Biomolecule Library

Chemistry Department - CSB/SJU

Welcome to the Biomolecule Library of the Chemistry Department.   The library contains interactive graphical images of interesting biological molecules.  The x, y, and z coordinates of many of these molecules come from the Protein Data Bank of the Brookhaven National Lab.  A list of interesting biomolecules are given below. Click on any and you will be taken to a new web page with three frames:

This web site consists of a number of frames:

The top frame - molecule.html - displays the molecule.  You can use the mouse buttons to manipulate the molecules, using the commands shown below:  


Mouse Commands

When you click on any of the molecules listed below, a black window containing the molecule will appear in your browser.  You should be able to see and rotate your molecule by placing the mouse cursor in the black window and using the commands given below:

In addition, you can change the rendering of the molecule by moving the mouse cursor within the area of the molecule. Click and hold the right mouse button, and a new menu will appear that will allow additional manipulation of the molecule. Experiment with these commands.  More detail instructions are given at the end of this page.

The right frame - commands.html - gives a list of commands which will alter the display of the structure and properties of the molecule.   Click on the different command buttons and  watch the changes!

The bottom frame - page1.html - displays the text associated with each molecule displayed in the top frame.  The text in this frame will describe the structure and function of the displayed molecule, and prompt you to change the view of the molecule by selecting different commands in the right frame.



Select from the list below to visualize a variety of biomolecules!




structure students
alpha helix an alphja helix from an antifreeze protein
twisted beta sheet a twisted beta sheet from the arabinose binding protein
beta barrel a beta barrel from triose phosphate isomerase
Supersecondary Structure:  helix-loop-helix EF Hand:  Ca binding motiff of calmodulin
Supersecondary Structure:   helix-loop-helix helix-turn-helix binding motiff from the lambd repressor
Supersecondary Structure:  beta-hairpin from bovine pancreatic trypsin inhibitor
Supersecondary Structure: beta-helix-beta from triose phosphate isomerase
alpha helical protein:  cytochrome B562; Cyto b562 with heme in oxidized state
alpha helical protein:   met-myoglobin; Met-Mb contains a heme with Fe3+
beta protein: superoxide dismutase; SOD with 8 antiparallel beta strands forming a barrel
beta protein: retinol binding protein; RBP with beta strands forming an up-down barrel
alpha/beta:  triose phosphate isomerase TPI has 8 parallel beta strands forming a barrel with strands connected by alpha helices
alpha/beta: hexokinase HK has open twisted beta sheet structure


structure students
Green Fluorescent Protein by Annelise and Jeremy - A protein that makes it's own fluorophore
Trp Repressor by Laura and Jessie - A protein-DNA complex involved in regulation of Trp synthesis.
HIV-1 NEF-SH3/SRC by Shawn Alderman, Matt Rose, and Kim Switlick - An HIV proteins meets a domain of a cell protein involved in signal transduction
Acetylcholinesterase by Steve Aldrich, Grant Seeger, and Jason Bartos - The enzyme that degrades acetylcholine at synaptic junctions
BAPP-Trypsin by Patty Hunt, Lisa Jungbauer, and Laura Melohn - A protein involved in Alzheimers interacts with a well known protease
Lysozyme by Kathy Thorson and John Geissler - A glycosidase with newly discovered properties
Barnase-Barstar by Josh Casey, liz Nesset, Marne O'Neill
Glutamine Synthase by Matt Nugent and Melissa Illies -
Glu-tRNA Sythase by Dan Ferraro, Ryan Fey, and Deb Wentz
Alcohol Dehydrogenase by Ryan Olson, Matt Tinguely, and Martin Klinkhammer
434 Repressor by Timothy Providence, Leonard Arthur and Francis Insaidoo
Hemoglobin Dimer by Brian Zachau and Kaarin Fossum


structure students
TATA:TATA Binding Protein Jeff Macalena and Aaron Kych.
DNA Polyerase I:  Klenow Frag. Alonzo Knowles and Brendon Scicluna.
Calmodulin:TFP complex Michelle and Nigel
Lac Repressor Karla Ziegelman and Rebecca Johnson
Ricin Jake Jedynak, Matt Schnobrich, and Sam Bugbee
Estrogen Receptor Alpha Chris Brueske and Huong Nyguen
RU486:Receptor Amy Luzum and Lars Liepold
Cytosine-5-methyltransferase Nicky Tuma and Juki Illie
Creatine Kinase Jess Asmussen and Dorian Nelson
Gal-4-Enhancer Adam Westman and Phil Ryan
Insulin Receptor Rebecca Johnson and Becky Keukle


