Hi
I am trying to thread a target rhodopsin sequence from humans to the template bovine rhodopsin structure (pdb1f88).
The rhodopsin crystal structure exists in the pdb file as a crystal dimer represented by chain A and B. Each chain is 348 amino acids, but there are missing residues on both chains.
I used the simple automodel script, and it worked well. When I tried to include both the ligands and the carbohydrates (hetatms) into the structure by setting env.io.hetatm = True, I get errors that do not make much sense to me. My structure pdb is different from the hetatm example pdb for in that the ligands hetatm residue numbers do not immediately follow the atom residue sequence.
Here is a summary of the heteroatoms that follow the seqres
HET NAG A 501 14 HET NAG A 502 14 HET NAG B 601 14 HET NAG B 602 14 HET MAN B 603 11 HET NAG A 701 14 HET NAG A 702 14 HET NAG B 801 14 HET NAG B 802 14 HET HG A 901 1 HET HG B 902 1 HET HG A 903 1 HET HG B 904 1 HET HG A 905 1 HET HG B 906 1 HET ZN A 907 1 HET ZN B 908 1 HET ZN B 909 1 HET ZN A 910 1 HET RET A 977 20 HET RET B 978 20
There are no amino acids residue numbers that flank the hetam numbers. That is, there is no amino acid numbers from 803 to 900. These entries are left unspecified.
All hetatms are described after chain B in the ATOM section.
ATOM 5067 OD1 ASN B 326 30.599 31.795 -7.049 1.00107.30 O ATOM 5068 ND2 ASN B 326 30.914 33.473 -8.519 1.00107.62 N TER 5069 ASN B 326 HETATM 5070 C1 NAG A 501 37.620 3.757 -28.808 1.00 65.21 C HETATM 5071 C2 NAG A 501 38.420 5.021 -29.058 1.00 65.24 C HETATM 5072 C3 NAG A 501 37.477 6.163 -29.455 1.00 66.66 C
I first tried to include all hetatms as '.' with the unspecified residues past the end of the protein (aa 348) replaced with '-'.
>P1;B._taurus structureY:B._taurus:1 :A: 977:A:ground state rhodopsin:Bovine: : MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLA VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT WVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----S ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTT LCCGKNP------STTVSKTETSQVAPA---------------------------------------------------- -------------------------------------------------------------------------------- --------------------..---------------------------------------------------------- -------------------------------------------------------------------------------- ------------------------------------------------------------..------------------ -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- --------------------.-.-.----.-------------------------------------------------- ----------------.*
It results in this error:
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 347 650 For alignment entry: 1 B._taurus
When I forgo the trailing '-' and simply append hetatms to the end in a series of '.':
>P1;B._taurus structureY:B._taurus:1 :A: 977:A:ground state rhodopsin:Bovine: : MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP------STTVSKTETSQVAPA........*
I get the following error:
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 347 650 For alignment entry: 1 B._taurus
I've seen the following thread and tried to follow the advice enclosed, but I am still having trouble. http://salilab.org/archives/modeller_usage/2008/msg00183.html http://salilab.org/archives/modeller_usage/2008/msg00186.html
The structure ID of bovine rhodopsin is pdb1f88.
Thanks in advance,