Molecular Machinery
A Tour of the Protein Data Bank

Scale (nm):
1
5
10
1nm (nanometer) = 10-6 millimeters
Small molecules
Digestive Enzymes
Blood Plasma
Viruses and Antibodies
Hormones
Channels, Pumps
and Receptors
Photosynthesis
Energy Production
Storage
Enzymes
Infrastructure
Protein Synthesis
DNA
About
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Extracellular
Membrane
Intracellular/Cytosol
Intracellular/Nucleus
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Style
Cartoon
Spheres
Trace
Ball and Stick
Color
Rainbow
Chain
Secondary Structure
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About the Molecular Machinery Viewer

This interactive view of molecular machinery in the PDB archive lets users select a structure, access a 3D view of the entry using Protein Viewer (PV; biasmv.github.io/pv), read a brief summary of the molecule’s biological role, and access the corresponding PDB entry and Molecule of the Month column.

Turning the“Auto Mode” option to “On” launches an automated tour of the structures that highlights the different categories of structures and the individual examples. The 3D view uses PV to rotate the molecule, change styles, and zoom in/out of the molecule. This mode can be used as a screensaver or as a kiosk display.

Click here to see the PDF Print Version of this poster (~23MB).

Authors: David S. Goodsell, Maria Voigt, Rob Lowe

About the Protein Data Bank archive

Cells build many complex molecular machines that perform the biological jobs needed for life. Some of these machines are molecular scissors that cut food into digestible pieces. Others then use these pieces to build new molecules when cells grow or tissues need to be repaired. Some molecular machines form sturdy beams that support cells, and others are motors that use energy to crawl along these beams. Some recognize attackers and mobilize defenses against infection.

Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. A few examples from the ~100,000 structures held in the PDB are shown here with each atom represented as a small sphere. The enormous range of molecular sizes is illustrated here, from the water molecule (H2O) with only three atoms to the ribosomal subunits with hundreds of thousands of atoms.