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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.


RCSB PDB Services and Impact

June Molecule of the Month

RCSB PDB Molecule of the Month
Proteins and Nanoparticles

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

Validation Services

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).

Deposit 3D macromolecular structure data to the PDB


PDB-Dev is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods

Explore the PDB Archive

Advanced Search

The Advanced Search interface enables queries by specific categories. Queries can be combined with AND or OR to construct complex searches.

Search categories:

  • IDs and keywords
  • Structure annotation
  • Deposition
  • Structure features
  • Sequence features
  • Chemical components
  • Biology
  • Methods
  • Publication
Start Advanced Search

Search by Sequences

Choose Option A or B to search for protein and nucleic acid sequences.  Read Tutorial | Advanced Sequence Searching

NOTE Parameters: BLAST method, E-value cutoff: 10.0, Mask Low Complexity: On.

Option A: Use PDB Sequence
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or Option B: Paste Sequence

Search by Ligands

Search ligands bound to macromolecules in the PDB by:

  • Identifier or Name
  • SMILES String, InChI or InChI Key
  • Chemical Formula or Molecular Weight
  • Chemical Substructure or Similarity
Start Ligand Search

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

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 Tuesday Jun 12 2018 there are 141209 structures.

Next data entry update in:

Search PDB Statistics

The PDB Statistics page lists the current holdings in the PDB and various growth statistics and histograms.

View PDB Statistics Page

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.

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.

PoseView

PoseView images are 2D diagrams that show a ligand and interacting residues.

Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions.

Access PoseView images in the Ligand Chemical Component section on an entry's Structure Summary.

Learn more about PoseView.

Protein Feature View

Provides a graphical summary of a full-length protein sequence from UniProt and how it corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models information from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder and hydrophobic regions are displayed.

Learn more about Protein Feature View.

Examples: Breast Cancer Type 1 ProteinGag-Pol Polyprotein, and Hemoglobin Alpha (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering a UniProt ID below.

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).

Sequence & Structure Alignment

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, Mammoth, TM-Align, 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.

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Protein Symmetry

The NGL symmetry view 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
    Symmetry Thumbnail for Hemoglobin 4HHB

    PDB ID:4HHB

  • Streptavidin
    Symmetry Thumbnail for Streptavidin 1STP

    PDB ID:1STP

  • Inovirus
    Symmetry Thumbnail for Inovirus 1IFD

    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 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.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

Download: Coordinates & Experimental Data

Enter PDB IDs separated by comma or white space. Note: The Download Tool is launched as a stand-alone application using the Java Web Start protocol. More Download Help 


Coordinates:

Experimental Data:

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Download: Sequences

Enter PDB IDs separated by comma or white space. Download Help 

Download a FASTA file containing all PDB sequences: uncompressedgzipped


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Download: Ligands

Enter ligand IDs separated by comma or white space. Download Help 

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FTP 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 ftp.wwpdb.org (data download details).

Major Directories

  • 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

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

Read More on FTP Services

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

RESTful Web Services

The RCSB PDB supports RESTful (REpresentational State Transfer) Web Services to make accessing data easier.

Generally we are trying to implement two types of services for our RESTful interface:

  • Search services: to return a list of IDs (e.g., PDB IDs, chain IDs, ligand IDs)
  • Fetch services: to return data given a ID (e.g. reports, descriptions, data items)
Read More on our RESTful Services

Molecular explorations
through biology and medicine

PDB-101 is an online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

Browse all PDB-101 resources by biological theme or start exploring:

  • Molecule of the Month

    Presents short accounts on selected molecules from the Protein Data Bank.

  • News and Events

    Upcoming meetings and events RCSB will hold

  • Educational Resources

    Access materials that promote exploration in the world of proteins and nucleic acids.

  • Guide to PDB Data

    Understanding PDB Data is a reference to help explore and interpret individual PDB entries.

  • Curricula

    Authentic, hands-on teaching materials, individual and group activities.

  • Geis Digital Archive

    View iconic illustrations by the gifted artist Irving Geis (1908-1997) in context with PDB structures and educational information.

Features & Highlights

New Architecture and Services Enable Faster Access to More Information

New Architecture and Services Enable Faster Access to More Information

Explore the improved display of PDB Statistics, structure funding information, and 3D views of ligands and electron density.
Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

A new FTP repository, ftp-versioned.wwpdb.org, now hosts versioned structural model files in PDBx/mmCIF and PDBML formats.
Improved Text Searching

Improved Text Searching

Simple text searches at rcsb.org are now easier and more accurate. Text searching from the top query bar has been redesigned and is now powered by the open source Apache Solr platform. Results are based on an indexing of PDBx/mmCIF data.

See new feature archive