User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions
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* First I changed chain X of 3b8a to chain A to match 1ig8 using [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] for the protein. I knew PDB Goodies ignored and left out the heteroatoms so I changed the few lines of the glucose ligand to chain a by hand. Th heterotoms will not be used by the Yale Morph server but I need them in the original file in order to be able to use fit or compare to add them in later. | * First I changed chain X of 3b8a to chain A to match 1ig8 using [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] for the protein. I knew PDB Goodies ignored and left out the heteroatoms so I changed the few lines of the glucose ligand to chain a by hand. Th heterotoms will not be used by the Yale Morph server but I need them in the original file in order to be able to use fit or compare to add them in later. | ||
* Submitted 1gi8 and the altered 3b8a to the Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] | * Submitted 1gi8 and the altered 3b8a to the Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] | ||
* When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein have several differences: | |||
1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47 | |||
|||||||.:|...|.:|||.:|||:.|.||||.||.|||:||||||| | |||
3b8a 1 SMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIP 50 | |||
1ig8 48 MIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLGGDRTFDTTQSKYRL 97 | |||
|||||||:||||||||::|||||||||||||||||.|:.|||||||||:| | |||
3b8a 51 MIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKL 100 | |||
1ig8 98 PDAMRTTQNPDELWEFIADSLKAFIDEQFPQGISEPIPLGFTFSFPASQN 147 | |||
|..||||::.:|||.|||||||.|:.||.... ::.:|||||||:||||| | |||
3b8a 101 PHDMRTTKHQEELWSFIADSLKDFMVEQELLN-TDTLPLGFTFSYPASQN 149 | |||
1ig8 148 KINEGILQRWTKGFDIPNIENHDVVPMLQKQITKRNIPIEVVALINDTTG 197 | |||
||||||||||||||||||:|.|||||:||.:|:||.:|||:|||||||.| | |||
3b8a 150 KINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRELPIEIVALINDTVG 199 | |||
1ig8 198 TLVASYYTDPETKMGVIFGTGVNGAYYDVCSDIEKLQGKLSDDIPPSAPM 247 | |||
||:||||||||||||||||||||||:|||.||||||:|||:||||.::|| | |||
3b8a 200 TLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPM 249 | |||
1ig8 248 AINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQTFEKMSSGYYLGEIL 297 | |||
|||||||||||||:||||||||:.:||:|||||||.||||:|||||||:| | |||
3b8a 250 AINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELL 299 | |||
1ig8 298 RLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARIEEDPFENLEDTDDL 347 | |||
||.|:::.::|.:.|:|||||..:|::||||||||||:|||||||||||: | |||
3b8a 300 RLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDI 349 | |||
1ig8 348 FQNEFGINTTVQERKLIRRLSELIGARAARLSVCGIAAICQKRGYKTGHI 397 | |||
||.:||:.||:.||||||||.||||.|||||:|||||||||||||||||| | |||
3b8a 350 FQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHI 399 | |||
1ig8 398 AADGSVYNRYPGFKEKAANALKDIYGWTQTSLDDYPIKIVPAEDGSGAGA 447 | |||
||||||||:||||||.||..|:||||||..:..| ||.|||||||||||| | |||
3b8a 400 AADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKD-PITIVPAEDGSGAGA 448 | |||
1ig8 448 AVIAALAQKRIAEGKSVGIIGA 469 | |||
||||||::||||||||:||||| | |||
3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470 | |||
According to help page, this shouldn't matter but they always seem to need to be identical to me for anything to work at the Yale Morph server. | |||
