Structure of PDB 5lqw Chain A Binding Site BS04

Receptor Information

>5lqw Chain A (length=2130) Species: 4932 (Saccharomyces cerevisiae)

KAEMPPEHLRKIINTHSDMASKNYNTDKKAFLGALKYLPHAILKLLENMP
HPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRREKRD
RTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVKDWL
YDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNYYYL
FDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRVPIR
SEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLEE
EELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKWFLQHPDEEYP
VKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTKYFQQTTIDWV
EAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTLTTKERKKSRL
GNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHYILNHIGQLTG
IYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQPAWRVWLNFL
RGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYYDLELRNSVMDD
ILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKIIERY
IKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQERQR
QIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKILVLA
LEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQRVFK
PVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNWIKP
SDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKIDFTL
LNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASFIFQ
YYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYTRYL
DRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSRMRL
IRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSMCGF
EVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKFDSR
IRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVKGET
RIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPAEKLIPT
IFRYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIP
RISTLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNL
NAYRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKK
LTHAQRTGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIP
TLKISLIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPR
KSYKMNSSAADITMESWEVSKPSLLHETNDSLITNKMWFDVQLRYGDYDS
HDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLK
PLIQNSMRTIMKANPALYVLRERIRKGLQIYQSPFLNSSNYAELFNNDIK
LFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVW
AGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHML
DFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRI
SSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWI
TIESQMRDLILTEYGRKYNVNISALTQTESKNEWRKSAIANTLLYLRLKN
IYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKV
KEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKF
MAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTDEGYQWGEEN
KDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQ
EGDYNFKYGIPLEFYNEMHRPVHFLQFSEL

Ligand information

>5lqw Chain 9 (length=54)

cugaauuaacaauggauucugguauguucuguacuaacaucgauugcuuc
auuc

..................................................
....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lqw Molecular architecture of the Saccharomyces cerevisiae activated spliceosome
• Resolution: 5.8 Å
• Binding residue (original residue number in PDB): R668 S1377 K1378 M1379
• Binding residue (residue number reindexed from 1): R503 S1212 K1213 M1214

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

External links

• PDB: RCSB:5lqw, PDBe:5lqw, PDBj:5lqw
• PDBsum: 5lqw
• PubMed: 27562955
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)