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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.


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Reports for released entries are available from Structure Summary pages.

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

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

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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.

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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

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    PDB ID:1IFD

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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.

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1D-coordinates API tutorial

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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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Go to the Ligands Downloads Page

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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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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.

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