Structure of PDB 5lj3 Chain C Binding Site BS02

Receptor Information
>5lj3 Chain C (length=882) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKEVEVLMETKNTQSPQTPLVEPVTERTKLQEHTIFTQLKKNIPKTRYNR
DYMLSMANIPERIINVGVIGPLHSGKTSLMDLLVIDSHKRIPDMSKNVEL
GWKPLRYLDNLKQEIDRGLSIKLNGSTLLCTDLESKSRMINFLDAPGHVN
FMDETAVALAASDLVLIVIDVVEGVTFVVEQLIKQSIKNNVAMCFVINKL
DRLILDLKLPPMDAYLKLNHIIANINSFTKGNVFSPIDNNIIFASTKLGF
TFTIKEFVSYYYAHSIPSSKIDDFTTRLWGSVYYHKGNFRTKPFENVEKY
PTFVEFILIPLYKIFSYALSMEKDKLKNLLRSNFRVNLSQEALQYDPQPF
LKHVLQLIFRQQTGLVDAITRCYQPFELFDNKTAHLSIPGKSTPEGTLWA
HVLKTVDYGGAEWSLVRIYSGLLKRGDTVRILDTSQSESRQKRQLHDIED
DETPSCEVEEIGLLGGRYVYPVHEAHKGQIVLIKGISSAYIKSATLYSVK
SKEDMKQLKFFKPLDYITEAVFKIVLQPLLPRELPKLLDALNKISKYYPG
VIIKVEESGEHVILGNGELYMDCLLYDLRASYAKIEIKISDPLTVFSESC
SNESFASIPVSNISVAAEPMDSKMIQDLSRPRKLSKILRTEYGWDSLASR
NVWSFYNLINDTLPDEISPELLSKYKEQIIQGFYWAVKEGPLAEEPIYGV
QYKLLSISVPSDVNIDVMKSQIIPLMKKACYVGLLTAIPILLEPIYEVDI
TVHAPLLPIVEELMKKRRGSRIYKTIKVAGTPLLEVRGQVPVIESAGFET
DLRLSTNGLGMCQLYFWHKIWRKVPGDVLDKDAFIPKLKPAPINSLSRDF
VMKTRRRKGISTGGFMSNDGPTLEKYISAELY
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 chain5lj3 Chain C Residue 1101 [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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PDB5lj3 Cryo-EM structure of the spliceosome immediately after branching.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		L142 H143 G145 K146 T147 S148 L189 S190 G217 K269 S315 T316 K317
Binding residue
(residue number reindexed from 1)		L72 H73 G75 K76 T77 S78 L119 S120 G147 K199 S245 T246 K247
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
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Cellular Component
External links
PDB RCSB:5lj3, PDBe:5lj3, PDBj:5lj3
PDBsum5lj3
PubMed27459055
UniProtP36048|SN114_YEAST Pre-mRNA-splicing factor SNU114 (Gene Name=SNU114)

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