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 PDBe main page in all its glory
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. More Useful than having Swiss Army Knife Fingers!
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. We want to look at some specific search tools though
The Protein DataBank
We want to look at some specific search tools though

31. Sequence similarity Search
The Protein DataBank
Sequence similarity Search

32. Sequence Similarity Search Results