Assignment 4 : PDB

1. How many unique protein chains are in this PDB

Unique protein chains: 3

2. What is the crystallization method used ?

Vapor Diffusion

3. What is the resolution of this PDB structure. Why is resolution of the structure important for inferring the function of the protein

Resolution is 2.08 Angstroms. Having a high resolution structure is important when looking at detailed interactions, such as enzymatic catalyis or protein-protein recognition. The reason for this is that at lower resolutions, the individual crystallographer is responsible for assigning atoms to density, and this may be incorrect for lower resolution structures. 2.08 Angstroms is medium to good quality resolution.

4. Find the UniProt ID of the SARS-CoV-2 Nucleoprotei

P0DTC9

5. PDB file downloaded and viewed in Emacs

ATOM      1  N   ASN A  48     -33.299 -23.939  10.450  1.00 49.28           N
ATOM      2  CA  ASN A  48     -32.686 -23.712   9.136  1.00 58.67           C
ATOM      3  C   ASN A  48     -32.797 -22.248   8.688  1.00 49.64           C

Download the FASTA File for PDB ID. Open the fasta file as a regular text file with your Text Editor.
1. Can you list the sequence of each protein chain along with it’s name using the FASTA file?

7CR5_1|Chain A|Nucleoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) RPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAE 7CR5_2|Chain B[auth H]|monoclonal antibody chain H|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYIMHWVRQAPGKGLEWVAVISYDGSNEAYADSVKGRFTISRDNSKNTLYLQMSSLRAEDTGVYYCARETGDYSSSWYDSWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK 7CR5_3|Chain C[auth L]|monoclonal antibody chain L|Homo sapiens (9606) QLVLTQSPSASASLGASVKLTCTLSSGHSNYAIAWHQQQPEKGPRYLMKVNSDGSHTKGDGIPDRFSGSSSGAERYLTISSLQSEDEADYYCQTWGTGIQVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS