Structure of PDB 3jb9 Chain B Binding Site BS02

Receptor Information
>3jb9 Chain B (length=904) Species: 284812 (Schizosaccharomyces pombe 972h-) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVVLHEDKQYYPSAEEVYGSNVDIMVQEQDTQPLSQPIIEPIRHKRIAIE
TTNVPDTVYKKEFLFGLLTGTDDVRSFIVAGHLHHGKSALLDLLVYYTHP
DTKPPKRRSLRYTDTHYLERERVMSIKSTPLTLAVSDMKGKTFAFQCIDT
PGHVDFVDEVAAPMAISDGVVLVVDVIEGVMINTTRIIKHAILHDMPIVL
VLNKVDRLILELRLPPNDAYHKLRHVIDEVNDNICQISKDLKYRVSPELG
NVCFASCDLGYCFTLSSFAKLYIDRHGGIDVDLFSKRLWGDIYFDSKTRK
FAKQSLDGSGVRSFVHFILEPLYKLHTLTISDEAEKLKKHLSSFQIYLKP
KDYLLDPKPLLQLICASFFGFPVGFVNAVTRHIPSPRENAARKASQSYIG
PINSSIGKAILEMSREESAPLVMHVTKLYNTVDANNFYAFARVYSGQVKK
GQKVKVLGENYSLEDEEDMVVAHIAEICVPCARYRLHVDGAVAGMLVLLG
GVDNSISKTATIVSDNLKDDPYIFRPIAHMSESVFKVAVEPHNPSELPKL
LDGLRKTNKSYPLSITKVEESGEHTIFGTGEMYMDCLLYDLRTLYSEIEI
RVSDPVARFCETAVDTSSIKCFSDTPNKKNRITMVVEPLEKGISNDIENG
KVNINWPQKRISEFFQKNYDWDLLASRSIWAFGPDDRGTNILRDDTLSTD
VDKNVLNSVKEYIKQGFQWGTREGPLCDETIRNVNFRLMDVVLAPEQIYR
GGGQIIPTARRVCYSSFLTASPRLMEPVYMVEVHAPADSLPIIYDLLTRR
RGHVLQDIPRPGSPLYLVRALIPVIDSCGFETDLRVHTQGQAMCQMVFDH
WQVVPGDPLDKSIKPKPLEPARGSDLARDFLIKTRRRKGLVEDVSTTRYF
DQEM
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain3jb9 Chain B Residue 1000 [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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PDB3jb9 Structure of a yeast spliceosome at 3.6-angstrom resolution
Resolution3.6 Å
Binding residue
(original residue number in PDB)		G153 K154 S155 S192 K271 D273 S323 D325
Binding residue
(residue number reindexed from 1)		G86 K87 S88 S125 K204 D206 S256 D258
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:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0140727 siRNA-mediated pericentric heterochromatin formation
Cellular Component
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005721 pericentric heterochromatin
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071014 post-mRNA release spliceosomal complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3jb9, PDBe:3jb9, PDBj:3jb9
PDBsum3jb9
PubMed26292707
UniProtO94316|SN114_SCHPO Pre-mRNA-splicing factor cwf10 (Gene Name=cwf10)

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