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Mining PSI Structures: JCSG Ligand Server

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Presentation on theme: "Mining PSI Structures: JCSG Ligand Server"— Presentation transcript:

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 Disorder: The idea here is to develop a script that would quantify the side chain disorder so that trimming of the side chain can be done in a more objective manner than simply by looking at the density. And similarly for NCS-mismatch: develop a script to automatically identify NCS-mismatches and deviations instead of looking at every residue in the aligned structure.

3 Introduction and History
Herb’s compilation of JCSG data Porting Excel sheet to Web server Automating tasks

4 Examples of Use

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

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

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

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

9 Non-metal 21 in PSI,12 in JCSG
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 Cryo # of times used # of times observed in structure EDO 230 179 (77.8 %) GOL 213 93 (43.7 %) MPD 66 23 (34.8 %) PEG200 56 18 (32.0 %) PEG400 35 10 (28.6 %)

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

13 Organisms (265, 94)

14 Structures by PSI Centers

15 Unique Ligands (25) in PSI Structures
PDB ID Ligand Name ID Center 1KPH, 1KPI Didecyl-Dimethyl-Ammonium 10A TBSGC 1X92 D-Glycero-D-Mannopyranose-7-Phosphate M7P MCSG 1LW4 3-Hydroxy-2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl- Pyridin-4-Ylmethyl)-Amino]-Butyric Acid TLP NYSGXRC 2B4B N-Ethyl-N-[3-(Propylamino)Propyl]Propane- 1,3-Diamine B33 1O8B Beta-D-Arabinofuranose-5'-Phosphate ABF 1RTW (4-Amino-2-Methylpyrimidin-5-Yl)Methyl Dihydrogen Phosphate MP5 NESG 1TUF Azelaic Acid AZ1 2PUZ N-(Iminomethyl)-L-Glutamic Acid NIG 2OU3 1h-Indole-3-Carbaldehyde I3A JCSG 2OSU 6-Diazenyl-5-Oxo-L-Norleucine DON 1M33 3-Hydroxy-Propanoic Acid 3OH 2Q09 3-[(4s)-2,5-Dioxoimidazolidin-4-Yl]Propanoic Acid DI6 1N2H, 1N2I Pantoyl Adenylate PAJ 2GVC 1-Methyl-1,3-Dihydro-2h-Imidazole-2-Thione MMZ 1BVR Trans-2-Hexadecenoyl-(N-Acetyl-Cysteamine)- Thioester THT 1Y80 Co-5-Methoxybenzimidazolylcobamide B1M SECSG 2A3L Coformycin 5'-Phosphate CF5 CESG 1VR0 (2r)-3-Sulfolactic Acid 3SL 2NW9 6-Fluoro-L-Tryptophan FT6 1Y0G 2-[(2e,6e,10e,14e,18e,22e,26e)-3,7,11,15,19,23,27,31- Octamethyldotriaconta-2,6,10,14,18,22,26,30- Octaenyl]Phenol 8PP 1QPR 5-Phosphoribosyl-1-(Beta-Methylene) Pyrophosphate PPC 1Z2L Allantoate Ion 1AL 1XKL 2-Amino-4h-1,3-Benzoxathiin-4-Ol STH 1P44 5-{[4-(9h-Fluoren-9-Yl)Piperazin-1-Yl]Carbonyl}- 1h-Indole GEQ 2OD6 10-Oxohexadecanoic Acid OHA

16 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_ ) from Nostoc Punctiforme PCC (2OU3) 10-Oxohexadecanoic acid (OHA) bound to Ferredoxin-like protein (JCVI_PEP_ ) from an environmental metagenome (unidentified marine microbe) (2OD6)

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

18 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

19 Unique binding modes observed in different PFAM families
PSI Non-PSI Total PF01070 FMN-dependent dehydrogenase 8 PF00881 DHOdehase 9 17 PF00258 Flavodoxin _1 3 13 16 PF00724 Oxidored._FMN 2 10 PF01613 Flavin reductase-like 7 PF01180 Nitroreductase 1 PF01243 Pyridox._oxidase 14 21

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

21 (Flavin reductase-like)
PF01613 (Flavin reductase-like) PF01180 (Nitroreductase) PF01243 (Pyridox._oxidase)

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
And finally, thanks to Chris and Ashley for many discussions. The NVS script is now part of Chris’s QC script. The disorder script will soon be added to it.

25 JCSG Annual Meeting 2007

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