Small Molecules
ethanol
methanol
methane
ice
imidazole
liquid
water
water
(single molecule)
liquid water
(movie)
Amino Acids and Peptides
alanine
arginine
asparagine
aspartate
cysteine
glutamate
glutamine
glycine
histidine
isoleucine
leucine
lysine
methionine
phenylalanine
proline
serine
threonine
tryptophane
tyrosine
valine
S,S-alanylalanine
R,S-alanylalanine
S,R-alanylalanine
R,R-alanylalanine
Proteins
a-helix
b-sheet
b-turn
bacteriorhodopsin
bovine
pancreatic trypsin inhibitor (BPTI)
bovine
pancreatic trypsin inhibitor (BPTI) with crystallographic waters
carbonic
anhydrase
chymotrypsin
(dimer)
collagen
cytokine-receptor
complex (interleukin-6 with fragments of GP130)
enolase
globin(single
chain)
green
fluorescent protein
hemoglobin
(tetramer)
hexokinase
insulin
(NMR structure)
insulin
(single structure)
lysozyme
lysozyme-antibody
complex
myoglobin
nucleosome
core particle (DNA complexed with histones)
ribonuclease
Many more protein structures are available from the Protein Data Bank.
Saccharides
amylose
cellulose
D-glucose
deoxyribose
(open form)
deoxyribose
(closed form)
glucose
(open form)
glucose
(pyranose form)
glucose
(furanose form)
sucrose
trehalose
Lipids
arachidonic
acid
cholesterol
glycerol
lauric
acid
oleic
acid
progesterone
phospholipid
(DPPC)
stearic
acid
testosterone
Nucelotides, Nucleosides, Nucleic
Acids
adenine
guanine
cytosine
uracil
thymine
purine
adenosine
cytosine
dAMP
dCMP
dTMP
AMP
cAMP
CMP
ATP
GMP
UMP
section
of a RNA
a
single A-T base pair
a
single G-C base pair
B-DNA
A-DNA
section
of a DNA
DNA
double helix
double
stranded RNA
nucleosome
core particle (DNA complexed with histones)
There are repositories of structural files available on the web including the following:
Protein Data Bank
(PDB) - Hosted by the Research Collaboratory for Structural Bioinformatics
Cambridge Structural Database
-
Primarily small molecules
The Nucleic Acid Database
Klotho: Biochemical Compounds
Declarative Database - Small molecules