www.rcsb.org Open in urlscan Pro
128.6.159.248  Public Scan

Form analysis
1 forms found in the DOM

Name: feedbackfrm — POST

<form id="feedbackfrm" name="feedbackfrm" action="" method="POST">
  <fieldset class="hidden parameters">
    <input id="projectkey" name="projectkey" value="HELP" type="hidden">
    <input id="issuetype" name="issuetype" value="Bug" type="hidden">
  </fieldset>
  <div class="row">
    <!-- NAME -->
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="fname-group" class="form-group">
        <label for="fname">First Name</label>
        <input type="text" class="form-control input-sm reqd" id="fname" name="fname">
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="lname-group" class="form-group">
        <label for="lname">Last Name</label>
        <input type="text" class="form-control input-sm reqd" id="lname" name="lname">
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="email-group" class="form-group">
        <label for="email">Email</label>
        <input type="text" class="form-control input-sm reqd" id="email" name="email">
      </div>
    </div>
  </div>
  <!-- ISSUE -->
  <div id="subject-group" class="form-group">
    <label for="subject">Subject</label>
    <input type="text" class="form-control input-sm reqd" id="subject" name="subject">
  </div>
  <div id="description-group" class="form-group">
    <label for="description">Question, Comment, Feedback or Other</label>
    <textarea class="form-control input-sm reqd" id="description" name="description" rows="4"></textarea>
  </div>
  <!-- FILE UPLOAD -->
  <div id="file-group" class="form-group">
    <label for="file">Attach File(s)</label>
    <br>
    <small>Use CTRL or Shift keys to select more than one file (<span id="maxuploads"></span> files max)</small>
    <input type="file" id="file" name="file" class="form-control input-sm" multiple="">
  </div>
  <!-- Privacy Policy -->
  <div class="checkbox">
    <label>
      <input type="checkbox" checked="" name="privacyPolicyAgreement" id="privacyPolicyAgreement"> I agree to the <a href="https://www.rcsb.org/pages/privacy-policy" target="_blank">Help Desk Privacy Policy</a>
    </label>
  </div>
  <!-- OPTIONAL -->
  <hr>
  <label>Optional: To help us learn more about our users, what is your:</label>
  <div class="row">
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="institution-type-group" class="form-group">
        <label for="instype">Institution Type</label>
        <select class="form-control" id="instype">
          <option>College/University</option>
          <option>Research Institute</option>
          <option>Industry</option>
          <option>Non-Profit Organization</option>
          <option>Government</option>
          <option>Hospital</option>
          <option>K12/Primary-Secondary Education</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="role-group" class="form-group">
        <label for="role">Role</label>
        <select class="form-control" id="role">
          <option>Graduate Student</option>
          <option>Postdoctoral Scholar</option>
          <option>Faculty</option>
          <option>Staff</option>
          <option>Software Developer</option>
          <option>Undergraduate Student</option>
          <option>High School Teacher</option>
          <option>High School Student</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="rsrch-intrst-group" class="form-group">
        <label for="rsrch-intrst">Main Research Interest</label>
        <select class="form-control" id="rsrch-intrst">
          <option>Biology and Biochemistry</option>
          <option>Molecular Biology and Genetics</option>
          <option>Computer Science</option>
          <option>Chemistry</option>
          <option>Microbiology</option>
          <option>Pharmacology and Toxicology</option>
          <option>Immunology</option>
          <option>Physics</option>
          <option>Clinical Medicine</option>
          <option>Neuroscience and Behavior</option>
          <option>Engineering</option>
          <option>Plant and Animal Science</option>
          <option>Materials Science</option>
          <option>Environment/Ecology</option>
          <option>Mathematics</option>
          <option>Social Sciences, General</option>
          <option>Agricultural Sciences</option>
          <option>Space Science</option>
          <option>Economics and Business</option>
          <option>Geosciences</option>
          <option>Psychiatry/Psychology</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="modal-footer">
      <button type="button" id="jira-fdbck-close" class="btn btn-default btn-sm" data-dismiss="modal">Close</button>
      <button id="jira-fdbck-submit" type="button" class="btn btn-primary btn-sm">Submit</button>
    </div>
  </div>
</form>

Text Content

Warning You are using a web browser that we do not support. Our website will not
work properly. Please update to a newer version or download a new web browser,
such as Chrome or Firefox.
MyPDB
 * Sign in with Google
 * Sign in with Facebook
 * Sign in with ORCID

