Structure of PDB 7abf Chain A Binding Site BS01

Receptor Information
>7abf Chain A (length=1656) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQ
IRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFK
RMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQP
LRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKA
FFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEY
KIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHR
HSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFN
LRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHR
PPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKN
LNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHV
QYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLI
YYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEG
RVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIP
WKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKN
LGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPI
PFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPH
EALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQY
LWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNV
MLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHT
NSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQ
DIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENI
VGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFV
SVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERT
AQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFR
EAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGL
GMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPW
ESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQK
DRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMI
QALGGVEGILEHTLFKGTYFPTWEGLFWQIPNRRFTLWWSPTINRANVYV
GFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQ
ELDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSK
DVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPT
GVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRK
GLQLYS
Ligand information
>7abf Chain 5 (length=58) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuucucuucagaucgcauaaaucuuucgccuuuuacuaaagauuuccgug
gagaggaa
<<<<<<<<<<........<<<<<<<<...........>>>>>>>>...>>
>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7abf Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		W134 F279 E280 R419 N457 H461 R462 P463 P464 Y471 R474 Y594 K595 Y596 K597 R635 F639 R642 G643 L647 M1307
Binding residue
(residue number reindexed from 1)		W72 F217 E218 R357 N395 H399 R400 P401 P402 Y409 R412 Y532 K533 Y534 K535 R573 F577 R580 G581 L585 M1232
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:7abf, PDBe:7abf, PDBj:7abf
PDBsum7abf
PubMed33243851
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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