Structure of PDB 9fmd Chain A Binding Site BS03

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 6 (length=97) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gugcucgcuucggcagcacauauacuaaaauuggaacgauacagagaaga
uuagcauggccccugcgcaaggaugacacgcaaauucgugaagcguu
<<<<<.<<....>>>>>>>...............................
......<<...<<<.....>>>....>>...................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB9fmd Mechanism for the initiation of spliceosome disassembly.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		Q39 K48 K480 K511 E534 K536 K537 R539 G541 A543 W651 N654 R658 R663 K666 V668 K670 T671 T673 Q675 R676 S679 L683 T1793 N1797 T1799 K1801 A1828 K1831
Binding residue
(residue number reindexed from 1)		Q15 K24 K456 K487 E510 K512 K513 R515 G517 A519 W627 N630 R634 R639 K642 V644 K646 T647 T649 Q651 R652 S655 L659 T1755 N1759 T1761 K1763 A1790 K1793
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
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)

[Back to BioLiP]