Name: Jyoti Rana

3522411029
Practicals on structural Bioinformatics
03/02/2025

CHIMERA

AIM: Generation of Publication quality images

METHOD:
1. Open the browser
2. Search for the URL given for PubMed articles
3. Read the article and find for the protein of interest
4. Open uniport (https://www.uniprot.org/)
5. Under structure select PDB id with lowest resolution
6. Open PDB (https://www.rcsb.org/)
7. Search for the selected PDB id
8. Download the 3D structure of protein
9. Open chimera software
10. Select fetch by id and use the PDB id for the same
11. Go to action select colors and make the background color to white
12. Go to select, and choose a chain of choice
13. Delete rest of the chain
14. Go to tools, under depiction change the color of the secondary structures
15. Go to select, under residue select HOH
16. From action, under atoms and bonds delete those
17. Download 300 dpi image
18. Go to select, under residue choose a ligand of choice
19. Go to action, under atoms and bonds select show
20. From action select focus
21. From tools, using depiction give 2D labels to proteins, and using structure analysis
find H-bonds
22. Download 300 dpi image
23. Go to select and select the whole chain
24. Go to action and select surface and solid
25. Go to action and under surface select show
26. Adjust its side view using lightning control under tools
27. View its columbic view from structure/binding analysis under tools
28. Download 300 dpi image

A. RESULT:
Q1) Read the abstract of the paper:
https://pubmed.ncbi.nlm.nih.gov/37998358/

1) What is the name and function of the protein?

The name of the protein is TEM8.
Functions of the protein includes angiogenesis, epithelial-to-mesenchymal transition, and
cell migration.

2) Is its 3d structure available? if available:

a) Download the lowest resolution structure.

3D structure of 3N2N

b) Name of that Pdb Id, Resolution obtained, Experimental method used, Deposited date
 Pdb ID: 3N2N
 Resolution: 1.80 Å
 Experimental method used: X-RAY DIFFRACTION
 Deposited date: 2010-05-18
c) Select only one chain
d) Make the background color as white
e) Show various secondary structures with various colours
f) Color each secondary structure with different color
g) Generate publication quality image of 300 dpi.
 Secondary structure in protein TEM8. Alpha helix as orange and Beta plates as purple

3) What are the residues that are interacting with the ligand.
a) Focus the window pane towards the active site (that contains the ligand
as peptide/metal ions/small molecule)
b) Label those binding site residues by adjusting the zone to 5A from the
ligand and color it based on element.
c) Find the hydrogen bonding distance between protein and ligand
d) Adjust the ‘Viewing control’ parameter under the ‘Tools’. Generate
high quality image by adjusting side view, effects, and lighting.
e) Generate publication quality image of 300 dpi and save it in .tiff
format.
 Bond length present between protein and ligand

4) Generate columbic surface view of the protein. If ligand is small

molecule, make it to ball and stick.

Columbic surface view of the protein

CONCLUSION
 B. RESULT:
Q1) Read the abstract of the paper:
https://pubmed.ncbi.nlm.nih.gov/39389489/
1) What is the name and function of the protein.
The protein is MAO-B.
2) Is its 3d structure available? if available:
a) Download the lowest resolution structure.

Structure of 1S3E

b) Name of that Pdb Id, Resolution obtained, Experimental method used, Deposited date
 PDB ID: 1S3E
 Resolution: 1.60 Å
 Experimental method used: X-RAY DIFFRACTION
 Deposited date: 2004-01-13
c) Select only one chain
A-chain selected
d) Make the background color as white
e) Show various secondary structures with various colours
f) Color each secondary structure with different color
g) Generate publication quality image of 300 dpi.
 Secondary structure present in chain-B of MAO-B

3) What are the residues that are interacting with the ligand.
a) Focus the window pane towards the active site (that contains the ligand
as peptide/metal ions/small molecule)
b) Label those binding site residues by adjusting the zone to 5A from the
ligand and color it based on element.
c) Find the hydrogen bonding distance between protein and ligand
d) Adjust the ‘Viewing control’ parameter under the ‘Tools’. Generate
high quality image by adjusting side view, effects, and lighting.
e) Generate publication quality image of 300 dpi and save it in .tiff
format.
 Binding site residue and bond length between ligand and protein

4) Generate columbic surface view of the protein. If ligand is small

molecule, make it to ball and stick.

Columbic view of the chain.

CONCLUSION:

C. RESULT:
Q1) Read the abstract of the paper:
https://pubmed.ncbi.nlm.nih.gov/37504963/
1) What is the name and function of the protein.
The protein is MMP-9.
Function: Matrix metalloproteinase that plays an essential role in local proteolysis of the
extracellular matrix and in leukocyte migration.
2) Is its 3d structure available? if available:
a) Download the lowest resolution structure.

3D structure of 1ITV

b) Name of that Pdb Id, Resolution obtained, Experimental method used, Deposited date
 PDB ID: 1ITV
 Resolution: 1.95 Å
 Experimental method used: X-RAY DIFFRACTION
 Deposited date: 2002-02-11
c) Select only one chain
d) Make the background color as white
e) Show various secondary structures with various colours
f) Color each secondary structure with different color
g) Generate publication quality image of 300 dpi.
 Secondary structure present in the protein

3) What are the residues that are interacting with the ligand.
a) Focus the window pane towards the active site (that contains the ligand
as peptide/metal ions/small molecule)
b) Label those binding site residues by adjusting the zone to 5A from the
ligand and color it based on element.
c) Find the hydrogen bonding distance between protein and ligand
d) Adjust the ‘Viewing control’ parameter under the ‘Tools’. Generate
high quality image by adjusting side view, effects, and lighting.
e) Generate publication quality image of 300 dpi and save it in .tiff
format.
 Binding site residue and bond length between ligand and protein

4) Generate columbic surface view of the protein. If ligand is small

molecule, make it to ball and stick.

Columbic view of the chain.

CONCLUSION:
 D. RESULT
Q1) Read the abstract of the paper:
https://pubmed.ncbi.nlm.nih.gov/37788831/
1) What is the name and function of the protein.
Name of protein is Aldo-keto reductase family 1 member B1
Function:
 Catalyzes the NADPH-dependent reduction
 Displays enzymatic activity towards endogenous metabolites

2) Is its 3d structure available? if available:

a) Download the lowest resolution structure.

3D structure of 1PWM from PDB

b) Name of that Pdb Id, Resolution obtained, Experimental method used, Deposited date
 PDB ID: 1PWM
 Resolution: 0.92 Å
 Experimental method used: X-RAY DIFFRACTION
 Deposited date: 2003-07-02
c) Select only one chain
d) Make the background color as white
e) Show various secondary structures with various colours
f) Color each secondary structure with different color
g) Generate publication quality image of 300 dpi.

Secondary structure of ALR2

3) What are the residues that are interacting with the ligand.
a) Focus the window pane towards the active site (that contains the ligand
as peptide/metal ions/small molecule)
b) Label those binding site residues by adjusting the zone to 5A from the
ligand and color it based on element.
c) Find the hydrogen bonding distance between protein and ligand
d) Adjust the ‘Viewing control’ parameter under the ‘Tools’. Generate
high quality image by adjusting side view, effects, and lighting.
e) Generate publication quality image of 300 dpi and save it in .tiff
format.
 Bond length between protein and ligand

4) Generate columbic surface view of the protein. If ligand is small

molecule, make it to ball and stick.

Columbic surface view

CONCLUSION: