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

Submitted URL: http://rcsb.org/
Effective URL: https://www.rcsb.org/
Submission: On June 07 via manual from PH — Scanned from DE

Form analysis 1 forms found in the DOM

Name: feedbackfrmPOST

<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
 *  * 
    * 
    * 
    * 
    * 


220,760 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

3D Structures



Include CSM



Advanced Search
|
Browse Annotations
Help

 * 
 * 
 * 
 * 
 * 
 * 

 * 
 * 
 * 
 * 
 * 


  Access Computed Structure Models (CSMs) of available model organismsLearn 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.

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



JUNE MOLECULE OF THE MONTH



INJECTISOME


   


   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 Jun 04 2024
 1.  
 2.  
 3.  
 4.  
 5.  
 6.  
 7.  
 8.  
 9.  
 10. 


8XAW

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

CRYO-EM STRUCTURE OF AN ANTI-PHAGE DEFENSE COMPLEX BOUND TO AMPPNP AND DNA AT
STATE 1


8K7P

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

STAPHYLOCOCCUS AUREUS LIPASE -PSA COMPLEX


8UDL

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

HUMAN MITOCHONDRIAL DNA POLYMERASE GAMMA BINARY COMPLEX


8YYQ

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

STRUCTURE OF THE HITB F328L MUTANT


8P5H

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

KINASE DOMAIN OF MUTANT HUMAN ULK1 IN COMPLEX WITH COMPOUND CCT241533


8KAJ

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

CRYSTAL STRUCTURE OF SPYCAS9-CRRNA-TRACRRNA COMPLEX BOUND TO 16NT TARGET DNA


9B5C

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

UBIQUITIN E1-UB-E2 TETRAHEDRAL TRANSTHIOLATION INTERMEDIATE MIMIC (DOUBLY
UB-LOADED) - CONSENSUS MAP AND MODEL


8UO6

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

HIV-1 REV RESPONSE ELEMENT (RRE) STEM-LOOP II (SLII)


8JRN

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

STRUCTURE OF E6AP-E6 COMPLEX IN ATT1 STATE


8P5M

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

SARS-COV-2 SPIKE RBD IN COMPLEX WITH MAB-23 (FAB)


FEATURES & HIGHLIGHTS

REGISTER FOR JUNE 13 VIRTUAL OFFICE HOUR: GENERATING DSN6 AND MTZ FILES

DSN6 formatted map files will not be offered after June 28, 2024. MTZ files
available from EDMAPS.rcsb.org will be discontinued in the Fall. Join us for a
Virtual Office Hour to learn more about this transition, and how you can
generate the data you need.

NOTICE: NGL VIEWER DEPRECATION

As of June 28, 2024, the NGL molecular viewer will be removed from RCSB.org.
Users are encouraged to use Mol* for 3D visualization.

SWITCH FROM MMTF TO BCIF

As of July 2, 2024, RCSB PDB will no longer serve PDB data in the MMTF
compression format. Users should switch to BCIF.

ANNOUNCEMENT: EDMAPS.RCSB.ORG SHUTDOWN

DSN6 formatted map files will not be offered after June 28, 2024. MTZ files
available from EDMAPS.rcsb.org will be discontinued in the Fall. Join us for a
Virtual Office Hour to learn more about this transition.

REGISTER NOW FOR A WEBINAR ON UNDERSTANDING PDB VALIDATION: WHICH EXPERIMENTAL
STRUCTURES SHOULD I RELY ON?

Join us on May 14 to learn about primary PDB structure quality metrics,
including those in the validation slider graphic; how PDB structure quality
varies across the archive; and identify good structure(s) for research from
RCSB.org

COMING SOON: ANNOTATION OF PROTEIN MODIFICATIONS IN THE PDB

By the end of 2024, wwPDB will roll out updated atomic coordinate files as well
as updated CCD files containing additional annotation describing protein
chemical modifications (PCMs) and post translational modifications (PTMs)

REGISTER NOW FOR A VIRTUAL DEEP DIVE INTO COMPUTED STRUCTURE MODEL EXPLORATION
AT RCSB.ORG

Join us on April 30 as we demonstrate how RCSB.org serves as your gateway to
structural data exploration. Learn how to navigate predicted 3D protein models
in the context of experimentally-determined PDB structures.

