Structure of PDB 5mq0 Chain A Binding Site BS02

Receptor Information

>5mq0 Chain A (length=1914) Species: 4932 (Saccharomyces cerevisiae)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPFNSIDRVIFRVPIRSEYKV
AFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLEDFAPLL
AEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKWFLQHPDE
EYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTKYFQQTTI
DWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTLTTKERKK
SRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHYILNHIGQ
LTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQPAWRVWL
NFLRGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYYDLELRNSV
MDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKII
ERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQE
RQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKIL
VLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQR
VFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNW
IKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKID
FTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASF
IFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYT
RYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSR
MRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSM
CGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKF
DSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVK
GETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPASDL
SWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWAEYA
TKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHRIRR
EFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEHTLF
KGTGFNSWEGLFWQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHG
KIPTLKISLIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETV
HPRKSYKMNSSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDV
QLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDA
YGNWFNGLKPLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLN
SSNYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKT
GHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVT
RKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQM
VLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKS
YHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGQ
NIKAPSVKRQKMAE

Ligand information

>5mq0 Chain E (length=16)

uaagugaucuagaaag

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mq0 Structure of a spliceosome remodelled for exon ligation.
• Resolution: 4.17 Å
• Binding residue (original residue number in PDB): K351 V516 V520 Q523 K524 R614 Y667 R668 Y671 R678 S1377 K1378 M1379 P1380 Y1620 V1621 G1636 K1637
• Binding residue (residue number reindexed from 1): K225 V354 V358 Q361 K362 R452 Y505 R506 Y509 R516 S1215 K1216 M1217 P1218 Y1434 V1435 G1450 K1451

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:5mq0, PDBe:5mq0, PDBj:5mq0
• PDBsum: 5mq0
• PubMed: 28076345
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)