The Practical

The database table

The database table which you will access has some data extracted from the PDB. Each row contains the following data:

Field	Type
pdb_code	varchar(4)
name	varchar(255)
date	date
description	text
source	varchar(255)
authors	text
resolution	float
exp_method	enum('XR','NM','EM','SD','ND','FL','FD','TM')
n_chains	smallint(6)
n_residues	smallint(6)

Tasks

Your practical tasks are to write Python/PEP249 scripts as follows:

Task 1

Count the number of entries in the table. The SQL required to count the rows in the table is:

select count(*) from protein where source = 'Homo sapiens'

The results should look like this:

Expected results

There were 3218 rows

Task 2

Extract and print the source, resolution and description for PDB code 1DM5. The SQL required to extract the data is:

select source, resolution, description from protein where pdb_code = '1DM5'

The results should look like this:

Expected results

PDB Code:    1DM5
Species:     Hydra vulgaris
Resolution:  1.93
Description: ANNEXIN XII E105K HOMOHEXAMER CRYSTAL STRUCTURE

Task 3

Extract the PDB code, resolution and name for all proteins from the species Leishmania major and print the results on multiple lines. The SQL required to extract the data is:

select pdb_code, resolution, name from protein where source = 'LEISHMANIA MAJOR'

The results should look like this:

Expected results

1E7W 1.75 DIHYDROFOLATE REDUCTASE
1E92 2.20 PTERIDINE REDUCTASE
1EZR 2.50 HYDROLASE
1LML 1.86 LEISHMANOLYSIN
1OKG 2.10 TRANSFERASE
1R75 1.86 STRUCTURAL GENOMICS, UNKNOWN FUNCTION

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