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Tutorial-3D Protein Structure Visualisation and Analysis

molecular computational biology tutorial questions and answers. visualisation also included

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sitinurrafiqah1602
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1K views

Tutorial-3D Protein Structure Visualisation and Analysis

molecular computational biology tutorial questions and answers. visualisation also included

Uploaded by

sitinurrafiqah1602
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Tutorial

STBC2012 3D Protein Structure Visualisation and Analysis

Name and matric number: SITI NUR RAFIQAH BINTI MOHAMMAD TAJUDIN

Date: 15/06/2023

Protein Structure Validation and Visualisation

Visit the RCSB Protein Data Bank (PDB) (https://www.rcsb.org/). Type PDB ID 4wjt in the
search area.

1. From the result page, what is the name of the protein and the resolution of the crystal
structure?

- the name of the protein is Stationary Phase Survival Protein YuiC from B subtilis
complexed with NAG

- Resolution is 1.21 Å

2. Check the quality of the protein structure of 4wjt using Ramachandran plot. Hint: look
at wwPDB validation full report or do it at Rampage: Ramachandran plot analysis
(http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) or MolProbity.

Favoured region (%): 97

Allowed region (%): 3

Outliers (%): 0

Is the protein structure in good quality?


- yes
3. Download the 4wjt_A PDB file (text) and save it on your Desktop. Open the PDB file
using ChimeraX. The structure should display in ribbon representation. Colour the
protein structure in yellow. Change the background to white. Display the protein
structure here.

4. Display the protein structure in an electrostatic potential surface representation.


Select the protein molecule, then click electrostatic
5. Based on the literature, the putative conserved catalytic residues are D129, D151 and
D162. Select and display these residues as ball and stick representation in a zoom-in
image. Label the residues (type ”label sel”).
Structure analysis

6. Download the PDBID 2ae0. Open it in ChimeraX. Superpose both 4wjt_A and 2ae0
protein structures and display the figure here.

7. What is the RMSD between the two-superposed structure?

- RMSD between 44 pruned atom pairs is 0.681 angstroms; (across all 102 pairs:
20.274)
8. Display the ligand N-acetylglucosamine (NAG) of 4wjt_A in ball and stick display
style and the NAG-binding pocket in an electrostatic potential surface representation.

9. Open PDBsum (www.ebi.ac.uk/pdbsum/) in your browser. Type 4wjt as the PDBID


code. Click on the “ligand” tab. What are the ligands bound on the structure?

- NAG

- DMS

- 3P9
10. Download the LigPlot diagram as a PDF file and display the protein-ligand interaction
here.

11. Open PDBePISA (www.ebi.ac.uk/pdbe/pisa/) in your browser. Load 4wjt as the


search molecule. What is the area of the dimeric protein interface? What kind of
interactions formed between the dimer?

- 3955.0 Å2

- Covalent

12. From all the analyses you have done, what is the possible function of this protein?

- Breaking chemical bonds to form new double bonds or ring structure

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