Structure of PDB 7pmq Chain D Binding Site BS03

Receptor Information
>7pmq Chain D (length=455) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFSTLNVLPPAQLTNLNELGYLTMTPVQAAALPAILAGKDVRVQAKTGSG
KTAAFGLGLLQQIDASLFQTQALVLCPTRELADQVAGELRRLARFLPNTK
ILTLCGGQPFGMQRDSLQHAPHIIVATPGRLLDHLQKGTVSLDALNTLVM
DEADRMLDMGFSDAIDDVIRFAPASRQTLLFSATWPEAIAAISGRVQRDP
LAIEIDSTDALPPIEQQFYETSSKGKIPLLQRLLSLHQPSSCVVFCNTKK
DCQAVCDALNEVGQSALSLHGDLEQRDRDQTLVRFANGSARVLVATDVAA
RGLDIKSLELVVNFELAWDPEVHVHRIGRTARAGNSGLAISFCAPEEAQR
ANIISDMLQIKLNWQTPPANSSIATLEAEMATLCIDGGKKAKMRPGDVLG
ALTGDIGLDGADIGKIAVHPAHVYVAVRQAVAHKAWKQLQGGKIKGKTCR
VRLLK
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 chain7pmq Chain D Residue 500 [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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PDB7pmq Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
Resolution3.22 Å
Binding residue
(original residue number in PDB)		Y23 T27 Q30 G50 S51 G52 K53 T54 E90 D306 R334
Binding residue
(residue number reindexed from 1)		Y21 T25 Q28 G48 S49 G50 K51 T52 E88 D304 R332
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:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0019843 rRNA binding
GO:0033677 DNA/RNA helicase activity
GO:0034458 3'-5' RNA helicase activity
GO:0043531 ADP binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7pmq, PDBe:7pmq, PDBj:7pmq
PDBsum7pmq
PubMed37221012
UniProtP21693|DBPA_ECOLI ATP-dependent RNA helicase DbpA (Gene Name=dbpA)

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