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. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. 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. September Molecule of the Month SARS-CoV-2 RNA-dependent RNA Polymerase

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

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. 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 Search icon to see results matching multiple fields.

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. Go to Advanced Search

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 there are 168889 structures. Access new data entries this week

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Search Ligands Search ligands bound to macromolecules in the PDB by: SMILES String, InChI

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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

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 glycoprotein, H-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). Launch 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. Select Associated Chain ID ... Select Associated Chain ID ... - Select Comparison Method - blast2seq Needleman-Wunsch Smith-Waterman

Protein Symmetry 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. Hemoglobin PDB ID:4HHB

Streptavidin PDB ID:1STP

Inovirus PDB ID:1IFD View Symmetry

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.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. For examples, view the Structure Summary pages for 1CBS (1.8Å structure of a small protein and a ligand , an entry with better overall quality relative to all X-ray structures) and 1FCC (a 3.2Å structure with worse overall quality relative to all X-ray 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: PDB

PDBx/mmCIF

PDBML/XML

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

HTTP/HTTPS 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