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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.


July Molecule of the Month

RCSB PDB Molecule of the Month
Myelin-associated Glycoprotein

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.

As you enter a term, you will see suggestions appearing in the dropdown menu that appears below the search bar. The suggestions are grouped by attribute name, indicating in the specific field or fields in which the search term was found.

You can click on an item in the dropdown menu to see results matching only that particular attribute, or click the
Search icon to see 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.

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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

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 Jul 07 2020 there are 166301 structures.

Next data entry update in:

Explore the PDB Archive

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 by Ligands

Search ligands bound to macromolecules in the PDB by:

  • Identifier or Name
  • SMILES String, InChI or InChI Key
  • Chemical Formula or Molecular Weight
  • Chemical Substructure or Similarity
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Search by Drugs & Drug Targets

Drugs & Drug Targets in the PDB have been mapped to DrugBank.

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

  • Drug: Atorvastatin (Lipitor)

Search for Drugs & Drug Targets

3D Structure Viewers

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

A 3D View (NGL) User Guide is available.

Pathway View

Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.

Maps can be accessed from the Protein View (see example P29401), and the main Pathway View page.

RCSB Saguaro 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 RCSB Saguaro Protein Feature View.

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

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

Human Gene View

Illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB structure protein chains (selected from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.

Learn more about Gene View.

Examples: Breast Cancer 1 (early onset) and Hemoglobin, Alpha 1 (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering an HGNC Human Gene Symbol below (examples).

Sequence & Structure Alignment

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, 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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Protein Symmetry

The JSmol symmetry display mode (select the 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 Position to Protein

Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location (i.e., the site of a SNP).

Example of SNP in Breast Cancer 1 Gene

A TGT-to-GGT transversion in codon 64 of the BRCA1 gene leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure.

Access the Mapping Tool
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.

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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Download: Sequences

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Download: Ligands

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FTP 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 at FTP archive, ftp.wwpdb.org (data download details) and Versioned FTP, ftp-versioned.wwpdb.org (Versioning details).

Major Directories

  • The directory pub/pdb is the entry directory for the ftp site.
  • 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 FTP Archive is available at ftp://ftp-versioned.wwpdb.org (See announcement). 

Read More on FTP Services

HTTP/HTTPS Services

PDB structure files, chemical component files, and several other files are available for download via http/https. These URLs are useful in scripted downloads using utilities such as wget.

Downloadable Files

  • PDB Structure Files
  • Ligand Files
  • Secondary Structure Files
  • SIFTS Files
Read More on our HTTP/HTTPS 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.

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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

Introducing a New Molecular Display

Introducing a New Molecular Display

Using Mol* for 2D image generation gives a more modern look
Sequence Motif Searching

Sequence Motif Searching

Use Advanced Search to find short sequence patterns in PDB structures
Enter the Coronavirus CellPAINT Contest

Enter the Coronavirus CellPAINT Contest

Show us how you can illustrate coronavirus with a new version of CellPAINT
Announcement: Legacy MyPDB Will Be Discontinued October 2020

Announcement: Legacy MyPDB Will Be Discontinued October 2020

Users should migrate to the new and improved version that uses third-party authentication
Announcement: Legacy RCSB PDB APIs Will Be Discontinued November 2020

Announcement: Legacy RCSB PDB APIs Will Be Discontinued November 2020

Users should migrate to new and improved APIs. Please contact us with any questions.
June 1: Retirement of Protein Workshop and Ligand Explorer

June 1: Retirement of Protein Workshop and Ligand Explorer

The 3D viewer Mol* has been updated to include features from these tools.
New APIs Replace REST Services

New APIs Replace REST Services

REST.rcsb.org services will be deprecated on May 14, 2020.
Welcome to the Next Generation RCSB.org

Welcome to the Next Generation RCSB.org

Explore significantly revised and updated tools for searching and exploring PDB data
COVID-19/SARS-CoV-2 Resources

COVID-19/SARS-CoV-2 Resources

PDB data and related resources provide a starting point for structure-guided drug discovery and understanding of COVID-19
Improve Your Coordinates, Keep Your ID (Phase II)

Improve Your Coordinates, Keep Your ID (Phase II)

PDB versioning, which enables depositors to update entries while retaining their original PDB ID, is now available for all structures.

See new feature archive