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.

October Molecule of the Month

RCSB PDB Molecule of the Month
Capsaicin Receptor TRPV1

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.

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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 Oct 20 2020 there are 170172 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 Ligands

Search ligands bound to macromolecules in the PDB by:

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Ligand Search

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 Mol* from any entry's Structure Summary page.

A 3D View (Mol*) 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 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 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).

Pairwise Structure Alignment

The standalone Mol* viewer application allows for calculating pairwise structure alignments.

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB.

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


  • Streptavidin
    Symmetry Thumbnail for Streptavidin 1STP


  • Inovirus
    Symmetry Thumbnail for Inovirus 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 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

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


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.


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

Sequence Alignments in Search Results

Sequence Alignments in Search Results

For Sequence Similarity searches, display search results as "Polymer Entities" to view amino acid mismatches.

Build Customize Tabular Reports of PDB Data

Build Customize Tabular Reports of PDB Data

After searching for a set of structures, create a table of information by selecting the columns of your choice. Tables can be saved in CSV or JSON formats.

Documentation for New and Improved APIs

Documentation for New and Improved APIs

Learn the concepts and syntax behind these new services. Legacy APIs will be discontinued November 2020

Search by Chemical Formula or Descriptor

Search by Chemical Formula or Descriptor

Use Advanced Search>Chemical Search for small-molecule searching by formulae or descriptors (SMILES, InChI)

Updated Validation Reports for Released PDB Structures

Updated Validation Reports for Released PDB Structures

Reports now include recalculated percentiles, 2D diagrams highlighting ligand quality, map and model fit for EM entries, and calculated map coefficients used for X-ray data validation.

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

Explore Sequence-Structure Relationships

Explore Sequence-Structure Relationships

Protein Feature View maps PDB structures and corresponding UniProtKB sequences and other annotations in an updated interface

Real Time Structural Search of the PDB

Real Time Structural Search of the PDB

A new paper describes a novel method that detects similarity between protein shapes and that works equally fast for any size of proteins or assemblies

Access Improved Carbohydrate Data at the PDB

Access Improved Carbohydrate Data at the PDB

A new data representation for carbohydrates in PDB entries and reference data improves the Findability and Interoperability of these molecules in macromolecular structures. Lists of PDB entries, CCDs, PRDs, and non-PDB compatible entries are available.

Integrating PDB Data with NIH Common Fund Data Resources

Integrating PDB Data with NIH Common Fund Data Resources

Access information from PHAROS (important drug target protein families: GPCRs, ion channels and kinases), GTEx (tissue-specific gene expression and regulation) and IMPC (data related to mouse phenotypes).

See new feature archive
  • American Public Health Association Film Festival

    American Public Health Association Film Festival

    The video Fighting Coronavirus with Soap has been selected to be screened along with other films and PSAs in the COVID-19 session  » 10/25/2020

  • PDB Turns 49

    PDB Turns 49

    Today is the anniversary of the 1971 announcement of the PDB. wwPDB is celebrating by looking ahead to golden anniversary symposia and events planned for 2021  » 10/20/2020

  • Happy Birthday, Irving Geis

    Happy Birthday, Irving Geis

    Celebrate Geis' birthday (October 18, 1908) with a tour of the Tour the Geis Digital Archive developed in collaboration with HHMI.  » 10/18/2020

  • Join Us at the STEMteachersEXPO

    Join Us at the STEMteachersEXPO

    RCSB PDB will be part of Strengthening virtual Chemistry and Biology Instruction Through 3D Modeling on Saturday October 24  » 10/16/2020

  • Fall Newsletter Published

    Fall Newsletter Published

    New publications; updated validation reports; exploring sequence-structure relationships; from Boot Camp to Poster Prize; and more. The Education Corner describes Using PDB Structures to Visualize Science by medical illustrator Veronica Falconieri.  » 10/13/2020

  • Dexamethasone and Cytokine Storms

    Dexamethasone and Cytokine Storms

    New in Resources to Fight the COVID-19 Pandemic: Preventing too much of a good thing during SARS-CoV-2 infection  » 10/12/2020

  • 2020 Nobel Prize in Chemistry

    2020 Nobel Prize in Chemistry

    Congratulations to PDB depositors Emmanuelle Charpentier and Jennifer A. Doudna on the award for the development of a method for genome editing. Read more about Cascade and CRISPR at Molecule of the Month  » 10/07/2020

  • Award-Winning Image

    Award-Winning Image

    This image of RNA Polymerase was selected as a national finalist in the 2019 Wiki Science Competition in the United States. The jury selected 36 finalists across six categories from 1,144 submissions.  » 10/06/2020

  • Structural Biology and Nobel Prizes

    Structural Biology and Nobel Prizes

    Next week, Nobel Prizes will be announced that highlight achievements in physics, chemistry, physiology or medicine, literature, and for peace.  » 09/29/2020

  • Poster Prize Awarded at ACA

    Poster Prize Awarded at ACA

    Congratulations to Takahiro Yamauchi for Crystal and Solution structures of Proliferating Cell Nuclear Antigen from Crenarchaeon aeropyrum pernix and an honorable mention to Ravi Yadav for Structural basis of Neisserial lactoferrin binding protein B function  » 09/24/2020

Molecule of the Month

Capsaicin Receptor TRPV1

Capsaicin Receptor TRPV1

TRPV1 is an ion channel that senses heat and contributes to pain sensation.

Read More

Quarterly News (see archive)

Issue 86 - October 2020

New publications; updated validation reports; exploring sequence-structure relationships; from Boot Camp to Poster Prize; and more. Fall 2020 Issue

Annual Reports

2019 Annual Report

Download the 2019 Annual Report (PDF) for an overview of activities relating to Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education.

Annual Report Archive