Structure of PDB 6qdv Chain C Binding Site BS03

Receptor Information
>6qdv Chain C (length=899) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVVLHEDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKPVKTKKFTLM
EQTLPVTVYEMDFLADLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHP
EIRKRYDQDLCYTDILFTEQERGVGIKSTPVTVVLPDTKGKSYLFNIMDT
PGHVNFSDEVTAGLRISDGVVLFIDAAEGVMLNTERLIKHAVQERLAVTV
CINKIDRLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLILSPLLG
NVCFSSSQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRK
FTKKAPTSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTK
EELKLNIRPLLRLVCKKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTG
GVDSDLGEAMSDCDPDGPLMCHTTKMYSTDDGVQFHAFGRVLSGTIHAGQ
PVKVLGENYTLEDEEDSQICTVGRLWISVARYHIEVNRVPAGNWVLIEGV
DQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSELPKMLD
GLRKVNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKV
ADPVVTFCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVV
QITWNRKKLGEFFQTKYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVD
KALLGSVKDSIVQGFQWGTREGPLCDELIRNVKFKILDAVVAQEPLHRGG
GQIIPTARRVVYSAFLMATPRLMEPYYFVEVQAPADCVSAVYTVLARRRG
HVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSVFHHWQ
IVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSIKFFDD
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6qdv Chain C Residue 1501 [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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PDB6qdv A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		T143 D204
Binding residue
(residue number reindexed from 1)		T88 D149
Annotation score1
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6qdv, PDBe:6qdv, PDBj:6qdv
PDBsum6qdv
PubMed30705154
UniProtQ15029|U5S1_HUMAN 116 kDa U5 small nuclear ribonucleoprotein component (Gene Name=EFTUD2)

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