Structure of PDB 8arp Chain D Binding Site BS01

Receptor Information
>8arp Chain D (length=444) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NQPQELIKPNWDEELPKLPTFEKNFYVEHESVRDRSDSEIAQFRKENEMT
ISGHDIPKPITTFDEAGFPDYVLNEVKAEGFDKPTGIQCQGWPMALSGRD
MVGIAATGSGKTLSYCLPGIVHINAQPLLAPGDGPIVLVLAPTRELAVQI
QTECSKFGHSSRIRNTCVYGGVPKSQQIRDLSRGSEIVIATPGRLIDMLE
IGKTNLKRVTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWP
KEVKQLAADYLNDPIQVQVGSLELSASHNITQIVEVVSDFEKRDRLNKYL
ETASQDNEYKTLIFASTKRMCDDITKYLREDGWPALAIHGDKDQRERDWV
LQEFRNGRSPIMVATDVAARGIDVKGINYVINYDMPGNIEDYVHRIGRTG
RAGATGTAISFFTEQNKGLGAKLISIMREANQNIPPELLKYDRR
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 chain8arp Chain D Residue 2001 [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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PDB8arp Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		F133 T159 S161 G162 K163 T164 L165 E205 R422
Binding residue
(residue number reindexed from 1)		F81 T107 S109 G110 K111 T112 L113 E153 R370
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:0003729 mRNA binding
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0008186 ATP-dependent activity, acting on RNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0030515 snoRNA binding
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000380 alternative mRNA splicing, via spliceosome
GO:0006364 rRNA processing
GO:0006369 termination of RNA polymerase II transcription
GO:0042254 ribosome biogenesis
GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8arp, PDBe:8arp, PDBj:8arp
PDBsum8arp
PubMed36894019
UniProtP24783|DBP2_YEAST ATP-dependent RNA helicase DBP2 (Gene Name=DBP2)

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