Structure of PDB 7abf Chain r Binding Site BS01

Receptor Information
>7abf Chain r (length=844) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YEMDFLADLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRYDQ
DLCYTDILFTEQERGVGIKSTPVTVVLPDTKGKSYLFNIMDTPGHVNFSD
EVTAGLRISDGVVLFIDAAEGVMLNTERLIKHAVQERLAVTVCINKIDRL
ILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLILSPLLGNVCFSSSQ
YSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKAPTS
SSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLNIR
PLLRLVCKKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDLGE
AMSDCDPDGPLMCHTTKMYSTDDGVQFHAFGRVLSGTIHAGQPVKVLGEN
YTLEDEEDSQICTVGRLWISVARYHIEVNRVPAGNWVLIEGVDQPIVKTA
TITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSELPKMLDGLRKVNKS
YPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVVTFC
ETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNRKK
LGEFFQTKYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGSVK
DSIVQGFQWGTREGPLCDELIRNVKFKILDAVVAQEPLHRGGGQIIPTAR
RVVYSAFLMATPRLMEPYYFVEVQAPADCVSAVYTVLARRRGHVTQDAPI
PGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSVFHHWQIVPGDPLD
KSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPM
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 chain7abf Chain r 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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PDB7abf Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		L138 H139 G141 K142 T143 C144 P206 G207 K259 Q313
Binding residue
(residue number reindexed from 1)		L25 H26 G28 K29 T30 C31 P93 G94 K146 Q200
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030623 U5 snRNA binding
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0042220 response to cocaine
GO:0071466 cellular response to xenobiotic stimulus
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0043231 intracellular membrane-bounded organelle
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 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:7abf, PDBe:7abf, PDBj:7abf
PDBsum7abf
PubMed33243851
UniProtQ15029|U5S1_HUMAN 116 kDa U5 small nuclear ribonucleoprotein component (Gene Name=EFTUD2)

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