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 2

3. Comparing two ligand binding sites
What is the environment around alpha-D-mannose and beta-D-mannose? 3

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 ? 5

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. Results
Sequences
3Dmotif
Ligand environment
Ligand bonds

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

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

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

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

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

30. 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

31. PDBesite Results Page
Some uses of the data obtained from PDBesite analysis:
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