Exercises for Chapter 3 – Structural Bioinformatics Databases of General Use

Use of PDBe

Sodium-potassium pumps take almost 1/5 – 2/3 of energy produced within cells. In this exercise, we will try to find, how can be such important protein analyzed from the structural point of view. Search PDBe for Na+/K+ ATPase structures for the one with best resolution and obtain:
      1. PDB ID with resolution and source organism,
      2. present ligands,
      3. number of individual chains,
      4. secondary structure of gamma subunit,
      5. functions and other GO annotations.
Macromolecules are usually present in PDB database as an asymmetric unit, whereas biological function can be provided by macromolecular assembly. Prime examples of such behavior are viral capsid proteins.
      1. Find how many viral capsid proteins are needed for building of empty canine parvovirus viral capsid.
      2. PDBe contains also data from electron microscopy (EM) therefore it is possible to compare experimental EM data directly with built atomistic model. One of canine parvovirus capsid proteins was resolved using EM. Try to compare built in model with EM volume map from EMDB. Does the EM map support preferred theoretical assembly from previous question?

Use of RCSB and ChEMBL

Human protein kinases are regulation proteins important not only for cell cycle, however their involvement in the cell cycle regulation is their key property for certain class of cancerostatic therapeutics in current development and clinical  trials. In this exercise, we will look into a prime example of kinase inhibitor – roscovitine. Look for roscovitine among ligands in RCSB.
      1. Find its 2D structure.
      2. With what proteins it was crystalized? List their PDB ID as well as protein name.
      3. The typical target for roscovitine is cyclin-dependent kinase 2 (CDK2), look into the complex of ligand id RRC with CDK2 and list all amino acids, with which it interacts.
      4. How active inhibitor is roscovitine? Find any values indicating how well will roscovitine bind to CDK2.
      5. Finally – look into ChEMBL for CDK2 inhibitors, which undergo clinical trials.

Use of PDBsum

Let’s return to sodium-potassium pump – PDBsum can be also used for further analysis, which is not present in PDBe, nor in RCSB, so let’s have once again have a look on PDB ID 2zxe:
      1. Identify ligand clusters present in sodium-potassium pump α subunit.
      2. Is the structure of cholesterol present in the structure correct?
      3. Identify catalytic residues.
      4. Which parts of β subunit are the least conserved?
      5. Does FXYD protein have more protein-protein contacts to α or β subunit? What type of amino acids form majority on the interfaces? Are there present inter-protein disulphide bonds?

Use of CATH

CATH database sorts structures into homologous CATH superfamilies, where it collects common properties of proteins within given superfamily.
    1. Find CATH superfamily for cytochrome P450 proteins.
    2. Decode CATH code for this family with structural description.
    3. What are the most typical GO terms annotated with this superfamily?
    4. What is the typical reaction catalyzed by this enzyme?
    5. Use Gene3D to find how frequent this protein domain is between species. Which kingdom uses this domain the most?
    6. Identify the smallest and largest representatives of this domain family?

Solutions to exercises

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