The PDB requires that a single poly peptide have single chain id. See page 5 of the wwPDB annotation / processing procedures guide http://www.wwpdb.org/documentation/wwPDB-A-2012May30.pdf
One thing you could do would be to number the second domain starting a 1170 which would sort-of preserve the biological numbering. You could also number domain one as 1200-1300 and the second domain as 2170-2350 if you like. If you use refmac with non-continuous residue numbering, be sure to include a LINKR statement so the peptide bond between the two domains is properly restrained. Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Meindert Lamers Sent: Tuesday, October 23, 2012 9:55 AM To: [email protected] Subject: [ccp4bb] Convention on residue numbering of fusion proteins? Dear all, Is there any convention on the numbering of residues in a fusion protein? I have a structure of two domains fused together but would like to keep the biological numbering intact. 1st domain: residue 200-300 (protein A). 2nd domain: residue 170-350 (protein B). The fusion is between A300 and B170 Is it OK to label them chain A and B and create a LINK between the two (thus keeping the biological residue number intact). Or do I have to start the 2nd domain with residue number 301 (and loose all biological information). Many thanks, Meindert -- ************************** Meindert H. Lamers Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH United Kingdom tel +44 (0)1223 402401 fax +44 (0)1223 213556 web: http://www2.mrc-lmb.cam.ac.uk/groups/mlamers/ **************************
