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.
The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
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?
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
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:
Browse by Annotation
PDB entries have been annotated by various ontologies and hierarchical classification schemes.
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- MeSH (Medical Subject Headings)
- Molecular Function
- Protein Symmetry
- Source Organism
Explore the PDB Archive
Search ligands bound to macromolecules in the PDB by:
- SMILES String, InChI
- Chemical Formula
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)
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.
Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.
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.
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.
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.
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.
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 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
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:
- 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
Enter ligand IDs separated by comma or white space. Download Help
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).
- 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. 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.
- PDB Structure Files
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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 Importin alpha 2 in complex with LSD1 NLS
Cryo-EM structure of Arabidopsis thaliana MSL1 A320V
Crystal Structure of the Thorarchaeaota 2DGel3/rabbit actin complex
BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212P
rrn anti-termination complex without S4
GluN1b-GluN2B NMDA receptor in non-active 1 conformation at 3.95 angstrom resolution
Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII)
Crystal structure of branching enzyme D434A mutant from Cyanothece sp. ATCC 51142
CutA in complex with A3 RNA
Poliovirus (Type 1 Mahoney), receptor-catalysed 135S particle incubated with anti-VP1 mAb at RT for 1 hr
Features & Highlights
Integrating PDB Data with NIH Common Fund Data ResourcesAccess 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).
Introducing a New Molecular DisplayUsing Mol* for 2D image generation gives a more modern look
Sequence Motif SearchingUse Advanced Search to find short sequence patterns in PDB structures
Enter the Coronavirus CellPAINT ContestShow us how you can illustrate coronavirus with a new version of CellPAINT
Announcement: Legacy MyPDB Will Be Discontinued October 2020Users should migrate to the new and improved version that uses third-party authentication
Announcement: Legacy RCSB PDB APIs Will Be Discontinued November 2020Users should migrate to new and improved APIs. Please contact us with any questions.
June 1: Retirement of Protein Workshop and Ligand ExplorerThe 3D viewer Mol* has been updated to include features from these tools.
New APIs Replace REST ServicesREST.rcsb.org services will be deprecated on May 14, 2020.
Welcome to the Next Generation RCSB.orgExplore significantly revised and updated tools for searching and exploring PDB data
See new feature archive
- Summer Newsletter Published » 07/28/2020
- Resources to Fight the COVID-19 Pandemic » 07/21/2020
- Drug Discovery Today » 07/14/2020
- Coming July 29: Improved Carbohydrate Data at the PDB » 07/07/2020
- Impact of the Protein Data Bank Across Scientific Disciplines » 06/30/2020
- PDB-101 Coronavirus Resources » 06/23/2020
- RCSB PDB in the Time of COVID-19 » 06/16/2020
- Coronavirus CellPAINT Contest Winners » 06/08/2020
- Education Corner: Biomolecular Modeling in Elementary and Middle School » 06/02/2020
Molecule of the Month
Quarterly News (see archive)
RCSB PDB in the Time of COVID-19; improving carbohydrates; retiring Legacy Web Services; and more. Summer 2020 Issue