A Structural View of Biology
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Deposition Preparation Tools
- pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs
- SF-Tool: Convert structure factor files among various formats
- Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands
Data Format Conversion
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).
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.
Questions about your deposition?
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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.
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.
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.
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.
Next data entry update in:
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Explore the PDB Archive
Search ligands bound to macromolecules in the PDB by:
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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)
Mol* 3D Viewer
Launch Mol* from the Structure Summary page for any entry.
A standalone version of Mol* is available. Users can upload their custom files into this tool.
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.
This feature is available in Structure Summary pages and Instance Sequence pages.
Genome ViewIllustrates 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.
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.
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.
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.The full wwPDB Validation Report PDF is available for download. 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
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:
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- Biological Assemblies in PDB
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Experimental Data Files can be downloaded in the following formats:
- Structure Factors
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- Chemical Shifts
- NMR Restraints v2
By entering PDB IDs, sequences can be downloaded in FASTA format.
Sequences can be provided for any of these identifiers:
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By entering chemical component IDs, SDF files with ligand coordinates can be downloaded.
Downloads are provided for:
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- Ideal coordinates from Chemical Component Dictionary
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).
- 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. Read More on File Download 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.More
Crystal structure of Nematocida HUWE1
Perdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE
Lysozyme 056 from Deep neural language modeling
Cryo-EM structure of RecBCD with undocked RecBNuc and flexible RecD
Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees Celsius
Paired helical filament extracted from PrP-CAA Patient brain tissue
H-Ras Q61L in complex with GppNHp (state 1) after structural transition by humidity control
Cryo-EM structure of the KdpFABC complex in an E1-ATP conformation loaded with K+
Rabbit muscle Glycogen Phosphorylase T state
Features & Highlights
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
Integrating PDB Data with Glycosylation Resources
Access information related to PDB structures from GlyTouCan, GlyCosmos, and GlyGen
Explore Genome-Protein Relationships
See alignments between PDB entity sequences and their reference genomes
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
Mol* appears on the cover of Nucleic Acids Research; thanks to outstanding student contributors Áron and Sukolsak
Sequence Redundancy Statistics
See the growth in the number of unique protein sequences in the PDB
Access Membrane Protein Annotations
Membrane annotations from OPM, PDBTM, and MemProtMD have been integrated with PDB data.
Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive
Scientific Software Developers and Postdocs
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.
Consistent Format for Validation and Coordinate Data
Validation reports for all new entries are now distributed in PDBx/mmCIF format.
PDB users and software developers should adopt this format for future applications.
See new feature archive
The 2021 ACA Transactions Symposium will celebrate 50 years of the PDB (July 30-31); RCSB PDB biocurators and student researchers will also present during the meeting » 07/26/2021
A new Structure perspective describes how 50 years of access to the PDB has accelerated scientific advances in protein structure architecture and prediction » 07/16/2021
PDB50 anniversary celebrations; consistent format for PDB data; sequence redundancy statistics; Education Corner on Expanding Online Educational Resources at the CCDC. » 07/15/2021
New painting: Myoglobin in a Whale Muscle Cell » 07/06/2021
EMDB, the primary archive for experimentally-determined maps and tomograms obtained using 3DEM, is now an official partner in the wwPDB collaboration. » 06/24/2021
A symposium on Understanding Enzyme Function in 3D: Celebrating 50 Years of the Protein Data Bank will be held as part of the American Chemical Society Fall 2021 meeting » 06/22/2021
PDB-101's Guide helps non-experts navigate through the PDB. A new chapter describes how carbohydrates are represented in the archive. » 06/15/2021
Awards were made for best posters in the categories of High School, Undergraduate, Graduate, and Postdoctoral Scholars. » 06/08/2021
A new Structure perspective describes how 50 years of access to the PDB has accelerated scientific advances in protein structure architecture and prediction » 06/07/2021
RCSB PDB's Maria Voigt describes how to use Digital and Physical 3D Models of Proteins » 06/01/2021
Molecule of the Month
Quarterly News (see archive)
PDB50 celebrations; consistent PDB data format; sequence redundancy statistics; and more. Summer 2021 Issue