PDB Connector PfamID column

Dear colleague,

I am using the very useful PDB Connector node.

Unfortunately, I face one issue. In the report table, I want to filter on the "Pfam ID" column, but for some structures, it is empty. (ex: 1R0P)

Moreover, for a multiple chain structure, the first chain can contain a value, but the others, which are identical to the first, not. (ex: 2G1T)

Do you have an idea how to improve this point?

Thanks for helping,

Emilie

Dear Emilie,

Thanks for you post - I'm glad you are finding the node useful.

I checked out the 2 structure ID's you mentioned, and I see the same thing, so I also checked them on the PDB website itself.

1r0p : There is no PFam ID for this structure on the PDB website.  If you think that there should be an ID for the structure, I would suggest contacting the PDB via their website (http://www.rcsb.org/pdb/home/contactUs.do) .  They are normally pretty quick to give an initial answer - it may be that there is a delay in providing the external IDs (Also worth noting that the PDB-Europe entry for 1r0p is annotated with the PFam ID - http://www.ebi.ac.uk/pdbe-srv/view/entry/1r0p/primary - it may be a synchronisation issue across sites)

2g1t : Again, I see the same issue.  I also checked by posting this ID into their webservices demo page (http://www.rcsb.org/pdb/software/wsreport.do), and here is the result:

"2G1T","A","3.30.200.20 [232-317]#1.10.510.10 [318-499]","Phosphorylase Kinase; domain 1#Transferase(Phosphotransferase) domain 1","","","","PF07714 [242-492]","Pkinase_Tyr","Protein tyrosine kinase"
"2G1T","B","3.30.200.20 [230-317]#1.10.510.10 [318-499]","Phosphorylase Kinase; domain 1#Transferase(Phosphotransferase) domain 1","","","","","",""
"2G1T","C","1.10.510.10 [318-499]#3.30.200.20 [232-317]","Transferase(Phosphotransferase) domain 1#Phosphorylase Kinase; domain 1","","","","","",""
"2G1T","D","3.30.200.20 [226-317]#1.10.510.10 [318-499]","Phosphorylase Kinase; domain 1#Transferase(Phosphotransferase) domain 1","","","","","",""
"2G1T","E","","","","","","","",""
"2G1T","F","","","","","","","",""
"2G1T","G","","","","","","","",""
"2G1T","H","","","","","","","",""

So, it appears that their webservice only returns the PFam ID with the first chain associated with it.  I will contact them about this, as it would appear to be an error in their webservice.

In the meantime, I've attached a simple workflow which offers a workaround for the second issue.

Yours,

Steve

Dear Steve,

I have just seen that PDB Connector Node is now ok. It seems that the PDB database was corrected.

So thank you for your help,

Emilie

Emilie,

Sorry - yes, the nice people over at RCSB PDB fixed a few bugs that this identified in their webservices.  Meant to post an update, but forgot - sorry!

Thanks for the bug report.

Steve