search - Sequence Search

Chemical Sketch Tool

You can search the PDB archive for a specific ligand or similar ligands based on the 2D chemical drawing of a molecule. In doing so you don’t have to know the specific chemical descriptors (e.g., SMILES and/or InChI) because they will be automatically generated. You can also edit a molecule that is drawn or loaded into the tool to add or remove atoms or groups of atoms and then use the new molecule to query the PDB archive.

Chemical Sketch Tool

Chemical Sketch Documentation

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 Tue Jun 28 2022 there are 192095 structures.

PDB Data Distributions

This feature on the PDB Data Distributions page allows you to quickly view the archive in a series of pie charts. Each chart displays a statistical drilldown of the data in the below categories:

  • Scientific Name of Source Organism
  • Taxonomy
  • Polymer Entity Type
  • Refinement Resolution (Å)
  • Release Date
  • Enzyme Classification Name
  • Symmetry Type
  • SCOP Classification
  • In addition, the drilldown data includes links to the Search Results page, where the data can be explored in greater detail.

    Search PDB Statistics

    The PDB Statistics page lists the current holdings in the PDB and various growth statistics and histograms.

    View PDB Statistics Page

    Search Ligands

    Search ligands bound to macromolecules in the PDB by:

    • SMILES String, InChI
    • Chemical Formula
    Ligand Search

    Search by Drugs & Drug Targets

    Drugs & Drug Targets in the PDB have been mapped to DrugBank. They have been made available through the integrated search system. You can find some search examples under the help examples page.

    • Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase

    • Drug: Atorvastatin (Lipitor)

    Go to Advanced Search

    Mol* 3D Viewer

    Launch Mol* from the Structure Summary page for any entry.

    standalone version of Mol* is available. Users can upload their custom files into this tool.

    A detailed Mol* User Guide is available.

    Protein Feature View

    Provides a graphical summary of biological and structural protein features of PDB entities and how they correspond to UniProtKB  sequences. It loads features from RCSB PDB webservices and third party resources such as UniProtKB, CATH or SCOPe.

    Learn more about  Protein Feature View.

    Examples: SARS-CoV-2 spike glycoproteinH-Ras, and BRCA1

    This feature is available in Structure Summary pages and Instance Sequence pages.

    Genome View

    Illustrates the correspondences between PDB Entity sequences and genomes. When the relationships between PDB Entities and genes are available, PDB Entity sequences are mapped to their genome positions to show which regions of a gene are available in the Entity coordinates.

    Learn more about Genome View.

    Examples: Breast Cancer 1 (early onset)SARS-CoV-2 spike glycoprotein and H-Ras (shown image).

    This feature is available from the Structure Summary page Genome tab.

    Pairwise Structure Alignment

    The protein structure alignment tool allows for calculating pairwise structure alignments using different alignment methods. See the detailed documentation at this help page. Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB.

    Also, the standalone Mol* viewer application allows for calculating pairwise structure alignments based on sequence alignment. See detailed instructions on how to superpose structures at the Mol* help page.

    Protein Symmetry

    The Mol* symmetry display mode (select the Assembly Symmetry button) highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.

    • Hemoglobin
      Symmetry Thumbnail for Hemoglobin 4HHB

      PDB ID:4HHB

    • Streptavidin
      Symmetry Thumbnail for Streptavidin 1STP

      PDB ID:1STP

    • Inovirus
      Symmetry Thumbnail for Inovirus 1IFD

      PDB ID:1IFD

    Structure Quality

    Structure Summary pages provide access to information about structure quality.

    The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks (black vertical boxes) are calculated with respect to all X-ray structures available prior to 2011. Resolution-specific percentile ranks (white vertical boxes) are calculated considering entries with similar resolution.

    This graphic is from the wwPDB Validation Report , which provides a more detailed assessment of the quality of a structure and highlights specific concerns. These reports were created using the recommendations of wwPDB Validation Task Forces.PDFs of Ramachandran plots (created by MolProbity) are provided to offer an independent method to evaluate the conformational quality of protein structures.

    Map Genomic Locations to/from PDB

    The 1D-coordinates API provides means to map between genomic coordinates and PDB positions. Find more information about this and other APIs in the webservices page.

    1D-coordinates API tutorial
    Analyze Biological Assemblies image

    EPPIC Biological Assemblies

    EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.

    PDB Citation MeSH Network Explorer

    The National Library of Medicine assigns MeSH (Medical Subject Headings) from a controlled vocabulary to index articles for PubMed. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches. The PDB Citation MeSH Network Explorer flattens these trees into co-occurence networks of MeSH terms associated with PDB entries. Each node on the graph is a publication, and nodes are linked when they share MeSH terms. 

