Answers.Body: <p>As per google search:</p>
  <p><a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/" rel="nofollow noreferrer">Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody </a> paper :</p>
  <blockquote>
  <p>......Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG 1 antibody prone to self-interaction...</p>
  </blockquote>
  <p>that points to  ---&gt; <a href="https://www.rcsb.org/structure/8TJT" rel="nofollow noreferrer">8TJT The Fab fragment of an anti-glucagon receptor (GCGR) antibody </a></p>
  <p>or using this database: <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab" rel="nofollow noreferrer">SAbDab (The Structural Antibody Database)</a> , citation <a href="https://academic.oup.com/nar/article/42/D1/D1140/1044118" rel="nofollow noreferrer">Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146</a></p>
  <blockquote>
  <p>SAbDab is a database of antibody structures that updates on a weekly basis. Each structure is annotated with a number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations.
  Use the database to:
  Inspect individual structures
  Create and download datasets for analysis
  Search the database for structures with similar sequences to your query
  Monitor the known structural repetoire of antibodies
  SAbDab has been built by the Oxford Protein Informatics Group (OPIG) under an open-innovation agreement.
  If you use our tools, please cite our paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]</p>
  </blockquote>
  <p>and <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/" rel="nofollow noreferrer">searching the database with the option Search structures by attribute and  keyword query </a> using keyword  <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/?ABtype=All&amp;method=All&amp;species=All&amp;resolution=&amp;rfactor=&amp;antigen=All&amp;ltype=All&amp;constantregion=All&amp;affinity=All&amp;isin_covabdab=All&amp;isin_therasabdab=All&amp;chothiapos=&amp;restype=ALA&amp;field_0=Title&amp;keyword_0=aggregation" rel="nofollow noreferrer">&quot;aggregation&quot; </a> in title</p>
  <p>you get these results:</p>
  <pre><code>pdb
  8cpe
  7nxx
  3upc
  3upc
  5lwf
  4m3j
  3upa
  1ohq
  4n1h
  </code></pre>
  <p>and as per comments above 3UPA seems to be a good candidate: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/" rel="nofollow noreferrer">Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-10T17:01:41.933Z
Answers.Text: Thanks @pippo1980 much appreciated. To other site members please upvote this response, it's really helpful. 3UPA is certainly cool.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-10T16:16:19.313Z
Answers.LastActivityDate: 2024-12-10T16:16:19.313Z
Answers.UserDisplayName: pippo1980
Body: <p>I working on (perhaps more specifically, just worked on) antibody self-aggregation, IgG. So this is where one antibody sticks to the Fc or Fab region of another antibody and so on ... resulting in antibody complexes.</p>
  <p>There are experimental data-sets examining self-aggregation, AC-SINS (Affinity-Capture Self-Interacting Nanoparticle Spectroscopy) is one such test and thats cool. However, to make progress on understanding the results I <em>really really</em> need to see a crystal structure, NMR structure etc ... of self-aggregation.</p>
  <p>I am having an extremely difficult time navigating <a href="https://www.rcsb.org" rel="nofollow noreferrer">PDB</a> attempting to find this.</p>
  <p>My request is either:</p>
  <ol>
  <li>Does anyone know a PDB code that directly points to my specific request <em>OR</em></li>
  <li>Anyone have advanced insight into navigating the key word database searches on PDB to find this?</li>
  </ol>
  <p>I can see antibody structures - about 6000 to 7000 of them. How do I filter this for the few examples required here?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-09T21:36:45.140Z
Comments.Text: [Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody](https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/) --> [8TJT The Fab fragment of an anti-glucagon receptor (GCGR) antibody](https://www.rcsb.org/structure/8TJT)
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-09T21:45:02.063Z
Comments.Text: [this search for title word "aggragation" ina a subset of PDB ... I guess/hope](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/?ABtype=All&method=All&species=All&resolution=&rfactor=&antigen=All&ltype=All&constantregion=All&affinity=All&isin_covabdab=All&isin_therasabdab=All&chothiapos=&restype=ALA&field_0=Title&keyword_0=aggregation)
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-09T23:31:43.863Z
Comments.Text: Excellent! Thanks @pippo1980 3UPA is just the ticket and https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/ is cool. Could you provide this answer as a response below? This resolves the issue as well as I could have hoped (slightly better to be honest). Note to mods, please do not delete these comments! until they are formal answers.
Comments.UserDisplayName: M__
Tags: <protein-structure><database><pdb><antibody><igg>
Title: Antibody self-aggregation: PDB structures
ThreadText: # Antibody self-aggregation: PDB structures
  
