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.
Openings with RCSB PDB at UCSD
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?
Explore the PDB Archive
The Advanced Search interface enables queries by specific categories. Queries can be combined with AND or OR to construct complex searches.
- IDs and keywords
- Structure annotation
- Structure features
- Sequence features
- Chemical components
Search by Sequences
NOTE Parameters: BLAST method, E-value cutoff: 10.0, Mask Low Complexity: On.
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
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 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.
- Access new data entries this week
- Access new structure publications this week
- Search unreleased entries
Next data entry update in:
Browse by Annotation
PDB entries have been annotated by various ontologies and hierarchical classification schemes.
- Anatomical Therapeutic Chemical Classification System
- Membrane Proteins
- Protein Modification
- Protein Symmetry
- Biological Process, Cell Component, Molecular Function
- Enzyme Classification
- Transporter Classification
- Source Organism
- Genome Location
- MeSH (Medical Subject Headings)
- SCOP and CATH
Search PDB Statistics
The PDB Statistics page lists the current holdings in the PDB and various growth statistics and histograms.
- Summary Table of Released Entries
- Growth of Released Structures Per Year
- Growth of X-ray Structures Per Year
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.
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.
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.
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.
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: 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
Enter PDB IDs separated by comma or white space. Download Help
Enter ligand IDs separated by comma or white space. Download Help
- 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
- Ligand Files
- Secondary Structure Files
- SIFTS Files
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)
Wild-type HIV-1 protease in complex with Lopinavir
Crystal structure of Bacillus cereus FlgL
To be published
Crystal structure of Xanthomonas campestris FlgL (space group C2)
Crystal structure of the PI3KC2alpha C2 domain in complex with IP6
Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD.
Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure
Lysozyme structure determined from SFX data using a Sheet-on-Sheet chipless chip
N-Terminal Domains of Cardiac Myosin Binding Protein C Cooperatively Activate the Thin Filament.
Bacteroides uniforms beta-glucuronidase 2 bound to D-glucaro-1,5-lactone
Features & Highlights
New Architecture and Services Enable Faster Access to More InformationExplore 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 ManagementA new FTP repository, ftp-versioned.wwpdb.org, now hosts versioned structural model files in PDBx/mmCIF and PDBML formats.
Improved Text SearchingSimple 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
- Fall Newsletter Published » 10/09/2018
- Create a Nobel-Themed Bean Bag Toss » 10/04/2018
- 2018 Nobel Prize in Chemistry » 10/03/2018
- 2018 Nobel Prize in Physiology or Medicine » 10/01/2018
- Structural Biology and Nobel Prizes » 09/28/2018
- Explore Distance, Angle, and Dihedral Measurements » 09/25/2018
- Celebrating National Postdoc Appreciation Week » 09/17/2018
- Public Symposium on Superbugs: Evolutionary Insights from the PDB » 09/14/2018
- Meet PDB in VR with Nanome » 09/10/2018
Molecule of the Month
Quarterly News (see archive)
PDB Benefits Global Health, Science, Economy; Explore Distance, Angle, and Dihedral Measurements; Meet PDB in VR with Nanome; and more. Fall 2018 Newsletter