Protein Modeling: Bovine eNOS N368D single
mutant with L-N(omega)-Nitroarginine-(4R)-Amino-L-Proline Amide Bound
Part 1: Selecting a Protein-Hetero Compound Complex
Protein title :Bovine eNOS N368D single mutant with
L-N(omega)-Nitroarginine-(4R)-Amino-L-Proline Amide Bound
PDB ID : 1ZZS
Hetero compound's name :
L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE AMIDE
Het Code : DP9
L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE
AMIDE Hetero Compound
Figure1 Hetero compound,DP9
Hetero compound in Chemsketch 2D
Hetero compound in Chemsketch 3D
Hetero compound in DSV
Chem3D file of
overlay hetero-compound in Here
I
picked the protein named: Bovine eNOS N368D single mutant with
L-N(omega)-Nitroarginine-(4R)-Amino-L-Proline Amide Bound from the protein data
bank web site : Bank. There are many hetero compounds in that are embedded
within this protein such as ACETATE ION (ACT),
L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE AMIDE ( DP9), GLYCEROL(GOL),
5,6,7,8-TETRAHYDROBIOPTERIN(H4B), PROTOPORPHYRIN IX CONTAINING FE(HEM), and
ZINC ION(ZN). I chose the hetero compound which has the HET code is DP9 to work
on this project.
I
extracted the hetero compound from the protein, and I sketched its structure in
ChemSketch. After that I converted it to
3D in Chemsketch to have more detailed picture about this hetero compound. I also have a copy of hetero compound in DSV
program in order to fix its structure incase its extracted structure is not the
same as its original that embed within the protein(1ZZS).
Part 2: Hetero Compound Presents within Protein:
Figure 2, Protein and hetero compound
This is a picture which shows the hetero compound, L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE
AMIDE (DP9) lies within the protein, Bovine eNOS N368D single mutant with
L-N(omega)-Nitroarginine-(4R)-Amino-L-Proline Amide Bound (1ZZS).
-------------------------00000------------------------
Part 3:
Steric Enery Calculation: (is Here)
-------------------------00000------------------------
Part 4:
Superimposing the Extracted Hetero Compound: (Here)
-------------------------00000------------------------
Part 5:
Protein-Ligand Interaction (Here)
-------------------------00000------------------------
Part 6: Bibliographic Information: (Here)
-------------------------00000------------------------
Part 7:
Organization and sumarization: (Here)
Protein Project (part 1-7) in MS
word format: Here
Protein Project (part 1-7) printable
format: Here
Bibliographic Information:
1.
The Protein, Bovine eNOS N368D single mutant
with L-N (omega)-Nitroarginine-(4R)-Amino-L-Proline Amide Bound is retrieved
from the RCSB
Protein Data Bank, and its PDB ID : 1ZZS
The Li, H., Flinspach, M.L., Igarashi, J., Jamal, J., Yang, W.,
Litzinger, E.A., Huang, H., Erdal, E.P., Silverman, R.B., Poulos, T.L.Exploring
the Binding Conformations of Bulkier Dipeptide Amide Inhibitors in Constitutive
Nitric Oxide Synthases. Biochemistry v44 pp. 15222-15229, 2005. http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZZS
2.
KeithM.
Channon, Tetrahydrobiopterin: Regulator of Endothelial Nitric Oxide Synthase in
Vascular Disease, Trends in Cardiovascular MedicineVolume 14, Issue 8, ,
November 2004, Pages 323-327.
3. The wiring diagram and
Ligplot of the Protein-Hetero compound were obtained from the PDBSum Website:
Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new summaries
and analyses
of the known 3D structures of proteins and nucleic acids.Nucleic Acids Res.,
33, D266-D268.