Jump to: CHIME/Rasmol, SwissPDB Viewer, MAGE, PDB, NDB, NIH
All macromolecular structures (proteins, DNA, and RNA) are deposited at the Protein Structure Database. Using simple or fancy search engines, one can search for your structure of interest. Entries are added daily, so check often.
To view the structures, you can use a variety of free software. Rasmol is one of the older and still widely used programs, and is available on Mac, PC, and Unix versions. A spin-off of Rasmol, CHIME runs within WEB browsers (best to stick with Netscape). Those programs will let you rotate, color, and zoom on existing protein structures. You can also save images and save scripts which will get you to specific orientations, etc.
A newer program, SwissPDB Viewer, similarly allows viewing structures and has a fancier interface. It allows for some fancier outputs (e.g., special 3D renderings). It also allows some simple homology modeling and allows you to rotate side chains, etc (note that as soon as you do these things, you have left the world of experiment and have entered a potential fantasy land). With homology modeling, you can take a sequence that is related to a protein of known structure and try to predict its structure by aligning the sequences onto the structure.
Res Collab for Structural Bioinformatics - The New Home of the PDB!
Nucleic Acids Database -- a part of the Biological Structure Resournce
IMB Jena Image Library of Biological Macromolecules
NIH
Free Visualization/Modeling Software 
Other Databases
Structure Checking/Exploring Tools
Other Stuff
Physical Models:
DNA/RNA Thermo and Modeling
Homology and other Modeling
Moose - Macromolecular Structure Query
Protein Structure Prediction - Cambrdige
Pedro's List of Sites
The Representation of Molecular Models - Rendering Techniques
Visualizing/comparing aligned structures
Principles of Protein Structure - Course
"Biomolecular Structures" - an Internet course
Molecular Modeling - A Primer
Amber Home Page, or here...
Visual Molecular Dynamics
2D to 3D Coordinate Conversions
Biosym Technologies / Molecular Simulations Inc. (MSI) - Insight II
TMAP - Membrane Protein Prediction Service
Argos Aligned Seq Struct Prediction Service
Argos - WEBMol - Java structure viewer
Argos - Surface calculations
BioSCAN sequence analysis server
Fred Hutchinson Cancer Research Center -- Blocks Protein Search Server
ExPASy Molecular Biology Server
DNAcers
Secondary Structure of Proteins - UMass
Great Teaching Tools/Examples
DNA/Protein Sequence Searching Tools
Brookhaven Protein Database Server (OLD!)