structure students
Zif268:DNA Complex Becky Guza and Anna Selmecki
Cytochrome P450 Bridget Charbonneau, Greg Hockin
Chymotrypsin Dan Welna and Sara Wilcox
Carboxypeptidase A Kristi Kragseth and Teresa Abraham
Leucine Zipper Bryan Johnson and Beth Cody
RNase A Barry Voight and Erik Hanson
Chondrotin Sulfate Stephen Lasslo and Eric Molstead
Glucose in Solution Nate Schultz and Matt Stockinger
Prions Amy Geissler and Aaron Mohs
N-Linked Complex CHO's Jenny Klein and Jenny Meyers
Glyceraldehyde-3-phosphate dehydrogenase Tom Warrington and Minh Ha
Cyclooxygenase Nana Gyimah and Blair Schwartz


structure students
ATP/ADP Jessica Schomer
GroEL/ES Ben Steil and Pamela Carrol
Flavin dehydrogenase Nathan Hubbard and David Valencia
Cyclophilin Dustin Lorenz and Matt Hiemenz
hemagglutinin Matt O'meara and Mark Ridenour
nucleosome Chen Chau and Christina Fair
cytoC Jon Siverson and Paul Piehowski


structure students
Rubredoxin from pyroccus furious:  NMR and X-Ray Structure Adam Barker and Adam DeFoe
Apolactalbumin (w/o calcium) and Hololactalbumin Jessica and Tina Veeks
Potassium Channel Thu Nguyen & Gina Fasching
Chloride Channel Laura Nezworski and Monica Hurtubise
Gsa - Adenylate Cyclase Complex Ryan Bielat and Justin Bundy
Maltoporin Transport Protein Isaac Marsolek  and Ross Olness
Soybean Agglutinin Lectin Zach Tegels and Kyle Wilkes
Cytochrome C Oxidase Nate Rose and Brian White


structure Students

Succinate Dehydrogenase (Complex II) (INEN)

Bobby Teigen, Josh Day, Adam Benoit

Immunoglobulin 48G7 Germline Fab Antibody Complexed With Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid. (1AJ7)

Kat Cronin and Jon Freeman

Bacteriorhodopsin Crystallized From Bicelles (1KME)

John Eiser and Alexi Young

P-Selectin Lectin/EGF Domains (IG1Q)

Chad Powers and Anillisa Jordan

Cu(I) Form Of E. Coli Cuer, A Copper Efflux Regulator (1QO5)

Abe Cass and Jim Kuderer

 Nf-Kb(P50)2 Complexed To A High- Affinity RNA Aptamer (1OOA)

Christian Brekke and Don Harris

Lactose Permease, Crystal Structure Of Lactose Permease With Td (1PV7)

Meghan Lee and Steph McClure

Glycerol-3-Phosphate Transporter From E. Coli (1PW4)

Dave DeGrio and Peter Simone

Photosystem II (1FE1)

Megan Dunlavey, Britt Peterson

Photosystem I: A Photosynthetic Reaction Center and Core Antenna System From Cyanobacteria 1JBO

Tom Johnson and  Cathy Watson

Acetylcholine Receptor Pore (1OED)

Chris Downing, Maureen Handako

Hemoglobin/Myoglobin Comparisons

  • oxy and deoxymyoglobin (sperm whale):  1A6M and 1A6N

  • human deoxy Mb () and human deoxy Hb - alpha chain (2HHB)

  • human deoxy Hb alpha and human deoxy Hb beta chain:  (2HHB)

  • human deoxy Hb (2HHB) and human oxyHb (1HHO  dimer; )


Marc Roe and James Wollack


Molecular Systems


1AVDThree-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution. Jeff and Nick M
1RHZSecYEB Protein Translocase Complex .  Nick B and Glenise
 2BF1Unliganded gp120 core (HIV viral protein): 1GC1 gp120:cd4:antibody complex Susan and Danielle
1IRU:  Mammalian Proteasome    Steve and Noah
1T42: Self-splicing Group I intron with both exons   Katie, Matt, and Beau
1RRQ, S, T:  Adenine DNA glycosylase:8-oxyG DNA complex Pat and Marty
1RWTLight Harvesting Complex from Spinach Allison and Kara
1S5LPhotosystem II from cyanobacteria S. elongatus Brian and Cathy
2A79Mammalian Voltage-dependent Shaker family potassium channel Andrea, Claire and Ann