My name is Yoshitaka AISU

My name is Yoshitaka AISU.

E-mail address: (withheld)

Professor of my laboratory is Takahisa IKEGAMI.

My research project is not already decided. But, I will research the structure of any proteins by NMR

The name of my protein is ADP-ribosylation factor 6 (ARF6) and its function is cell invasion.

PDB code is 2D1X.

Resolution is 1.90Å, R-Value 0.216, and R-free 0.226.

Slide 1

This report is made available with the kind permission of the student who prepared it, Yoshitaka Aisu. It was prepared for the 2010 class at Osaka University, Japan (workshops.molviz.org). The only change is that the student’s email address was removed, and this paragraph was added. Each slide answers a specific question.

Slide 2

six protein chains, no DNA, no RNA.

Ligands Three letter codes SO4 Full name SULFATE ION

Slide 3

Slide 4A

only beta sheet

there is no disulfide bond.

3KJ6

2 disulfide bonds within chain L 2 disulfide bonds within chain H

2 disulfide bonds between chain L and chain H

Slide 4B

Slide 5

There is a hydrophobic core.

Slide 6

This protein is soluble .

Slide 7

salt bridge and hydrogen bond

Slide 8

High conserved GLU21:A - expected

High conserved VAL57:A - unexpected

Because GLU21 is near the legand SO4.

Slide 9

Asymmetric unit Biological unit PISA

6 chains 6 chains

conformation is difference between the AU and PISA.Author’s biological unit is 3 chains.

Slide 10

List the gap in 2D1X

chain A : 1-6chain P : 1-2chain P : 12-15chain B : 1-7

chain Q : 1-2chain Q : 12-15chain D : 1-7

Slide 11

Sandbox Reserved 3

change colors

Slide 12

red: negative charge

blue: positive charge

Slide 13

Number of energetically significant ARG/TYR cation-pi interactions: 2

ARG42:A with TYR49:C ARG4:Q with TYR12:D

Slide 14

Residue of high temperature Glu1:C

Thank you for your lecture.

See you , again.

I enjoy leaning computer science.