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 | + | * 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, according to FASTA sequence obtained for each PDB file from PDBsum, differ quite a bit: |
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Revision as of 05:50, 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, according to FASTA sequence obtained for each PDB file from PDBsum, differ quite a bit:
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 for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment but they always seem to need to be identical to me for anything to work at the Yale Morph server.