   --------------------------------------------------------------------------------

 * Documentation

Contact us
Toggle navigationRCSB PDB
 * Deposit 
   
      PREPARE DATA
   
    * PDBx/mmCIF file
    * pdb_extract
    * SF-Tool
    * Ligand Expo
    * MAXIT
   
      VALIDATE DATA
   
    * Validation Server
    * Validation API
    * Information for Journals
    * Validation Task Forces
   
      DEPOSIT DATA
   
    * wwPDB OneDep System
    * PDB-Dev
   
      HELP AND RESOURCES
   
    * Deposit FAQ
    * Validation FAQ
    * Tutorials
    * Annotation Policies
    * Processing Procedures
    * PDBx/mmCIF Dictionary
    * Chemical Component Dictionary
    * Biologically Interesting Molecule Reference Dictionary (BIRD)
    * BioSync/Beamlines/Facilities
    * Related Tools

 * Search 
   * Advanced Search
   * Sequence Similarity Search
   * Structure Similarity Search
   * Chemical Similarity Search
   * Chemical Sketch Tool
   * Browse by Annotations
   * New Entries
   * Unreleased Entries
   * PDB Statistics
 * Visualize 
   * Mol* (MolStar)
   * Sequence Annotations Viewer
   * Genome View
 * Analyze 
   * Pairwise Structure Alignment
   * Symmetry Resources in the PDB
   * Structure Quality
   * Grouping Structures
   * PDB Citation MeSH Network Explorer
   * PDB Statistics
   * EPPIC Biological Assemblies
   * External Data and Resources
   * Integrated Resources
   * Additional Resources
 * Download 
   * Coordinates and Experimental Data
   * Sequences
   * Ligands
   * File Download Services
   * Web Services
 * Learn 
   
     
   
   * Training Courses
   * Guide to PDB Data
   * Molecule of the Month
   * Educational Resources
   * Curricula
   * Browse
   * News
   * SciArt Galleries
   * Irving Geis
   * David Goodsell
 * About 
   * Contact Us
   * About RCSB PDB
   * Vision and Mission
   * Citation, Usage, Privacy Policies, Logo
   * News
   * PDB History
   * PDB50
   * User Community
   * Publications
   * RCSB PDB Advisory Committee
   * Team Members
   * Diversity, Equity, Inclusion, and Access
   * Service Status
 * Documentation 
   * General Help
   * 3D Structures in the Protein Data Bank
   * Computed Structure Models (CSM)
   * Search and Browse
   * Basic Search
   * Advanced Search
   * Browse Annotations
   * Visualize and Analyze
   * Sequence Viewers
   * Pairwise Structure Alignment
   * Exploring a 3D Structure
   * Grouping Structures
   * Programmatic Access
   * Additional Resources
   * Software Supporters
   * Deposition Resources
   * FAQs
   * Glossary
 * Careers
 * COVID-19
 *  * 
    * 
    * 
    * 


212,303 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

3D Structures



Include CSM



Advanced Search
|
Browse Annotations
Help

 * 
 * 
 * 
 * 
 * 
 * 

 * 
 * 
 * 
 * 


  New: More Computed Structure Models (CSM) availableLearn more
 * Welcome
 * Deposit
 * Search
 * Visualize
 * Analyze
 * Download
 * Learn


WELCOME

RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education
by providing access and tools for exploration, visualization, and analysis of:

Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive



Computed Structure Models (CSM) from AlphaFold DB and ModelArchive

These data can be explored in context of external annotations providing a
structural view of biology.

--------------------------------------------------------------------------------



NOVEMBER MOLECULE OF THE MONTH



ZAR1 RESISTOSOME


   


   PREPARE DATA

 * PDBX/MMCIF FILE
   
   Prepare data in PDBx/mmCIF format

 * PDB_EXTRACT
   
   Extract data 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

 * MAXIT
   
   Translate data between file formats and more

   


   VALIDATE DATA

 * VALIDATION SERVER
   
   Check your X-ray, NMR, or EM structures before depositing-standalone server

 * VALIDATION API
   
   Validate your structures via programmatic remote access before deposition

 * INFORMATION FOR JOURNALS
   
   Instructions to journal editors

 * VALIDATION TASK FORCES
   
   Recommendations from method-specific Validation Task Forces

   


   DEPOSIT DATA

 * WWPDB ONEDEP SYSTEM
   
   Deposit 3D macromolecular structure data to the PDB

 * PDB-DEV
   
   Deposit structural models obtained using integrative hybrid methods

   


   HELP AND RESOURCES

 * Deposit FAQ
 * Validation FAQ
 * Tutorials
 * Annotation Policies
 * Processing Procedures
 * PDBx/mmCIF Dictionary
 * Chemical Component Dictionary
 * Biologically Interesting Molecule Reference Dictionary (BIRD)
 * BioSync/Beamlines/Facilities
 * Related Tools



