Structure of PDB 6id0 Chain A Binding Site BS01

Receptor Information
>6id0 Chain A (length=1981) 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
GGPKFEPLVREFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYHT
PNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDDEEFELPEFV
EPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIPLVKNWYREH
CPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATKFFQS
TKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKE
RKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAH
VGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGW
RVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQRVESHFDLE
LRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGLPTP
IENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTRLYL
KAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKH
DTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRH
LLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRR
LFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESRFEKM
YEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGIIRGL
QFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEAAHP
IRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCW
PRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPN
LLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDD
ESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNTQEL
LDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMGHVL
IPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFIDSQR
VWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDK
GWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGI
LEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRF
TLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQK
IHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILLFAS
YKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKF
LDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIM
KANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTN
VYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLG
QLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVI
KGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFS
RLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLK
DLILADYGKKNNVNVASLTQSEIRDIILGME
Ligand information
>6id0 Chain B (length=98) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ugguuucucuucagaucgcauaaaucuuucgccuuuuacuaaagauuucc
guggagaggaacaacucugagucuuaacccaauuuuuugaggccuugc
...<<<<<<<<<<........<<<<<<<<.<.......>.>>>>>>>>..
.>>>>>>>>>>.....................................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6id0 Structures of the human spliceosomes before and after release of the ligated exon.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		G52 F53 V54 Q57 H97 I132 W134 G222 S223 T224 K267 F279 E280 R409 R417 R419 R420 D423 K428 N457 H461 P463 P464 K465 A466 K469 R470 R474 K595 Y596 K597 R600 Q601 R635 F639 F640 R642 G643 P646 T766 K1294 R1298
Binding residue
(residue number reindexed from 1)		G28 F29 V30 Q33 H73 I108 W110 G198 S199 T200 K243 F255 E256 R375 R383 R385 R386 D389 K394 N423 H427 P429 P430 K431 A432 K435 R436 R440 K561 Y562 K563 R566 Q567 R601 F605 F606 R608 G609 P612 T732 K1260 R1264
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA 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: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:6id0, PDBe:6id0, PDBj:6id0
PDBsum6id0
PubMed30728453
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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