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PDBemotif

PDBemotif. A web based integrated search service to understand ligand binding and secondary structure properties in macromolecular structures. PDBe-motif ( http://www.ebi.ac.uk/pdbe-site/PDBeMotif ). Integrated search system for protein and nucleic acid structures.

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PDBemotif

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  1. PDBemotif A web based integrated search service to understand ligand binding and secondary structure properties in macromolecular structures

  2. PDBe-motif (http://www.ebi.ac.uk/pdbe-site/PDBeMotif) • Integrated search system for protein and nucleic acid structures. • User can construct a query based on - a) Ligands and their 3D environment b) protein families (SCOP, CATH, UNIPROT, EC-number) c) protein secondary structures and different 3D motifs (PROSITE, beta turn, catalytic sites etc.) d) protein Φ/Ψ angle sequences • Results - a) Sequence multiple alignment b) 3D multiple alignment of fragments, motifs and protein chains. c) Interactions statistics d) Motifs characteristics and properties distribution charts. 2

  3. Comparing two ligand binding sites What is the environment aroundalpha-D-mannoseandbeta-D-mannose?

  4. Query based on binding environment What binds ASP ASP HIS LYS ?

  5. PDBesite-interaction between a ligand and a residue How does ATP generally interact with LYS in all structures ?

  6. The PDBe-motif Search Interface

  7. Different Search Options - • PDB Header Search – PDB ID, Experiment Type, author name …. • Molecule Binding – Ligand 3-letter code, metal site geometry – looking for covalent, H-bonds, Van der Waals, planar interactions – distribution against amino acids, nucleic acids, ligands, Prosite motifs etc. • Pair bonds – interactions statistics between a pair of residues (Ligand-aminoacid, ligand-ligand, ligand-nucleic acid etc.) • Motif binding – search for sequence pattern –distribute against ligands, secondary structures, 3D motifs • Search – combine different sources of data generate your query • Upload your own PDB file for analysis

  8. Starting a Search Using Sucrose Specific porin as an example to explore the site

  9. Sequences 3Dmotif Ligand environment Ligand bonds Results

  10. Secondary Structure pattern aa sequence Ligand binding Searching further based on Secondary structures

  11. 1a0t

  12. 3D-Motifs: Motif information for each chain and bound ligands presented individually

  13. Search Results for 1a0t –based on 3D motif configuration(195:IHWI,196:HWID) Predominant secondary structure element – beta sheets

  14. Predominantly beta sheet but tertiary structure quite different Something Interesting!!!! 1a0t 1ofm

  15. Both cases the 3D motif is engaged in interacting with hexose sugar moieties Significance in structure-function relationships

  16. Residues are colour coded based on their nature of interactions with the ligand Provides detailed 3dimensional information about the ligand binding environment Ligand Binding Environment

  17. Sucrose Binding • Aromatic amino acid sidechains (Tyr, Phe) are parallel to hexose/pentose sugar ring – helps in gliding mechanism • Lots of charged amino acids in the environment-facilitating the transport

  18. Calcium Binding Lots of negatively charged amino acids

  19. What type of PROSITE pattern is involved in binding a 4Fe-4S cluster?

  20. Interaction Statistics • Clicking on each bar returns a list of PDB entries • The bars are proportionally colour coded based on the nature of interactions between the ligand and motif

  21. How does GTP interact with LYS?

  22. Statistics -Binding Interactions GTP vs Lys Colour coded based on nature of interactions

  23. Combining Different Search Items

  24. Pattern search

  25. Search for Small Molecule

  26. Combining both the queries

  27. Multiple 3D Alignment of GXXXXGKT motif/Walker A motif Particular amino acid sequence giving rise to secondary structure pattern – defining role in cellular processes

  28. PDBe-Site – Another Useful Tool to Analyse Ligand Environment

  29. Search options in the PDBe-site page • Define search by ligand • Define search by sequence motif (pattern) • Define search by metal site geometry • Define search by environment • has same environment • has similar environment Upload your own PDB file for analysis !!

  30. Compare ligand environments. Analyze interactions between ligand and protein. Compare binding environment. Look for ligands within a certain environment. Superpose binding sites and ligands. Predict what could bind that empty pocket in your structure PDBesite Results Page Some uses of the data obtained from PDBesite analysis:

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