Structure of PDB 6ff4 Chain A Binding Site BS02

Receptor Information
>6ff4 Chain A (length=2238) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEEKLQEKARKWQQLQAKRYAEKRKVDAQKEDMPPEHVRKIIRDHGDMTN
RKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITGAISF
VNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDY
ADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQRW
QFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPK
FEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVH
LTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDDEEF
ELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIPLVK
NWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKA
TKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVK
TLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGL
QYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGPGCG
FWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQRVE
SHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKV
PGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGR
LTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFP
PLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEAL
SRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWY
EADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLE
SRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSY
GIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIA
TEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGY
NNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVY
SKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQC
FLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAV
VNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGML
SMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESE
FIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRH
TLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQAL
GGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTNAQRSGLNQ
IPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFR
AHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCAD
ILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIER
YARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQ
AMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIW
FVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWA
GQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLD
FPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTIS
SYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIK
VEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEIFSSKTEWRVRAI
SAANLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYL
YGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWI
HTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAY
KLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSS
WNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLN
Ligand information
>6ff4 Chain 5 (length=70) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ucugguuucucuucagaucgcauaaaucuuucgccuuuuacuaaagauuu
ccguggagaggaacaacucu
.....<<<<<<.<<<........<<<<<<<<...........>>>>>>>>
...>>>.>>>>>>.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ff4 Structure and Conformational Dynamics of the Human Spliceosomal BactComplex.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		A56 H97 G222 S223 T224 K267 E280 R409 R417 R419 R420 D423 P425 K428 K452 N457 H461 P464 K469 R470 R474 K595 Y596 K597 R600 Q601 R635 F639 R642 G643 P646 L647 V767 D768 K769 R1298
Binding residue
(residue number reindexed from 1)		A28 H69 G194 S195 T196 K239 E252 R381 R389 R391 R392 D395 P397 K400 K424 N429 H433 P436 K441 R442 R446 K567 Y568 K569 R572 Q573 R607 F611 R614 G615 P618 L619 V739 D740 K741 R1270
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:6ff4, PDBe:6ff4, PDBj:6ff4
PDBsum6ff4
PubMed29361316
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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