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Getting the Most out of the PDBe

Getting the Most out of the PDBe. The Protein Databank can be accessed from two URLs: The North American DB: RCSB.org The European Molecular Biology Laboratory: pdbe.org

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Getting the Most out of the PDBe

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  1. Getting the Most out of the PDBe • The Protein Databank can be accessed from two URLs: • The North American DB: RCSB.org • The European Molecular Biology Laboratory: pdbe.org • Both sites contain the same information, but the interfaces are completely different and offer different interpretations of the data • Before we can start mining these databases though, we need to look at what the databases hold…

  2. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… We can find information about the protein itself, the original organism, the expression host, the authors and the journal in which the structure was published in the first part of the header. (The numbers adjacent to the REMARK comments change with each section type)

  3. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… The next REMARKS tell us about the actual experimental data used to determine the structure.

  4. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… The next REMARKS tell us about the actual experimental data used to determine the structure. The next REMARKS tell us about the parameters of the model

  5. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… The next REMARKS tell us some more about the actual experimental data used to determine the structure. The next REMARKS tell us about the Symmetry and Spatial Relationships within the model

  6. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… Then we read about residues for which no electron density was observed Then we learn about possible problems in the model

  7. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… Then we learn some more about the model

  8. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… The we have the amino acid sequence of every protein molecule found in the Unit Cell Note: There are two chains (A and B)

  9. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… Then we have the secondary structural assignments This is how Chimera knows what to select when you type: “sel :/isHelix” or “sel :/isSheet”

  10. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… Certain amino acids are involved in cis- peptide bonds… And then we have the coordinates of all the residues! Finally.

  11. What is a PDB File? Let’s go ahead and look at 3gtn.pdb… Always scan to the end of the file. Hetero atoms, Water molecules (HOH) and ligands are down here. You can actually cut these coordinates out and paste them into a fresh document of you’d like.

  12. What is a PDB File? Remember: A PDB file is just a text file containing information that other programs can parse. You can learn a lot about your proteins from the PDB file, so always open them up and look at them when you download them from…

  13. The Protein DataBank The PDBe main page in all its glory

  14. The Protein DataBank The first three options on the main tab set are DEFINITELY worth looking at

  15. The Protein DataBank Lost?

  16. The Protein DataBank Questions?

  17. The Protein DataBank More Useful than having Swiss Army Knife Fingers!

  18. If you typed in a PDB ID Code from the BioBar… The Journal article describing the structure…

  19. If you typed in a PDB ID Code from the BioBar… Experimental Details

  20. If you typed in a PDB ID Code from the BioBar… Details about the Primary and Secondary Structures the Protein (IMPORTANT!!!)

  21. If you clicked the “Protein” Button on the Main Entry Page… Follow all the Links!

  22. If you typed in a PDB ID Code from the BioBar… Details about any ligands that may be bound

  23. A Thought on the number of Chains in the Files Protein Structure Files OFTEN Contain more than one molecule (crystallization effect, NMR ensemble) THIS DOES NOT MEAN THAT THE BIOLOGICALLY RELEVANT UNIT HAS QUATERNARY STRUCTURE

  24. The PDBsum Link: The Most Important Thing You’ve never used…

  25. The PDBsum Page for 3gtn These links can provide you with access to a variety of information!

  26. The Protein Tab of PDBsum for 3gtn Primary/Secondary Structure Overlay Topology Diagram Down here there are interesting links as well!

  27. PDBsum: Conserved Residue Information Conserved residues from a multiple structural alignment (You don’t have any control over this though…)

  28. Shut the Front Door! Predicted Binding Sites?! (From Volume Analysis)

  29. Boom! That was my head exploding after I clicked on the ‘Links’ tab

  30. The Protein DataBank We want to look at some specific search tools though

  31. The Protein DataBank Sequence similarity Search

  32. Sequence Similarity Search Results

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