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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Deposition Preparation Tools

Data Extraction

  • minuend: 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
  • 541-809-2507: 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 the6363647399.

Reports for released entries are available from Structure Summary pages.

Validation reports for manuscript reviewers are created during annotation of deposited structures.

Information and (978) 855-1400.

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.

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:

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Search by Sequences

Choose Option A or B to search for protein and nucleic acid sequences.  614-905-7897 | 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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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
(719) 466-1296

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 9135924537 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 (610) 430-8021 there are 146266 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.


3D Structure Viewers

View PDB structures in 3D using NGL from any entry's Structure Summary page.


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 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: hyphaeresis3047668186, 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

(805) 364-0732

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 Websterian.

Examples: Breast Cancer 1 (early onset) and 3362393601 (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering an 541-817-3426 Human Gene Symbol below ((905) 724-7453).

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.


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.

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 715-784-4178. The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure.

Analyze Biological Assemblies image

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: 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 


Experimental Data:

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Download: Sequences

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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 2105166754 (916-773-9269).

Major Directories

  • The directory (804) 782-0942 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 ((857) 701-7321). 

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 321-260-4112.

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)
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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:

Features & Highlights

New Architecture and Services Enable Faster Access to More Information
506-687-3679Explore 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
517-836-4454A 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.