Protein 3D-structure analysis Exercises

Practicals Find update frequency for RCSB PDB: weekly. When was the last update? How many protein structures are there in wwPDB?

Practicals How many NEW structures were deposited in 2010 vs 2011? Hint: try this at PDBe vs RCSB PDB Much easier at RCSB PDB:

Practicals How many structures determined by X-ray crystallography, NMR, Electron microscopy? Use Advanced Query at RCSB PDB

Find the structure with the highest resolution at RCSB PDB axLabel=5&numOfbars=10&name=Resolution

How many structures determined by X-ray crystallography, NMR, Electron microscopy? Use advanced Query at PDBe

At RCSB PDB, find structures with imatinib as ligand. How many structures contain this ligand? What type of proteins contain this ligand? Use advanced query. Verify using the PDB ID for imatinib=STI Answer: Protein kinases

Amongst proteins with bound imatinib, there are structures for p38. Find the official protein and gene name of p38 Most easily done via the UniProt entry Find the UniProt AC for p38.

Find structures for a human protein kinase with bound ADP and a resolution between 2 and 2.5 A: Use main query window, find structures with ligand ADP, then use options (Species, Resolution, Enzyme classification, …) to filter the result

Identifiy the residues that form hydrogen bonds with the product, via PDBsum and from the RCSB PDB website: e.g. 2IJM bin/pdbsum/RunLigplot.pdf?pdb=2ijm&pdf=YES&file=ligplot02_01 and Ligand Explorer from RCSB PDB (shown below)

At RCSB PDB, find structures for proteins similar to p38 Query: p38 imatinib in main search window, choose 3HEC: You get kinases

find structures for proteins similar to p38 via the DALI database (FSSP link on PDBsum page). What kind of proteins do you recover?

Sequence: Use the sequence of human PLK4 to find a matching structure (advanced search tools)

Get sequence:

Look at protein structure classification in CATH and SCOP (e.g. via links for 3BRB from PDB or PDBsum). The aim is essentially to see that there are quantitative means to classify domain structures No hit in SCOP, so try keyword search, or start at top of hierarchy lmb.cam.ac.uk/scop/search.cgi?ver=1.75&key=kinase&search_type=scop

How many PDB structures are represented in CATH and in SCOP? What is the reason for the difference relative to the total number of experimental structures? Check their home pages: More automated procedures can handle more data – human beings can handle less data, but using your brains adds extra value

Starting with the structure for human FTO, find other proteins with similar 3D-structure via PDB or DALI (FSSP) : What kind of proteins do you find (function, taxonomy)? Answer: dioxygenases, more specifically ALPHA-KETOGLUTARATE- DEPENDENT DIOXYGENASE Taxons: Mammalia (alkB homologs), and bacteria (alkB from E.coli) What are their ligands? Answer: alpha-ketoglutarate and iron

Do an alignment based on the 3D-structure and check if the ligand- binding residues are conserved. Do this with entries from closely related/different taxons. A)Get the ligand-binding sites using PDBsum, UniProt annotation, or Ligand explorer B) Get an alignment from RCSB PDB or DALI pw_fatcat&mol=3LFM.A&mol=2IUW.A Very low sequence identity, but secondary structure is almost the same. Binding sites for catalytic iron (HxD and H) are boxed

Can you get the same proteins, doing a normal BLAST search with FTO? Answer: No, they are too different Have a look at the domain structure (InterPro) of FTO and the proteins that you identified. Compare InterPro lines: they are different

Find 3D-structures for transthyretin at RCSB PDB, then look for proteins with similar 3D-structure Similar structure: 2H6U What is the function of transthyretin, respectively of other proteins with similar structure? Have a look at the corresponding UniProt entries! How are they classified at CATH / at SCOP? Use text search NB: the proteins are too similar to be distinguished by these means

More things to do (facultative) Find protein structures with aspirin as ligand Find the chemical structure for aspirin Get all structures with the ligand aspirin. How many are there? -Go to CHEBI, get Smiles for aspirin CC2078A6?chebiId=CHEBI:15365http:// 01CC2078A6?chebiId=CHEBI: Go to RCSB PDB, use advanced search (smiles) -You can also try and draw “aspirin” using CHEBI