Structure of PDB 8v87 Chain 3 Binding Site BS02

Receptor Information
>8v87 Chain 3 (length=656) Species: 1247190 (Saccharomyces cerevisiae BY4741) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFPSFGLSKIVLNNIKRKGFRQPTPIQRKTIPLILQSRDIVGMARTGSG
KTAAFILPMVEKLKSHSGKIGARAVILSPSRELAMQTFNVFKDFARGTEL
RSVLLTGGDSLEEQFGMMMTNPDVIIATPGRFLHLKVEMNLDLKSVEYVV
FDEADRLFEMGFQEQLNELLASLPTTRQTLLFSATLPNSLVDFVKAGLVN
PVLVRLDAETKVSENLEMLFLSSKNADREANLLYILQEIIKIPLATSEQL
QKLQNSNLPSEKATILFVPTRHHVEYISQLLRDCGYLISYIYGTLDQHAR
KRQLYNFRAGLTSILVVTDVAARGVDIPMLANVINYTLPGSSKIFVHRVG
RTARAGNKGWAYSIVAENELPYLLDLELFLGKKILLTPMYDSLVDVMKKR
WIDEGKPEYQFQPPKLSYTKRLVLGSCPRLDVEGLGDLYKNLMSSNFDLQ
LAKKTAMKAEKLYYRTRTSASPESLKRSKEIISSGWDAQNAFFGKNEEKE
KLDFLAKLQNRRNKETVFEFTRNPDDEMAVFMKRRRKQLAPIQRKATERR
ELLEKERMKSFKDPTFFLSHYAPANGFANDAAQAAYDLNSDDKVQVHKQT
AIIGESGQKIAASFRSGRFDDWSKARNFKHKQMKAPKMPDKHRDNYYSQK
KKVEKA
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 chain8v87 Chain 3 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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PDB8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Resolution2.66 Å
Binding residue
(original residue number in PDB)		F157 T183 G184 S185 G186 K187 T188
Binding residue
(residue number reindexed from 1)		F21 T47 G48 S49 G50 K51 T52
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:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis
GO:1902626 assembly of large subunit precursor of preribosome
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8v87, PDBe:8v87, PDBj:8v87
PDBsum8v87
PubMed38632236
UniProtQ12389|DBP10_YEAST ATP-dependent RNA helicase DBP10 (Gene Name=DBP10)

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