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Welcome

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

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Reports for released entries are available from Structure Summary pages.

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

Information and&nbspexample Validation Reports (at wwpdb.org).

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

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Advanced Search - Sequence Search

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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&nbspdistinct polymer and, where appropriate, the InChI string(s) for each&nbspdistinct ligand and the&nbspcrystallization pH value(s).

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As of&nbspTue Oct 05 2021 there are 182949 structures.

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Examples:&nbspSARS-CoV-2 spike glycoprotein,&nbspH-Ras, and&nbspBRCA1

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

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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&nbspGenome View.

Examples:&nbspBreast 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.

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

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

Protein Symmetry

The Mol* symmetry display mode (select the&nbspAssembly 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

    PDB ID:4HHB

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    PDB ID:1STP

  • Inovirus

    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&nbspwwPDB&nbspValidation Report&nbsp, 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&nbspRamachandran 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&nbspwebservices page.

1D-coordinates API tutorial

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.

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Experimental Data Files can be downloaded in the following formats:

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Go to the Ligands Downloads Page

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

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Annual snapshots of PDB Archive are&nbspavailable.&nbsp

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

Read More on File Download Services

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User Survey: Tell RCSB PDB About Your Interests

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PDBx/mmCIF data files to include PI information

PI name, email, and ORCiD ID will be publicly available in PDBx/mmCIF data files starting September 24, 2021

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Pairwise Structure Alignment

Comparisons can be made for any protein in the PDB archive and/or uploaded data files.

Improved Access to Chemical Component Definitions and Archive Inventories

Individual Chemical Component Dictionary entries and new archive inventory lists are now available

Explore Ligand Quality

New graphics summarize quality assessments

Small Molecule Search Results Options

For any search, retrieve small molecule information about associated chemical components and peptide-like antibiotic and inhibitor molecules

PDB adopts a standard Creative Commons open source license

PDB data can be copied, modified, and distributed, even for commercial purposes, all without asking permission

Search by Funding

Use Advanced Search to find structures by Funding Agency or Country

Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files

Journals, PDB users, and software developers should review code and begin to prepare for the change in format of PDB IDs and inclusion of PDB DOIs in PDBx/mmCIF files

PDBx/mmCIF data files to include PI information

PI name, email, and ORCiD ID will be publicly available in PDBx/mmCIF data files starting September 24, 2021


See new feature archive

Molecule of the Month

Fifty Years of Open Access to PDB Structures

The Protein Data Bank is celebrating its golden anniversary!

Read More

Quarterly News (see archive)

Issue 91 - October 2021

PDB50; Opioids and Pain Signaling Video; Explore Ligand Quality; User Survey; and more; Education Corner on The SARS-CoV-2 Virion: Magnifying the Miniscule with Models of Digital, Plastic, and Paper.&nbspFall 2021 Issue

Annual Reports

2020 Annual Report

Download the 2020 Annual Report (PDF) for an overview of activities relating to Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education.

Annual Report Archive