EXERCISES
Protein Data Bank Europe@EBI
1a. Go to the PDBelite webpage (http://www.ebi.ac.uk/msd-srv/msdlite/).
Try and construct a query to retrieve the PDB entry which were solved using X-Ray crystallography
method between 1.5-2.8 Angstrom resolution, has TRANSFERASE as a keyword, and pyridoxal phosphate
(PLP) as a bound ligand and click search.
(hint: type the above parameters e.g. 1.5-2.8, transferase and PLP in the corresponding empty sections of
the query page. Also on the results part, if you are interested in viewing certain information click on those
options. For example if you are interested in know which organism the protein comes from click on
“UniProt acc num”, if you are interested in knowing who the author is click on “Entry Author” or if you
want to know what type of assembly the protein forms (e.g. monomer, dimmer, hexamer etc ) then click on
“Assembly Type”.)
1b. From the list of PDB entries returned by the above query, explore the PDB ID code “1daa”. What is the
name and source of the protein in PDB entry 1daa? How many chains are there? Do you think this protein
acts as an enzyme? If yes, what is the EC number? What is the Uniprot accession ID for this protein? Are
there any related structures available in the database? How can you find them?
(hint: to find the related entries, click on the “Cross references” button on the atlas page for PDB entry
1daa. Under this section look under the Uniprot section for “Other entries”).
1c. Explore the structure of 1daa using Astex viewer visualization. Can you explore the binding
environment for PLP using Astex viewer? How many amino acid residues are in the immediate binding
environment of PLP within a distance of 3.6 Angstroms?
(hint: In the visulaisation section of the Atlas page for 1daa, click on the option saying “View the PDB
entry using AstexViewer™@PDBe-EBI”. This will display the structure of 1daa. On the different options
displayed on the left hand column of Astex viewer, click on the “Chemistry Option” for PLP. This will
display the neighbouring residues of PLP. If you manipulate the distance bar on top of this page you can
visualize the residues which are at maximum distance of 3.6 Angstrom from PLP).
2a. Using the PDBechem service find the ligands which has the following substructure in common.
(hint: draw the above structure using “nonstereosmile option” .This search may take up to few minutes)
2b. How many ligands do you find containing the above substructure?
2c. Check the ligand BSP from the Results list. What is the chemical formula for this ligand? Which PDB
entry is this ligand associated with?
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2d. Go to the Atlas page for the associated PDB entry and find out what type of protein does this ligand
bind to? Are there any other ligands present in this PDB entry? If yes, what are they? What is the source of
this protein?
3a. Using the PDBemotif service find out which of the ligands has 4 histidines in their binding
environment.
hint: go to the 3D Environment search page for PDBE motif and type 'HIS HIS HIS HIS' in the option
provided for amino acids. Then click on “build statistics”
3b. Do you find any particular substructure of ligand predominantly having 4 histidines in their binding
environment?
hint: look at the structure of HEM, HEC ....
3c. Click on the bar for HEM to find out the list of PDB entries which has 4histidine residues. From the
Header information of the list of PDB ID codes what do is your primary guess for the function of HEM
binding proteins?
3d. From the list of PDB entries, find out the ligand binding environment for 1a3o.
(hint: click on link 1a3o, and this will point towards the results page for 'SEQUENCES'
describing secondary structure elements for 1a3o. On the top of the page you will find the link 'Ligand
Environment', click on the link and this will take you to the page you are looking for.)
3e. What type of interaction does HEM has with amino acid HIS?
3f. Try to do a multiple 3d alignment between the ligand binding environment of HEM from PDB entry
1a3o and HEA from PDB entry 2dyr. What is the main difference between the ligands HEM and HEA?
(hint: Go to the ligand environment page for 1a3o as described before and check the box next to one of the
HEM ligand present in the PDB entry and click on 'ADD TO THE MULTIVIEW PAGE'. In a similar
manner for 2dyr, add the ligand HEA to the MULTIVIEW page. Check the boxes next to both the entries
in the MULTIVIEW RESULTS page and remember to check the box for align by 'environment'. Now you
will be able to view the superimposed binding environment for both the ligands)
3g. Which atom of HEM forms covalent interactions with the NE2 atom of HIS? If you want to find out all
possible interactions between HEM and HIS present in the PDB Archive how will you proceed?
(hint: In the ligand environment page for 1a3o, click on the colour-coded HIS residue(red). This will show
you all the interactions between HEM and HIS for this particular PDB entry. To search the entire PDB
archive for interactions between HEM and HIS, click on the green graph symbol located on the top of this
page.)
3h. How will you find out which amino acid side chains have maximum interactions with HEM across the
PDB archive?
(hint: click on the red graph symbol below HEM in the Ligand environment page for 1a3o)
4a. Type the PDB ID code 1E94 in the PISA submission page. How many protein chains are present in the
PDB entry?
4b. Click on the “assemblies” button and find out the probable quaternary structures for this entry. What
are the different types of complexes formed by the protein chains present in the PDB entry? For each of the
predicted assemblies, what is the solvation free energy gained upon the formation of these complex
structures? What is the total surface area and the buried surface area for these assemblies?
4c. Click on the “interfaces” button and find out for chains 1)A and B, 2)C and D, 3)E and F how many Hbonds and saltbridges are formed between them.
4d. Did you find any covalent or disulphide bonds between the protein chains?
5a. For PDB entry 1daa which you have explored before, run an PDBefold search for this entry. What is
the percentage of amino acid sequence identity between this entry and the PDB entry 1i1k? What is the
percentage of secondary structure identity between the above two proteins? What is the source of the
protein 1i1k? Why do you think their %secondary structure identity is so high compared to their %amino
acid identity?
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