 * ADVANCED SEARCH
   
   Complex boolean queries with values for a wide range of structure attributes

 * SEQUENCE SIMILARITY SEARCH
   
   Find similar protein and nucleic acid sequences using the mmseqs2 method

 * STRUCTURE SIMILARITY SEARCH
   
   Search protein structures by global shape similarity

 * CHEMICAL SIMILARITY SEARCH
   
   Find ligands bound to macromolecules by SMILES String, InChI, or Chemical
   Formula

 * CHEMICAL SKETCH TOOL
   
   Draw a molecule and use the SMILES or InChI string to search for molecules in
   the CCD

 * BROWSE BY ANNOTATIONS
   
   PDB entries in context of annotations by various ontologies and hierarchical
   classification schemes

 * NEW ENTRIES
   
   Search entries released since last Tuesday

 * UNRELEASED ENTRIES
   
   Search entries that are being processed, on hold waiting for release, or have
   been withdrawn

 * PDB STATISTICS
   
   PDB data distribution, archive growth, and more



 * MOL* (MOLSTAR)
   
   3D visualization for PDB structures and ligand binding sites. Access from
   each structure summary page.

 * SEQUENCE ANNOTATIONS VIEWER
   
   Graphical summaries of protein features and their relationships with
   UniProtKB entries. Access from each structure summary page.

 * GENOME VIEW
   
   Graphical summaries of the correspondences between PDB entity sequences and
   genomes. Access from each structure summary page.



 * PAIRWISE STRUCTURE ALIGNMENT
   
   Calculate pairwise structure alignments using various methods

 * SYMMETRY RESOURCES IN THE PDB
   
   Explore tools that display global, local, and helical symmetry among subunits

 * STRUCTURE QUALITY
   
   The slider graphic compares important global quality indicators for a given
   structure with the PDB archive

 * GROUPING STRUCTURES
   
   Explore conservation and trends in the structure properties, features, and
   functions

 * PDB CITATION MESH NETWORK EXPLORER
   
   Find connections between articles describing PDB structures using MeSH terms

 * PDB STATISTICS
   
   PDB data distribution, archive growth, and more

 * EPPIC BIOLOGICAL ASSEMBLIES
   
   EPPIC (Evolutionary Protein-Protein Interface Classifier) finds biological
   interfaces from crystal contacts

 * EXTERNAL DATA AND RESOURCES
   
   
   
   * • Integrated Resources
   * • Additional Resources



 * COORDINATES AND EXPERIMENTAL DATA
   
   Enter PDB IDs to download multiple files in batches containing one or more
   file formats

 * SEQUENCES
   
   Enter PDB IDs to download sequences in FASTA format

 * LIGANDS
   
   Enter the chemical component IDs to download SDF files with ligand
   coordinates

 * FILE DOWNLOAD SERVICES
   
   Download PDB archive or other related data files

 * WEB SERVICES
   
   The Data API and Search API are the two main APIs that power rcsb.org



Training, Outreach, and Education resources to build and support the broad PDB
user community

 * TRAINING COURSES
   
   Learn to effectively use tools for deposition, searching, analysis, and
   visualization of PDB data

 * GUIDE TO PDB DATA
   
   Guided reference for exploration and interpretation of PDB entries

 * MOLECULE OF THE MONTH
   
   Accounts of selected molecules from the PDB

 * EDUCATIONAL RESOURCES
   
   Resources promoting exploration in the world of proteins and nucleic acids

 * CURRICULA
   
   Authentic, hands-on teaching materials, individual and group activities

 * BROWSE
   
   Browse all PDB-101 resources by biological theme

 * NEWS
   
   Learn about educational offerings and outreach events

 * SCIART GALLERIES
   
   Molecular art for downloading and printing by
   
   * • Irving Geis
   * • David Goodsell





LATEST ENTRIES

As ofTue Nov 14 2023
 1.  
 2.  
 3.  
 4.  
 5.  
 6.  
 7.  
 8.  
 9.  
 10. 