EXPLORE MECHANISM AND CATALYTIC SITE ANNOTATIONS

Access Mechanism and Catalytic Site Atlas (M-CSA) annotations for PDB structures

TAKE THE EDMAPS.RCSB.ORG SURVEY

Please take this brief survey about usage of DSN6-formatted data files

REGISTER FOR THE APRIL 1 MOL* VIRTUAL OFFICE HOUR

Join RCSB PDB for quick tips on how to use Mol* for hiding/coloring/changing the
representation of parts of a structure


See new feature archive


 * NEWS


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

 * BIOCURATOR MILESTONE: >10,000 DEPOSITIONS PROCESSED
   
   Congratulations to wwPDB's Yuhe Liang on processing more than 10,000 PDB
   structures
   » 06/06/2024
   

 * MOLECULAR ORIGAMI: BUILD 3D PAPER MODELS OF PROTEIN DOMAINS
   
   Download printable alpha helices and beta strand templates for hands-on
   exploration of protein folding domains, including a TIM Barrel and a Beta
   Sandwich
   » 06/04/2024
   

 * REGISTER FOR THE JUNE 4TH WEBINAR
   
   RCSB PDB Director will present Protein Data Bank: From two epidemics & the
   global pandemic to mRNA vaccines & Paxlovid as part of Advancing Drug
   Discovery: A Webinar Series of the National Academies of Sciences,
   Engineering and Medicine
   » 05/31/2024
   

 * EXPLORE THE STRUCTURAL BIOLOGY OF EVOLUTION
   
   Evolution is a natural process that produces improved organisms without any
   need for intelligent intervention
   » 05/26/2024
   

 * EDUCATION CORNER: CREATING 3D PROTEIN MODELS AND VIDEOS
   
   Learn about Building and Animating Catalase in a High School Classroom with
   Emerson Newton
   » 05/20/2024
   

 * PDB-101 FOCUS: PEAK PERFORMANCE
   
   PDB-101 materials explore the structural biology of athletics and well-being
   » 05/16/2024
   

 * REGISTER FOR THE JUNE 3 MOL* VIRTUAL OFFICE HOUR
   
   Join RCSB PDB for quick tips on how to use Mol* in the pairwise structure
   alignment tool.
   » 05/13/2024
   

 * POSTER PRIZE AWARDED AT DISCOVERBMB
   
   The wwPDB Foundation awarded Angela Kayll (James Madison University) for her
   poster Solution Structure of the hMDH2-hCS Metabolon.
   » 05/08/2024
   

 * CELIA SCHIFFER ELECTED TO NATIONAL ACADEMY OF SCIENCES
   
   Schiffer is Chair of the wwPDB Foundation
   » 05/07/2024
   

 * VIDEO: HOW NEURONS COMMUNICATE
   
   Visit PDB-101 to watch An Introduction to Neurotransmission and Action
   Potential
   » 05/05/2024
   


MOLECULE OF THE MONTH

INJECTISOME

Salmonella bacteria inject a cocktail of effector proteins into cells to disable
their defenses.

Read More


QUARTERLY NEWS (SEE ARCHIVE)

ISSUE 101 - APRIL 2024

Training Opportunities; a Python Package to Access the Search API; a new Cancer
Molecular Animation; and more.

Building and Animating Catalase in a High School Classroom by Emerson Newton,
John H. Pitman High School.

 * Winter 2024 Issue
 * Fall 2023 Issue
 * Summer 2023 Issue
 * Spring 2023 Issue




ANNUAL REPORTS

2023 ANNUAL REPORT

Download the 2023 Annual Report (PDF) for an overview of recent activities,
including RCSB PDB APIs and pairwise alignment tools.

Annual Report Archive


PDB at a Glance
68,768
Structures of Human Sequences
17,775
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 U.S. National Science Foundation
(DBI-2321666), 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.

To update/release in-progress structure depositions: access OneDep

For questions/corrections to specific PDB entries, including citation updates:
contact deposit-help@mail.wwpdb.org

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