On Tuesday, July 25, 2023, Joel Subach <
mjsubach@alumni.ncsu.edu> wrote:
Hi Alphafold Multimer may be able to predict the entire oligomer depending on the residues, thanks:)
On Tuesday, July 25, 2023* , g.m.tuveri--- via modeller_usage <modeller_usage@salilab.org> wrote:
Hello, I'm trying to add some missing domains to a big homodimeric protein, pdb 8em4. I predicted the missing structures with Alphafold and now I want to create an entire model of 8em4 using multiple templates. I am using the following directives:
# Comparative modeling by the AutoModel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the AutoModel class
log.verbose() # request verbose output
class MyModel(AutoModel):
def special_restraints(self,aln):
# Constrain the A and B chains to be identical (but only restrain
# the C-alpha atoms, to reduce the number of interatomic distances
# that need to be calculated):
s1 = Selection(self.chains['A']).only_atom_types('CA')
s2 = Selection(self.chains['B']).only_atom_types('CA')
self.restraints.symmetry.append(Symmetry(s1, s2, 1.0))
def user_after_single_model(self):
# Report on symmetry violations greater than 1A after building
# each model:
self.restraints.symmetry.report(1.0)
env = Environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = ['.']
a = MyModel(env,
alnfile = 'ali_lrp2.ali', # alignment filename
knowns = ("8em4","domain1","domain2","domain3"), # codes of the templates
sequence = 'A0A6P5R9N9') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to calculate)
a.make() # do the actual comparative modeling
In ali_lrp2.ali I have aligned the entire lrp2 sequence with the known 8em4 sequence for the two monomers. Headers are the following:
>P1;A0A6P5R9N9
sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00
>P1;8em4
structureX:8em4:28:A:4414:B::: 2.83:-1.00
I don't report the sequences, but for each of the headers I am separating the two monomers with a /, for example
>P1;A0A6P5R9N9
sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00
AAAAAAAAAAAAAAAAAAAA/
BBBBBBBBBBBBBBBBBBBB*
>P1;8em4
structureX:8em4:28:A:4414:B::: 2.83:-1.00
AAAAAA-----AAA-AAAAA/
BBBBBB-----BBB-BBBBB*
Then I add the missing domain template sequence in the following way:
>P1;domain1
structureX:domain1::A::B::::
------AAAAA---------/
------BBBBB---------*
>P1;domain2
structureX:domain2::A::B::::
--------------A-----/
--------------B-----*
I keep obtaining knots, especially in the long domain. I made sure that the alignment is correct, but maybe the request of symmetry or the use of multiple templates are badly implemented.
I attach the long alignment file
>P1;A0A6P5R9N9
sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00
MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG
TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE
QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ
LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA
YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD
SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN
ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD
DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN
GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS
TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ
RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD
LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL
VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV
YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD
EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA
QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW
TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK
IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD
GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV
RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC
PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD
CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ
NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT
CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS
SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW
ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD
MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC
NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG
FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV
DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT
DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS
KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY
WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL
TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP
SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL
MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP
GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL
TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA
KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV
DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR
DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG
FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL
HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR
GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD
PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI
YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR
KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ
SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL
RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY
VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS
NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT
SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL
TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ
QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA
RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC
ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY
VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC
GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD
TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN
CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE
FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK
LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV
DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK
RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI
EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE
KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS
DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA
RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH
HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT
THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF
QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL
CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN
EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC
IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA
VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD
NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT
CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF
ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI
YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC
DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP
STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC
AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG
LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL
AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG
LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS
DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ
NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG
GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP
KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY
RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET
IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV
TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT
NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD
TANLVKEDSDV/
MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG
TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE
QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ
LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA
YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD
SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN
ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD
DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN
GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS
TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ
RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD
LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL
VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV
YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD
EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA
QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW
TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK
IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD
GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV
RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC
PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD
CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ
NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT
CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS
SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW
ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD
MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC
NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG
FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV
DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT
DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS
KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY
WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL
TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP
SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL
MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP
GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL
TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA
KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV
DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR
DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG
FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL
HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR
GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD
PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI
YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR
KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ
SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL
RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY
VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS
NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT
SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL
TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ
QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA
RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC
ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY
VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC
GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD
TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN
CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE
FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK
LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV
DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK
RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI
EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE
KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS
DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA
RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH
HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT
THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF
QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL
CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN
EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC
IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA
VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD
NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT
CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF
ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI
YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC
DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP
STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC
AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG
LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL
AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG
LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS
DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ
NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG
GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP
KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY
RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET
IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV
TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT
NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD
TANLVKEDSDV*
>P1;8em4
structureX:8em4:28:A:4414:B:MOL_ID 1; MOLECULE LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN CHAIN A, B; SYNONYM LRP-2,GLYCOPROTEIN 330,GP330,MEGALIN:MOL_ID 1; ORGANISM_SCIENTIFIC MUS MUSCULUS; ORGANISM_COMMON HOUSE MOUSE; ORGANISM_TAXID 10090: 2.83:-1.00
----------------------------CGSGNFRCDNGYCIPASWRCDG
TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE
QQNC----------------------------------------------
--------------------------------------------------
--------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD
SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE--
-----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD
DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN
GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS
TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ
RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD
LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL
VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV
YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD
EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA
QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW
TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK
IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD
GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV
RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC
PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD
CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ
NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT
CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS
SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW
ECDGHPDCIQGSDEHNGCVPKT----------------------------
--------------------------------------------------
NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG
FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM
DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT
DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS
KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY
WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL
TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP
SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL
ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP
GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL
TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA
KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV
DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR
DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG
FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL
HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR
GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD
PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI
YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR
KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ
SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL
RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY
VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS
NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT
SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL
TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ
QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA
RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC