User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods

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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.

Revision as of 05:37, 7 January 2012

MORPH

  • First I changed chain X of 3b8a to chain A to match 1ig8 using 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 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.

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Wayne Decatur

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