Modelling of the test protein

The sequence of the test protein (Amino acid)

5’ APADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFS 3’

PDB ID obtained from the alignment results

Fig 1: BLAST was performed with query sequence as the test sequence and PDB as the database. The best-aligned protein was found to be 4HEF_A as highlighted in the figure.

Source: NCBI BLAST

FASTA sequence of the aligned protein

>pdb|4HEF|A Chain A, Beta-lactamase

APADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTAT

LAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPT

YAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKRDRPLR

VGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLK

RLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVK

IAYAILSGLE

The above sequence has been obtained from the NCBI repository. The test sequence given here belongs to the A chain of Beta-lactamase gene of Pseudomonas aeruginosa.

Details about the protein 

The above-stated protein with PDB ID 4HEF is the structure of avibactam bound to AmpC in the above-stated bacteria. Avibactum is a novel and covalent non-beta lactam beta-lactamase inhibitor which has been developed recently. According to a paper, the same structure has been found to be visible as a beta-lactamase enzyme bound to avibactam (Lahiri et al. 2013). X-ray analysis has been found to show the level of deacetylation mechanism favouring cyclization over the hydrolytic processes. The structure has also been found to reveal that similar binding modes are observed in both enzymes proving a broad-spectrum inhibitory activity of avibactam (Lahiri et al. 2013).

Three points of interest in the protein (Active sites, ligand binding sites, catalytic residue stretch, Signal peptide)

Fig 2: A- Shows the active site marked in red, signal peptide marked in grey and the functional region marked in blue, green and sea green. B- Shows the ligand-binding residue as a pink ball and stick part. The same has been labelled in the figures too. The point of interests was highlighted on the basis of protein data obtained from Uniprot details.

Source: RasMol

Fig 3: The command line used to highlight the point of interests in the protein structure

Source: RasMol

Key for the point of interests