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Mining PSI Structures: JCSG Ligand Server

Mining PSI Structures: JCSG Ligand Server. Abhinav Kumar Structure Determination Core. Outline. Introduction and history Examples of use (live) Statistics Unique ligands Binding mode studies Usage. Introduction and History.

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Mining PSI Structures: JCSG Ligand Server

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  1. Mining PSI Structures:JCSG Ligand Server Abhinav Kumar Structure Determination Core

  2. Outline • Introduction and history • Examples of use (live) • Statistics • Unique ligands • Binding mode studies • Usage

  3. Introduction and History http://smb.slac.stanford.edu/public/jcsg/cgi/jcsg_ligand_check.pl • Herb’s compilation of JCSG data • Porting Excel sheet to Web server • Automating tasks • Andrew’s script to produce the list of PSI structures released by PDB • Script to download the pdbs and extract relevant information • Database for the Ligand server

  4. Examples of Use

  5. Live • Examples of query entry • Executing search • Explanation of links in the search results • Summary

  6. PSI: solid bar JCSG: open bar 288 158 92 27 Distribution of Ligands Number of Structures and unique Compounds

  7. 18/22 (SECSG) Ligands 67/74 (JCSG)

  8. Co-factors 22 in PSI, 20 in JCSG Organics 22 in PSI, 6 in JCSG

  9. Ions Metal 24 in PSI,10 in JCSG Non-metal 21 in PSI,12 in JCSG

  10. Buffers (14,10) Precipitants (13,9) Cryos

  11. Cryo-protectant agents in JCSG Structures

  12. 12 9 6 5 9 10 9 4 7 5 10 10 11 7 10 13 15 8 6 9 14 11 Number of ligands 15 11 14 13 10 18 11 14 18 PFAMs (1292 in PSI, 392 in JCSG)

  13. Unique Ligands (25) in PSI Structures

  14. Examples of Unique Ligands (R)-2-Hydroxy-3-Sulfopropanoic acid (3SL) bound to the putative 2-phosphosulfolactatetitle 2 phosphatase from Clostridium Acetobutylicum (1VR0) Indole-3-Carboxaldehyde (I3A) bound to tellurite resistance protein of COG3793 (ZP_00109916.1) from Nostoc Punctiforme PCC 73102 (2OU3) 10-Oxohexadecanoic acid (OHA) bound to Ferredoxin-like protein (JCVI_PEP_1096682647733) from an environmental metagenome (unidentified marine microbe) (2OD6)

  15. Unknown Ligands (UNL) FB8805A (2Q9K) Protein of unknown function FK9436A (2OH1) Acetyltransferase Gnat family

  16. Binding Mode Studies • Several ligands/co-factors bound to the proteins • Binding mode studies for co-factors • FMN as an example • FMN bound in over 340 structures in RCSB • Binding mode variation in due to the torsional flexibility in the molecule

  17. Unique binding modes observed in different PFAM families

  18. PF01070 (FMN-dependent dehydrogenase ) PF00881 (DHOdehase) PF00258 (Flavodoxin _1) PF00724 (Oxidored._FMN )

  19. 1y30 PF01613 (Flavin reductase-like) PF01180 (Nitroreductase) PF01243 (Pyridox._oxidase)

  20. PF01264 Two structures of Chorismate Synthase 1qxo, 1um0

  21. First Structures in PFAMs for Protein-Ligand complexes

  22. Page Visits (36 different domains) Tracking since September 2007

  23. Scientific Advisory Board Sir Tom Blundell Univ. Cambridge Homme Hellinga Duke University Medical Center James Naismith The Scottish Structural Proteomics Facility Univ. St. Andrews James Paulson Consortium for Functional Glycomics, The Scripps Research Institute Robert Stroud Center for Structure of Membrane Proteins, Membrane Protein Expression Center, UCSF Soichi Wakatsuki Photon Factory, KEK, Japan James Wells UC San Francisco Todd Yeates UCLA-DOE, Inst. for Genomics and Proteomics GNF & TSRI Crystallomics Core Scott Lesley Mark Knuth Heath Klock Dennis Carlton Thomas Clayton Marc Deller Daniel McMullan Polat Abdubek Julie Feuerhelm Joanna C. Hale Thamara Janaratne Hope Johnson Edward Nigoghossian Linda Okach Sebastian Sudek Glen Spraggon Bernhard Geierstanger Sanjay Agarwalla Anna Grzechnik Connie Chen Dustin Ernst Regina Gorski Sachin Kale Amanda Nopakun Christina Puckett Tiffany Wooten Jessica Canseco Mimmi Brown Stanford /SSRL Structure Determination Core Keith Hodgson Ashley Deacon Mitchell Miller Herbert Axelrod Hsiu-Ju (Jessica) Chiu Kevin Jin Christopher Rife Qingping Xu Silvya Oommachen Henry van den Bedem Scott Talafuse Ronald Reyes Abhinav Kumar Christine Trame Debanu Das Winnie Lam UCSD & Burnham Bioinformatics Core John Wooley Adam Godzik Lukasz Jaroszewski Slawomir Grzechnik Sri Krishna Subramanian Andrew Morse Tamara Astakhova Lian Duan Piotr Kozbial Dana Weekes Natasha Sefcovic Prasad Burra Konstantina Bakolitsa Andrei Istomin Kyle Ellrott Josie Alaoen Cindy Cook Ex officio founding members JCSG-1 Raymond Stevens , TSRI Susan Taylor, UCSD Peter Kuhn, SSRL/TSRI Duncan McRee, TSRI/Syrrx Peter Schultz, TSRI/GNF TSRI, NMR Core Kurt Wüthrich Reto Horst Maggie Johnson Amaranth Chatterjee Michael Geralt Wojtek Augustyniak Pedro Serrano Bill Pedrini Biswaranjan Mohanty Jin-Kyu Rhee TSRI Administrative Core Ian Wilson Marc Elsliger Gye Won Han David Marciano Henry Tien Lisa van Veen The JCSG is supported by the NIGMS Protein Structure Initiative Grant U54 GM074898

  24. Acknowledgements Herb, Andrew, Ashley

  25. JCSG Annual Meeting 2007

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