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10. STRUCTURAL ANALYSIS OF Zn FINGER PROTEIN USING

RASMOL, PDBSUM AND Q-SITE FINDER

Objectives:

1. To analyze the Zn Finger proteinusing PDBsum.

2. To analyze the Zn Finger proteinusing RASMOL.3. To analyze the Zn Finger proteinusing Q-Site Finder.

Requirements:

1. http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/

2. http://rasmol.org/

3. http://bmbpcu36.leeds.ac.uk/qsitefinder/

Principle and Description:

The 3D configuration of the primary structure is defined as the tertiary structure, describingthe fold of the protein. Three dimensional structure of a protein is closely related to its biological

function. Therefore analysis of predicted protein structure is very important to know its function.This practical describes to analyze the tertiary structure of Zn Finger using the tools PDBsum,

RASMOL and Q-Site Finder.

PDBsum is a database of mainly pictorial summaries of the 3D structures of proteins and

nucleic acids. Its pages aim to provide an at-a-glance view of the contents of every 3D structure,

plus detailed structural analyses of each protein chain, DNA-RNA chain and any bound ligandsand metals.

RasMol is a molecular graphics program intended for the visualization of proteins, nucleic

acids and small molecules.

Q-Site Finder is used to do predict ligand binding site. Identifying the location of ligand

binding sites on a protein is of fundamental importance for a range of applications including

molecular docking, de novo drug design and comparison of functional sites. Here, we using.

Procedure 1:

1. Upload 3D structure of Zn Finger (1a1f) in PDBsum and submit.

2. Go carefully with all the links from the resultant page and answer the following queries.

Observation 1:

1. Mention the biological significance of Zn Finger protein.2. Retrieve the primary sequence in FASTA format.

3. Write about the secondary structure information and print the secondary structure.

4. Note Ramachandran plot statistics and print the Ramachandran plot.

5. Is there any ligand or metal ion present in the protein? If so write about the ligand or metalion.

6. Take print out of the ligand and its coordinated aminoacids.

Procedure 2:

1. Download and install the tool RASMOL in your local disk.

2. Upload the structure Zn Finger(1a1f) in RASMOL.3. Write the information about Zn finger.

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