Structure of PDB 5ylz Chain C Binding Site BS02

Receptor Information
>5ylz Chain C (length=878) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHPYGKEVEVLMETKNTQSPQTPLVEPVTERTKLQEHTIFTQLKKNIPKT
RYNRDYMLSMANIPERIINVGVIGPLHSGKTSLMDLLVIDSHKRIPDMSK
NVELGWKPLRYLDNLKQEIDRGLSIKLNGSTLLCTDLESKSRMINFLDAP
GHVNFMDETAVALAASDLVLIVIDVVEGVTFVVEQLIKQSIKNNVAMCFV
INKLDRLILDLKLPPMDAYLKLNHIIANINSFTKGNVFSPIDNNIIFAST
KLGFTFTIKEFVSYYYAHSIPSSKIDDFTTRLWGSVYYHKGNFRTKPFEN
VEKYPTFVEFILIPLYKIFSYALSMEKDKLKNLLRSNFRVNLSQEALQYD
PQPFLKHVLQLIFRQQTGLVDAITRCYQPFELFDNKTAHLSIPGKSTPEG
TLWAHVLKTVDYGGAEWSLVRIYSGLLKRGDTVRILDTSQSESREDDETP
SCEVEEIGLLGGRYVYPVHEAHKGQIVLIKGISSAYIKSATLYSVKSKED
MKQLKFFKPLDYITEAVFKIVLQPLLPRELPKLLDALNKISKYYPGVIIK
VEESGEHVILGNGELYMDCLLYDLRASYAKIEIKISDPLTVFSESCSNSR
LGEENLPGLSISVAAEPMDSKMIQDLSRNTLGKGQNCLDIDGIMDNPRKL
SKILRTEYGWDSLASRNVWSFYNGNVLINDTLPDEISPELLSKYKEQIIQ
GFYWAVKEGPLAEEPIYGVQYKLLSISVPSDVNIDVMKSQIIPLMKKACY
VGLLTAIPILLEPIYEVDITVHAPLLPIVEELMKKRRGSRIYKTIKVAGT
PLLEVRGQVPVIESAGFETDLRLSTNGLGMCQLYFWHKIWRKVPGDVLDK
DAFIPKLKPAPINSLSRDFVMKTRRRKG
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain5ylz Chain C Residue 1500 [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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PDB5ylz Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae
Resolution3.6 Å
Binding residue
(original residue number in PDB)		H143 G145 K146 S148 S190 G217 K269 D271 R272 T316 K317
Binding residue
(residue number reindexed from 1)		H77 G79 K80 S82 S124 G151 K203 D205 R206 T250 K251
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030623 U5 snRNA binding
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000349 generation of catalytic spliceosome for first transesterification step
GO:0000387 spliceosomal snRNP assembly
GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
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:0005829 cytosol
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071007 U2-type catalytic step 2 spliceosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ylz, PDBe:5ylz, PDBj:5ylz
PDBsum5ylz
PubMed29153833
UniProtP36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)

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