Structure of PDB 5xjc Chain D Binding Site BS01

Receptor Information
>5xjc Chain D (length=1722) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPK
PFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCA
PTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVG
SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGER
TYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSA
TLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQI
MNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLR
EGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFAD
KHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQML
GRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNA
EIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRR
LDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQ
LLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIE
EPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRG
WAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERL
YDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELT
ITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLIT
FFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLD
LQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTG
SGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNK
KVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVV
DEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHW
LGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKH
SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEK
LSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWG
MNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCV
IMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVD
YLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCIS
IEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAA
EYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQ
LSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAM
WSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQ
IADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIA
PLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHN
YTLYFMSDAYMGCDQEYKFSVD
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5xjc Chain D Residue 2201 [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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PDB5xjc An Atomic Structure of the Human Spliceosome
Resolution3.6 Å
Binding residue
(original residue number in PDB)		Q485 G508 K509 T510 E616 N820
Binding residue
(residue number reindexed from 1)		Q82 G105 K106 T107 E213 N417
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
Biological Process
GO:0000354 cis assembly of pre-catalytic spliceosome
GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
GO:0000398 mRNA splicing, via spliceosome
GO:0001649 osteoblast differentiation
GO:0006397 mRNA processing
GO:0008380 RNA splicing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0016020 membrane
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071006 U2-type catalytic step 1 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:5xjc, PDBe:5xjc, PDBj:5xjc
PDBsum5xjc
PubMed28502770
UniProtO75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)

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