Record of 3D Macromolecular Structure Observations
for Protein Explorer (Basic Level Form)

by Eric Martz, May 2000     Basic PDF     Advanced Level Form
Discovery in Protein Explorer offers a simpler list of questions.

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Protein Explorer development is supported by the National Science Foundation.

Your Name _______________________________________ PDB ID Code ________

Name of Molecule ______________________________________________________

  1. How many chains are there?
    Chain Name*
    Protein, DNA, or RNA?
    Number of Residues? **
    Alpha helices? ***
    Beta strands? Parallel/antiparallel? ***
    *Hint: click on the chain and look for the one-letter "name" in the message window.
    **Hint: use the Sequence display (click PE Site Map, then Sequences).
    ***Hint: in QuickViews, DISPLAY Cartoon, COLOR Structure.

  2. Is water present?


  3. Are bound ligands present (non-solvent "hetero" atoms)? If so, are they held by covalent or noncovalent bonds? To what types of residues? (Hint: SELECT Ligand, DISPLAY Contacts. Click on bonded atoms to identify their residues.)




  4. In soluble proteins, hydrophobic residues are buried in the cores of domains. Large hydrophobic patches on the surface may be sites of protein-protein interaction. Where do you see concentrations of hydrophobic residues? (Hint: DISPLAY Spacefill, COLOR Polarity3.)




  5. If there is protein bound to nucleic acid, which nucleotides are recognized in a sequence-specific manner? Which are bound nonspecifically to the backbone? (Hint: SELECT Protein, DISPLAY Contacts, click on bound atoms to identify residues.)




  6. Comments/special features?