Beruflich Dokumente
Kultur Dokumente
Contents
Introduction of protein structures
Using thymidine kinase as an example
Hydrophobic interaction
The physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water
An example of van der Waals force: Gecko climbs on the glass An example of hydrophobic interaction: Water drops on hydrophobic surface
NMR
DNAs/RNAs (2k7e)
EM
http://www.pdb.org/
1. Save the data on your PC 2. Open the file on a structure viewer program (swiss PDBviewer, pymol, and etc.)
Unknown Known
O
query
Known
Compound structure
Download page
General Terms
Main chain Residue Arginine Chain Secondary Structure (Ribbon)
Side chain
Gray: C atom Blue: N atom Red: O atom Atom radius
Workspace
Layer info Main window Viewer
Control panel
Translate
Rotate
control panel
Load PDB1
Load PDB2
GLU111
Render in solid 3D
Bond length
?A
1.52A
Bond length
?A
Bond length
?A
Helix
Change color
Polar
Hydrophobic
High B-factor
Low B-factor
Secondary Structure
Selected residues
Relative accessibility
Thymidine kinase
Press left button of mouse to select the ligand (THM, thymidine) of 1kim
1. Q125 recognize the thymine moiety 2. Activity was decreased by over 90% if Q125 mutated (Biochemistry, 2000.
39: p. 4105-4111)
M128 and Y172 sandwich the thymine moiety Stabilize the binding of substrate (JBC, 1999. 274: p. 31967-31973)
Surface preference
Discard surface
1kim
3vtk
Results of superimposition
Comparison of ligands
1kim: substrate(CPK)
Save files
Homework
Keyword
1. Capture a picture of N1 neuraminidase (ribbon) and its ligand (stick) 2. Capture a picture of H-bonds between protein and ligand
E-mail
pikihsu@gmail.com Mail title: _HW2