Native Protein Data Bank &
Gallery of Protein Structure Animations

Click on the links down the right side of the page to view animations of reassembled native protein structures. The structures are rendered by JSmol.

(All animations have now been converted to JSmol. There are no longer any security issues. However, JSmol is not as fast as Jmol was. For small to medium proteins and using a fast computer, JSmol is adequate. Please be patient with the processing of large proteins.)
 

While the primary criterion for docking these structures is D2 symmetry and quality of steric fit, they also mostly have a barrel structure within each subunit and its axis is directed towards the centre of the complex. This symmetry principle is described in this poster.

In places there is some overlap of side-chains resulting from minor structural changes during crystallisation. I have not attempted to correct these. What I am showing in structures with the "n1" prefix is "reassembly" rather than full restoration of the native protein. However, some later additions to the gallery will include oligosaccharide side chains, freely rotating auxiliary domains and polypeptide tethers that have been re-orientated away from the crystal structures to better reflect their probable locations in solution. Such cases will be clearly indicated with the "n2" prefix.


 
 
Dihydrodipicolinate Synthase,
DHDPS
From Bacillus anthracis, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
Dihydrofolate Reductases
(Type 1)
From Bacillus anthracis, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From Homo sapiens, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From Thermotoga maritima, JSmol animation
 
or click here to download pdb structure file for your own viewer.

 
Galactose Oxidase
From the fungus, Dactylium dendroides, JSmol animation
 
or click here to download pdb structure file for your own viewer.

 
Hemocyanin

Type II from the Horseshoe crab Limulus polyphemus
 
or click here to download pdb structure file for your own viewer.
 
Hemoglobins
From Homo sapiens, R conformation, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From Homo sapiens, T conformation, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From Homo sapiens, intermediate conformation or possibly the true R state, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From the high-altitude goose, Anser indicus, R conformation, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From the high-altitude goose, Anser indicus, T conformation, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
Immunoglobulins
IgG
IgG1, trans isomer, from Homo sapiens, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
IgG1, cis isomer, from Homo sapiens, JSmol animation
 
or click here to download pdb structure file for your own viewer.

 
Neuraminidases
Type N2 from Influenza Virus, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
Type N9 from Avian Influenza Virus, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From Micromonospora viridifaciens, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
Triose phosphate isomerases (TIM)
From Thermotoga maritima, JSmol animation
 
or click here to download pdb structure file for your own viewer.
 
From the yeast Saccharomyces cerevisiae
In preparation

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