8IR4

--------------------------------------------------------------------------------

CRYSTAL STRUCTURE OF THE SLF1 BRCT DOMAIN IN COMPLEX WITH A RAD18 PEPTIDE
CONTAINING PS442


8PUW

--------------------------------------------------------------------------------

CHAETOMIUM THERMOPHILUM LAS1-GRC3-COMPLEX


8PKW

--------------------------------------------------------------------------------

KELCH DOMAIN OF KEAP1 IN COMPLEX WITH A ORTHO-DIMETHYLBENZENE LINKED CYCLIC
PEPTIDE 5 (ORTHO-WRCDEETGEC)


8PV6

--------------------------------------------------------------------------------

CHAETOMIUM THERMOPHILUM PRE-60S STATE 3 - POST-5S ROTATION WITH RIX1 COMPLEX
WITH FOOT - COMPOSITE STRUCTURE


8PBC

--------------------------------------------------------------------------------

RAD51 FILAMENT ON SSDNA BOUND BY THE BRCA2 C-TERMINUS


8OUA

--------------------------------------------------------------------------------

CEREBLON ISOFORM 4 IN COMPLEX WITH NOVEL BENZAMIDE-TYPE CEREBLON BINDER 11F


8JUL

--------------------------------------------------------------------------------

CRYO-EM STRUCTURE OF SIDT1 IN COMPLEX WITH PHOSPHATIDIC ACID


8T90

--------------------------------------------------------------------------------

CRYSTAL STRUCTURE OF TERRESTRIVIRUS INOSITOL PYROPHOSPHATASE KINASE IN COMPLEX
WITH ADP AND MYO-(3OH)IP5


8TN8

--------------------------------------------------------------------------------

CRYSTAL STRUCTURE OF THE MURINE ASTROVIRUS CAPSID SPIKE AT 1.75 A


8JLR

--------------------------------------------------------------------------------

A77636-BOUND HTAAR1-GS PROTEIN COMPLEX


FEATURES & HIGHLIGHTS

DEPRECATION OF FTP FILE DOWNLOAD PROTOCOL IN THE PDB ARCHIVE

wwPDB plans to deprecate FTP download protocol on November 1st 2024

BACKBONE ANNOTATION AND STANDARDIZATION OF PEPTIDE RESIDUES IS NOW LIVE



EXPLORE ANTIBIOTIC RESISTANCE IN 3D

Annotations from the Comprehensive Antibiotic Resistance Database (CARD) have
been mapped to structures in the PDB archive

ACCESS COMPUTED STRUCTURE MODEL ANNOTATIONS

Gene Ontology terms (for Molecular Function, Cellular Component, and Biological
Process), InterPro protein family classifications, and Pharos disease
associations are available for CSMs at RCSB.org

DOWNLOAD PAE JSON FILES FOR ALPHAFOLD MODELS

Access Predicted Aligned Error files from Structure Summary Pages

ASBMB MEMBERS: REGISTER NOW FOR VIRTUAL EVENT

Learn about Teaching enzymology with the Protein Data Bank: from pandemic to
Paxlovid on October 19.

REGISTER NOW FOR OCTOBER VIRTUAL CRASH COURSES ON RCSB PDB APIS

Learn about Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine
Learning. Part 1 will introduce the Data and Search APIs. Part 2 will offer
hands-on exercises.

COMING SOON: PDB ENTRIES WITH NOVEL LIGANDS DISTRIBUTED ONLY IN PDBX/MMCIF AND
PDBML FILE FORMATS

PDB will run out of 3-character CCD IDs before the end of 2023. Afterwards, PDB
entries with novel ligands will not be distributed in the legacy PDB file
format.

TAKE THE TABULAR REPORTS SURVEY AND WIN

Please take this brief survey about RCSB.org tabular reports to be entered into
a drawing for a set of Bound Playing Cards.

TURNING GLOBAL DATA INTO GLOBAL KNOWLEDGE

RCSB PDB is highlighted in EdgeDiscovery, a publication that highlights research
and research computing initiatives in New Jersey and beyond


See new feature archive


 * NEWS


 * PUBLICATIONS
   
   * Published in Journals & Books
   
     --------------------------------------------------------------------------------
   
   * Molecule of the Month
   
     --------------------------------------------------------------------------------
   
   * Quarterly Newsletter
   * Annual Report
     

 * NOV 18-24: WORLD ANTIMICROBIAL AWARENESS WEEK
   
   PDB structures help us understand resistance to antibiotics and develop new
   ways to fight infection
   » 11/18/2023
   

 * NOV 17: WHO'S CERVICAL CANCER ELIMINATION DAY OF ACTION
   
   Visit PDB-101 to learn how the capsid protein of papillomavirus is used in
   vaccines that prevent cervical cancer
   » 11/16/2023
   

 * MEET RCSB PDB AT ABRCMS
   
   Visit the poster Enabling Computational Biology Research Using Python-Based
   Applications to learn about recent software development; meet Rutgers members
   in booth #511 to learn about the summer internships and gap year
   opportunities
   » 11/15/2023
   

 * NOVEMBER 14 IS WORLD DIABETES DAY
   
   PDB structures reveal how glucose levels are regulated in the body and
   provide new hope for combating the disease.
   » 11/13/2023
   

 * MOLECULAR LANDSCAPES
   
   New painting: Bacteriophage T4 Infection
   » 11/07/2023
   

 * EXPLORE THE STRUCTURAL BIOLOGY OF VIRUSES
   
   Visit PDB-101 to learn how insights provided by structural biology are used
   to develop new defenses against viral infection
   » 10/31/2023
   

 * MEET RCSB PDB AT SACNAS
   
   Learn about summer internship opportunities and more at booth #1235
   » 10/23/2023
   

 * HAPPY BIRTHDAY, PDB!
   
