Hi Sebastiano, Discuss things with the person who processes your deposition to the PDB. We did the same for an uncleaved influenza protein. Normally two chains but because it was uncleaved we provided a justification for numbering as two chains (pdb:1RD8). In order to make it consistent with the numbering for the existing structures, the pdb people were very obliging and agreed that things would be simpler for people to be able to compare with what was already out there. I used pdbset to change the numbering, added a link between the two virtual chains and together with the pdb people we put together a remark in the pdb header to describe what is going on. They were very helpful. Best wishes James
-----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sebastiano Pasqualato Sent: Tuesday, October 16, 2007 6:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] chain IDs and residue numbering in depositing chimeras PDB Dear all, I'm going to deposit to the PDB a structure in which a polypetidic chain is made up by the fusion of two portions of proteins. That is, it is a chimera of two proteins (say aa 1-100 of protein X fused to aa 50-150 of protein Y) Currently, this polypetidic chain has got a single chain ID and I've kept residue numbers growing without caring about the original residue numbers of the second protein (i.e. the chain A goes from residue 1 to 100, then 101 to 201 correspond to residues 50-150 of protein Y) Now, I've always found it nice to have the correct numbering on the residues, when I download a pdb, and was wondering if any of you could suggest me a way to have this in my structure. I wouldn't like to change the chain ID, a) beacuse what's crystallized was a single polypeptidic chain b) because many programs will not put a link between residues with different chain IDs A solution would be adding something like "1000" to the numbers of the residues of the second protein, but then again the residues numbers will jump from 100 to 1050 and there will be no link created by some programs (isn't it?)... How could I do? Any suggestion is warmly welcomed! Thanks in advance for the help, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310