EBI is an Outstation of the European Molecular Biology Laboratory. A web based integrated search service to understand ligand binding and secondary structure properties in macromolecular structures PDBemotif

PDBe-motif ( 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.

3 The PDBe-motif Search Interface

4 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

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

6 Results Sequences 3Dmotif Ligand environment Ligand bonds

7 1.Secondary Structure pattern 2.aa sequence 3.Ligand binding 4.Searching further based on Secondary structures

8 1a0t

9 3D-Motifs: Motif information for each chain and bound ligands presented individually

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

11 1ofm 1a0t Predominantly beta sheet but tertiary structure quite different Something Interesting!!!!

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

13 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

14 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

15 Calcium Binding Lots of negatively charged amino acids

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

17 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

18 How does GTP interact with LYS?

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

20 Combining Different Search Items

21 Pattern search

22 Search for Small Molecule

23 Combining both the queries

24

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

26 PDBe-Site – Another Useful Tool to Analyse Ligand Environment

Macromolecular Structure Database 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 Search options in the PDBe-site page Upload your own PDB file for analysis !!

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

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

Macromolecular Structure Database MSDsite query based on binding environment What binds ASP ASP HIS LYS ?

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