Structure of PDB 6j6q Chain A Binding Site BS02

Receptor Information

>6j6q Chain A (length=1913) Species: 559292 (Saccharomyces cerevisiae S288C)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIPHFGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKG
KMVRAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTN
HNKTKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYL
HLDYNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRL
GNVDAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKF
NKNLGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEI
VKTTTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWR
CWKANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVE
KTMVKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLE
SRSFSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIE
EAYDNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKIT
DAYLDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDV
SRGQSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVIN
FKDMSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNP
NEFMQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENP
DPNFENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSI
KWENAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDE
RTKQRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLIS
LFTYFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTP
KELGGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIF
RYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRI
STLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNA
YRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWEKSQIPNRRFTLWWSP
TINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIV
FDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVS
KPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTD
NVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPAL
YVLRERIRKGLQIYQSSYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVAT
KAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVR
SLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSID
KLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESA
KMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNIS
ALTQTEIKDIILG

Ligand information

>6j6q Chain B (length=57)

gugaucuagaaagguaugucuaaaguuacuuaugcucuuauuuacuaaca
aaaucaa

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Receptor-Ligand Complex Structure

Structure summary

• PDB: 6j6q Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): P347 Q523 T607 K608 R610 K611 R614 Y667 R668 Y671 M674 R678 S925 K926 R928 M972 S1325 K1330 S1377 K1378 M1379 P1380 R1521 K1535 Q1600 Y1620 K1637 R1650 E1817 R1904 S1906
• Binding residue (residue number reindexed from 1): P221 Q382 T466 K467 R469 K470 R473 Y526 R527 Y530 M533 R537 S784 K785 R787 M831 S1184 K1189 S1236 K1237 M1238 P1239 R1380 K1394 Q1438 Y1458 K1475 R1488 E1655 R1732 S1734

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:6j6q, PDBe:6j6q, PDBj:6j6q
• PDBsum: 6j6q
• PubMed: 30879786
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)