Structure of PDB 5y88 Chain A Binding Site BS04

Receptor Information
>5y88 Chain A (length=1903) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMV
RAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNK
TKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLD
YNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNV
DAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKN
LGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKT
TTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWK
ANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTM
VKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRS
FSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAY
DNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAY
LDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRG
QSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKD
MSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEF
MQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPN
FENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWE
NAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTK
QRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFT
YFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKEL
GGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYI
TTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTL
FQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRT
DVIQALGGIETILEHTLFKGTGFNSWEGLFWENRRFTLWWSPTINRANVY
VGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDICQILD
GELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPSLLHET
NDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSP
TGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVLRERIR
KGLQIYQYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTL
NPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQ
IIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKAT
EPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTI
TIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDI
ILG
Ligand information
Ligand IDIHP
InChIInChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
InChIKeyIMQLKJBTEOYOSI-GPIVLXJGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
ACDLabs 12.01
OpenEye OEToolkits 2.0.7		C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
CACTVS 3.385O[P](O)(=O)O[C@@H]1[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
FormulaC6 H18 O24 P6
NameINOSITOL HEXAKISPHOSPHATE;
MYO-INOSITOL HEXAKISPHOSPHATE;
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
ChEMBLCHEMBL1233511
DrugBankDB14981
ZINCZINC000169289809
PDB chain5y88 Chain A Residue 3000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5y88 Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae
Resolution3.46 Å
Binding residue
(original residue number in PDB)		R236 K517 H659 K684 Y688 K697 Y1620
Binding residue
(residue number reindexed from 1)		R110 K373 H515 K540 Y544 K553 Y1450
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000386 second spliceosomal transesterification activity
GO:0003723 RNA binding
GO:0003729 mRNA 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:0097157 pre-mRNA intronic binding
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000350 generation of catalytic spliceosome for second transesterification step
GO:0000387 spliceosomal snRNP assembly
GO:0000389 mRNA 3'-splice site recognition
GO:0000395 mRNA 5'-splice site recognition
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
Cellular Component
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005737 cytoplasm
GO:0046540 U4/U6 x U5 tri-snRNP complex
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:5y88, PDBe:5y88, PDBj:5y88
PDBsum5y88
PubMed28919079
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

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