PDB FILES FOR TEACHING BIOCHEMISTRY

We have accumulated many PDB files which we feel will be useful in teaching undergraduate Biochemistry. They are arranged according to subject. More information about PDB files can be found in the FAQ section.

Amino Acids: the twenty amino acids plus examples of an alpha-helix and a beta-sheet.
Nucleic Acids: the common DNA and RNA nucleotides, DNA base pairs, and examples of DNA
Cofactors: some common enzyme cofactors
Classic Proteins: 12 classical proteins often studied in Biochemistry
Nucleic Acid Binding Proteins: Eight common nucleic acid binding proteins
Krebs Cycle: most of the enzymes involved in the citric acid cycle
Gluconeogenesis and Glycolysis: most of the enzymes involved in gluconeogenesis and glycolysis
Photosynthesis: many of enzymes the involved in photosynthesis

Frequently asked questions about PDB-files

What are PDB files?

The PDB (Protein Data Bank, from Research Collaboratory for Structural Bioinformatics) format is the standard file format for the XYZ coordinates of atoms in a molecule.

Here are a few lines from the PDB file for the DNA base pair structure directly above.

HEADER    B-DNA
COMPND    G-C B-DNA BASE PAIR  
AUTHOR    GENERATED BY GLACTONE
SEQRES   1 A    1    G
SEQRES   1 B    1    C
ATOM      1  P     G A   1      -6.620   6.196   2.089
ATOM      2  OXT   G A   1      -6.904   7.627   1.869
ATOM      3  O2P   G A   1      -7.438   5.244   1.299
ATOM      4  O5'   G A   1      -5.074   5.900   1.839
ATOM      5  C5'   G A   1      -4.102   6.424   2.779
ATOM      6  C4'   G A   1      -2.830   6.792   2.049
ATOM      7  O4'   G A   1      -2.044   5.576   1.839
ATOM      8  C3'   G A   1      -2.997   7.378   0.649

The last three columns are the XYZ coordinates of the atoms.

How does one view the structures represented in PDB files

To view PDB structures you will need a PDB viewer. One of the best PDB viewers is a program called RasMol. RasMol was written and graciously released into the public domain by Dr. Roger Sayle of GlaxoWellcome.
Follow these instructions to download and install RasMol
1. Go to the RasMol Home Page.
2. Then go to Getting RasMol or Chime and their Manuals
3. Then go to Getting and installing RasMol
4. Now choose your operating system
5. Follow the detailed instructions for installing RasMol on your computer
6. You can also Configure Netscape to use RasMol as a viewer/helper application.
7. Don't forget to get the RasMol Manual

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