Structure of PDB 8qpa Chain A Binding Site BS02

Receptor Information
>8qpa Chain A (length=1971) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLEN
MPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREK
RDRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLD
WFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYF
YLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIR
QPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPL
INPISHRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALL
WAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYV
LNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLN
LLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTK
LVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMC
KDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNL
LARQFEGQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAW
RCWKANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATV
DKTVCKKNLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWL
ESRRFSPIPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLI
EQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKI
TDAYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWE
TSEGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVI
NYKDMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQM
PNDFLSFQDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEH
PDPNNENIVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTT
VQWENSFVSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQ
NEVTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTAL
IGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFY
TPKELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPN
LYRYIQPWESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIP
RINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNL
NNYRTDMIQALGGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKK
LTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIP
TLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPR
KSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLR
WGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGN
WFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQN
YGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQL
FLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKG
MLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLF
NLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHI
WPTLTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEIS
APSQQRQQIATSNYETQTFSS
Ligand information
>8qpa Chain 5 (length=79) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
acucugguuucucuucagaucgcauaaaucuuucgccuuuuacuaaagau
uuccguggagaggaacaacucugagucuu
.<<<...<<<<<<<<<<........<<<<<<<<...........>>>>>>
>>...>>>>>>>>>>.......>>>....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8qpa Structural insights into the cross-exon to cross-intron spliceosome switch
Resolution3.7 Å
Binding residue
(original residue number in PDB)		H97 K101 I132 W134 G222 S223 T224 Q226 K267 E280 L282 R284 R409 R419 R420 D423 P425 K452 N457 K460 H461 P464 K465 A466 Q467 K468 K469 R470 R474 K477 N542 K595 Y596 K597 R600 Q601 R635 F639 F640 R642 G643 P646 R763 K1294 I1301 M1307
Binding residue
(residue number reindexed from 1)		H42 K46 I77 W79 G167 S168 T169 Q171 K212 E225 L227 R229 R354 R364 R365 D368 P370 K397 N402 K405 H406 P409 K410 A411 Q412 K413 K414 R415 R419 K422 N487 K540 Y541 K542 R545 Q546 R580 F584 F585 R587 G588 P591 R696 K1227 I1234 M1240
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0017070 U6 snRNA binding
GO:0030619 U1 snRNA binding
GO:0030620 U2 snRNA binding
GO:0030623 U5 snRNA binding
GO:0070530 K63-linked polyubiquitin modification-dependent protein binding
GO:0097157 pre-mRNA intronic binding
GO:0140492 metal-dependent deubiquitinase activity
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0071222 cellular response to lipopolysaccharide
GO:0071356 cellular response to tumor necrosis factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0030532 small nuclear ribonucleoprotein complex
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071006 U2-type catalytic step 1 spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
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:8qpa, PDBe:8qpa, PDBj:8qpa
PDBsum8qpa
PubMed38778104
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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