  (Asked by: username_0 on 2024-12-08)
  
  I working on (perhaps more specifically, just worked on) antibody self-aggregation, IgG. So this is where one antibody sticks to the Fc or Fab region of another antibody and so on ... resulting in antibody complexes.
  
  There are experimental data-sets examining self-aggregation, AC-SINS (Affinity-Capture Self-Interacting Nanoparticle Spectroscopy) is one such test and thats cool. However, to make progress on understanding the results I *really really* need to see a crystal structure, NMR structure etc ... of self-aggregation.
  
  I am having an extremely difficult time navigating [PDB](https://www.rcsb.org) attempting to find this.
  
  My request is either:
  
  1. Does anyone know a PDB code that directly points to my specific request *OR*
  2. Anyone have advanced insight into navigating the key word database searches on PDB to find this?
  
  I can see antibody structures - about 6000 to 7000 of them. How do I filter this for the few examples required here?
  
  **Tags:** protein-structure, database, pdb, antibody, igg
  
  > **Comments:**
  > **username_1**: [Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody](https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/) --> [8TJT The Fab fragment of an anti-glucagon receptor (GCGR) antibody](https://www.rcsb.org/structure/8TJT)  
  > **username_1**: [this search for title word "aggragation" ina a subset of PDB ... I guess/hope](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/?ABtype=All&method=All&species=All&resolution=&rfactor=&antigen=All&ltype=All&constantregion=All&affinity=All&isin_covabdab=All&isin_therasabdab=All&chothiapos=&restype=ALA&field_0=Title&keyword_0=aggregation)  
  > **username_0**: Excellent! Thanks @username_1 3UPA is just the ticket and https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/ is cool. Could you provide this answer as a response below? This resolves the issue as well as I could have hoped (slightly better to be honest). Note to mods, please do not delete these comments! until they are formal answers.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-12-10. Score: 1 | Accepted answer
  
  As per google search:
  
  [Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody](https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/)  paper :
  
  > ......Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG 1 antibody prone to self-interaction...
  
  that points to ---> [8TJT The Fab fragment of an anti-glucagon receptor (GCGR) antibody](https://www.rcsb.org/structure/8TJT)
  
  or using this database: [SAbDab (The Structural Antibody Database)](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab) , citation [Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146](https://academic.oup.com/nar/article/42/D1/D1140/1044118)
  
  > SAbDab is a database of antibody structures that updates on a weekly basis. Each structure is annotated with a number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations.
  > Use the database to:
  > Inspect individual structures
  > Create and download datasets for analysis
  > Search the database for structures with similar sequences to your query
  > Monitor the known structural repetoire of antibodies
  > SAbDab has been built by the Oxford Protein Informatics Group (OPIG) under an open-innovation agreement.
  > If you use our tools, please cite our paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]
  
  and [searching the database with the option Search structures by attribute and keyword query](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/)  using keyword ["aggregation"](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/search/?ABtype=All&method=All&species=All&resolution=&rfactor=&antigen=All&ltype=All&constantregion=All&affinity=All&isin_covabdab=All&isin_therasabdab=All&chothiapos=&restype=ALA&field_0=Title&keyword_0=aggregation)  in title
  
  you get these results:
  
  ```
  pdb
  8cpe
  7nxx
  3upc
  3upc
  5lwf
  4m3j
  3upa
  1ohq
  4n1h
  
  ```
  
  and as per comments above 3UPA seems to be a good candidate: [Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody](https://pmc.ncbi.nlm.nih.gov/articles/PMC10813588/)
  
  > **Comments:**
  > **username_0**: Thanks @username_1 much appreciated. To other site members please upvote this response, it's really helpful. 3UPA is certainly cool.  
  
  ---
  
  