Structure of PDB 5gm6 Chain A Binding Site BS01

Receptor Information
>5gm6 Chain A (length=2200) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVR
AQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKT
KLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDY
NFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVD
AFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNL
GKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTT
TKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKA
NIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMV
KKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSF
SPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYD
NPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYL
DQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQ
SAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDM
SHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFM
QFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNF
ENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWEN
AFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQ
RTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTY
FREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELG
GLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYIT
TWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLF
QRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTD
VIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQR
TGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISL
IQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMN
SSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDS
HDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLK
PLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFN
NDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIH
TSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLE
VHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDW
LDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTD
EQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGKNEWRKSAIA
NTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIY
GMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGW
IHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLT
DEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWN
YTFMGTAFNQEGDYNFKYGIPLEFYNEMHRPVHFLQFSEELEAEQIDVFS
Ligand information
>5gm6 Chain D (length=117) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggaggucaacaucaagaacugugggccuuugccuauagaacuuauaacga
acaugguucuugccuuuuaccagaaccauccggguguugucuccauccau
auuuuuuggaacuuuuc
<<<<<.<<<<<<<.....<<<<<<<<....>>>>>>>>............
..<<<<<<<<...........>>>>>>>>...>>>>>>>>>>>>......
.................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5gm6 Structure of a yeast activated spliceosome at 3.5 angstrom resolution
Resolution3.5 Å
Binding residue
(original residue number in PDB)		Y128 P130 K174 K190 T205 R207 R284 T296 S297 K334 K340 E353 L355 R358 W402 F484 R488 R495 K503 K527 N528 N532 H535 P539 N541 K544 K546 K549 K670 Y671 K672 H675 R709 N713 R716 G717 H839
Binding residue
(residue number reindexed from 1)		Y2 P4 K48 K64 T79 R81 R158 T170 S171 K208 K214 E227 L229 R232 W276 F339 R343 R350 K358 K382 N383 N387 H390 P394 N396 K399 K401 K404 K525 Y526 K527 H530 R564 N568 R571 G572 H694
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000386 second spliceosomal transesterification activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0017070 U6 snRNA binding
GO:0030619 U1 snRNA binding
GO:0030620 U2 snRNA binding
GO:0030623 U5 snRNA binding
GO:0097157 pre-mRNA intronic binding
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000350 generation of catalytic spliceosome for second transesterification step
GO:0000387 spliceosomal snRNP assembly
GO:0000389 mRNA 3'-splice site recognition
GO:0000395 mRNA 5'-splice site recognition
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
Cellular Component
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005737 cytoplasm
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071013 catalytic step 2 spliceosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5gm6, PDBe:5gm6, PDBj:5gm6
PDBsum5gm6
PubMed27445306
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

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