    Download Coordinate & Experimental Data Files

    By entering PDB IDs, multiple files can be downloaded in batches containg one or more file formats.

    Coordinate Data Files can be downloaded in the following formats:

    • PDB
    • PDBx/mmCIF
    • PDBML/XML (Header only)
    • Biological Assemblies in PDB
    • Biological Assemblies in PDBx/mmCIF

    Experimental Data Files can be downloaded in the following formats:

    • Structure Factors
    • NMR Restraints
    • Chemical Shifts
    • NMR Restraints v2

    Go to the Downloads Page

    Download: Sequences

    By entering PDB IDs, sequences can be downloaded in FASTA format.

    Sequences can be provided for any of these identifiers:

    • Entry IDs
    • Entity IDs
    • Asym IDs

    Go to the Sequences Downloads Page

    Download: Ligands

    By entering chemical component IDs, SDF files with ligand coordinates can be downloaded.

    Downloads are provided for:

    • Coordinates of first chemical component instance from each PDB entry
    • Coordinates of all chemical component instances from each PDB entry
    • Ideal coordinates from Chemical Component Dictionary

    Go to the Ligands Downloads Page

    File Download Services

    Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at the main archive, ftp.wwpdb.org (data download details) and the versioned archive, ftp-versioned.wwpdb.org (Versioning details).

    Major Directories

    • The directory pub/pdb is the entry directory for the PDB archive.
    • The directory pub/pdb/data/structures/divided contains the current PDB contents including PDB, mmCIF, and PDBML/XML formatted coordinate files, structure factors and NMR restraints

    Annual snapshots of PDB Archive are available

    The Versioned Archive is available at https://ftp-versioned.wwpdb.org (See announcement). 

    Read More on File Download Services

    Web Services

    Programmatic access to individual structures and/or specific data items is provided through Web Service Application Program Interfaces (APIs).

    New Web Service APIs are being developed; users should register with the RCSB PDB API electronic list for announcements.

    Contact RCSB PDB with questions suggestions for specific services.


    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

      Accounts of selected molecules from the PDB.

    • 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

    Developers: Switch to Search API v2 Before July 13

    Developers: Switch to Search API v2 Before July 13

    Documentation about Search API v2 is available. V1 will not be supported after July 13, 2022.

    PDB Data Distributions

    PDB Data Distributions

    Explore PDB holdings by experimental method and molecular type, along with numbers for structures with experimental and small molecule data

    Subscribe to API News

    Subscribe to API News

    Stay up-to-date with web service developments and announcements from RCSB PDB

    Postdocs and Scientific Software Developers

    Postdocs and Scientific Software Developers

    Join RCSB PDB to design, develop, & deploy modern web and data applications & complex user interfaces. Help accelerate research and training in biology, medicine, & related disciplines. Positions at Rutgers and SDSC/UCSD.

    New Ways to Explore Similar Proteins

    New Ways to Explore Similar Proteins

    "Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study

    Distributing PDBx/mmCIF-Formatted Assembly Files

    Distributing PDBx/mmCIF-Formatted Assembly Files

    The PDB archive now distributes assembly files in PDBx/mmCIF format, allowing direct access and visualization of curated assemblies for all PDB entries.

    Explore Ligand Quality

    Explore Ligand Quality

    A new publication describes the graphical summaries of quality assessments available at RCSB.org

    Access Membrane Protein Annotations

    Access Membrane Protein Annotations

    New publication describes improved annotation, search and visualization of membrane proteins

    Search API v2 Now Available

    Search API v2 Now Available

    Developers should migrate to this new Search API. Limited V1 support extended until July 13, 2022.

    Developers: Switch to New Sequence Cluster Files by April 12

    Developers: Switch to New Sequence Cluster Files by April 12

    Sequence clustering based on polymer entity ID are now available to replace files organized by chain identifiers

    See new feature archive

    Molecule of the Month

    Non-Homologous End Joining Supercomplexes

    Non-Homologous End Joining Supercomplexes

    Lethal double-strand breaks in the DNA genome are repaired by NHEJ

    Read More

    Quarterly News (see archive)

    April 2022 newslettery

    Issue 93 - April 2022

    Announcements for Developers; New Structure Annotations; Award-winning PDB-101 images; and more; Education Corner on Python Scripting for Biochemistry and Molecular BiologySpring 2022 Issue

    Annual Reports

    2021 Annual Report

    Download the 2021 Annual Report (PDF) for an overview of recent RCSB PDB activities, publications, and a look back at celebrating 50 years of the PDB archive.

    Annual Report Archive