   Today is the anniversary of the 1971 announcement of the PDB.
   » 10/20/2023
   

 * POSTER PRIZE AWARDED AT THE PROTEIN SOCIETY
   
   The wwPDB Foundation made awards to Taylor M. Laflamme (Clark University) and
   Kevin Ramirez (University of California Merced) for their posters at The
   Protein Society Meeting in July 2023.
   » 10/18/2023
   

 * HAPPY BIRTHDAY, IRVING GEIS
   
   Celebrate Geis' birthday (October 18, 1908) with a tour of the Geis Digital
   Archive of his pioneering works of biomolecular art at PDB-101
   » 10/15/2023
   


MOLECULE OF THE MONTH

ZAR1 RESISTOSOME

Plants protect themselves from infection with immune system machines such as the
resistosome

Read More


QUARTERLY NEWS (SEE ARCHIVE)

ISSUE 99 - OCTOBER 2023

In this issue: Explore Bioenergy; Upload Structure Files to Search; Preparing
PDB Depositions; and more. In the Education Corner, learn about Empowering
Educators with Research-Grade Computational Tools

 * Summer 2023 Issue
 * Spring 2023 Issue
 * Winter 2023 Issue
 * Fall 2022 Issue




ANNUAL REPORTS

2022 ANNUAL REPORT

Download the 2022 Annual Report (PDF) for an overview of recent RCSB PDB
activities, including enabled access to ~1 million Computed Structure Models
(CSMs) from AlphaFoldDB and RoseTTAFold.

Annual Report Archive


PDB at a Glance
65,237
Structures of Human Sequences
16,815
Nucleic Acid Containing Structures
CSM at a Glance
999,251
AlphaFoldDB
69,326
ModelArchive
More Statistics
 * About
 * About Us
 * Citing Us
 * Publications
 * Team
 * Careers
 * Usage & Privacy

 * Help
 * Contact Us
 * Documentation
 * Website FAQ
 * Glossary
 * Service Status



RCSB PDB (citation) is hosted by

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

RCSB PDB is a member of the

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

 * RCSB Partners
 * Nucleic Acid Knowledgebase

 * wwPDB Partners
 * RCSB PDB
 * PDBe
 * PDBj
 * BMRB
 * EMDB

RCSB PDB Core Operations are funded by the National Science Foundation
(DBI-1832184), the US Department of Energy (DE-SC0019749), and the National
Cancer Institute, National Institute of Allergy and Infectious Diseases, and
National Institute of General Medical Sciences of the National Institutes of
Health under grant R01GM133198.

×


All questions and comments will receive a response in a timely manner.

Reporting an issue? Please attach a screenshot, if possible.

Access OneDep to update/release in-progress structure depositions

For questions/corrections to specific PDB entries, contact
deposit-help@mail.wwpdb.org to reach that help desk system.

First Name
Last Name
Email
Subject
Question, Comment, Feedback or Other
Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)
I agree to the Help Desk Privacy Policy

--------------------------------------------------------------------------------

Optional: To help us learn more about our users, what is your:
Institution Type College/University Research Institute Industry Non-Profit
Organization Government Hospital K12/Primary-Secondary Education Other
Role Graduate Student Postdoctoral Scholar Faculty Staff Software Developer
Undergraduate Student High School Teacher High School Student Other
Main Research Interest Biology and Biochemistry Molecular Biology and Genetics
Computer Science Chemistry Microbiology Pharmacology and Toxicology Immunology
Physics Clinical Medicine Neuroscience and Behavior Engineering Plant and Animal
Science Materials Science Environment/Ecology Mathematics Social Sciences,
General Agricultural Sciences Space Science Economics and Business Geosciences
Psychiatry/Psychology Other
Close Submit
×


Thank you for providing your feedback! Someone will be in touch with you
shortly. This window will automatically close in 5 seconds.
×


Apologies, our feedback server is currently unavailable and we are
troubleshooting the issue. In the meantime, please copy and paste the below
information into an email addressed to info@rcsb.org