Structure of PDB 9fmd Chain A Binding Site BS02

Receptor Information
>9fmd Chain A (length=2250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHG
DMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITG
AISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEP
PLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGST
YQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIP
GGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLP
HHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDD
DEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDI
PLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFR
SFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNL
KPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQL
ADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKG
PGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTK
QRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANI
PWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKK
NLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSP
IPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNP
HEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQ
YLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECN
VMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNH
TNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSF
QDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNEN
IVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSF
VSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKER
TAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYF
REAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGG
LGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQP
WESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQ
KDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDM
IQALGGVEGILEHTLFKGTYFPTWEGLFWETNAQRSGLNQIPNRRFTLWW
SPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHES
IVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWN
VSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYT
TDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANP
ALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRV
TIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAK
WKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSE
LQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLIL
ILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLIL
ADYGKKNNVNVASLTQSEIRDIILGMEISAPFSSKTEWRVRAISAANLHL
RTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPD
NPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWIHTQPNES
PQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGY
EWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMG
VRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA
Ligand information
>9fmd Chain 5 (length=92) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
guuucucuucagaucgcauaaaucuuucgccuuuuacuaaagauuuccgu
ggagaggaacaccaauuuuuugagccuugccuuggcaaggcu
<<<<<<<<<<<........<<<<<<<<...........>>>>>>>>...>
>>>>>>>>>>............<<<<<<<<....>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9fmd Mechanism for the initiation of spliceosome disassembly.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		K50 G52 F53 V54 D55 A56 H97 K101 I132 W134 R217 G222 S223 T224 K267 F279 E280 R409 R417 R419 R420 D423 P425 K428 K452 N457 H461 P464 K465 A466 Q467 K468 K469 R474 K595 Y596 K597 R600 Q601 R635 F639 F640 R642 G643 P646 L647 V767 D768 K1294 I1301
Binding residue
(residue number reindexed from 1)		K26 G28 F29 V30 D31 A32 H73 K77 I108 W110 R193 G198 S199 T200 K243 F255 E256 R385 R393 R395 R396 D399 P401 K404 K428 N433 H437 P440 K441 A442 Q443 K444 K445 R450 K571 Y572 K573 R576 Q577 R611 F615 F616 R618 G619 P622 L623 V743 D744 K1270 I1277
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:9fmd, PDBe:9fmd, PDBj:9fmd
PDBsum9fmd
PubMed38925148
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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