Structure of PDB 8h5y Chain A Binding Site BS02

Receptor Information
>8h5y Chain A (length=564) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIFTLRPYQQEAVDATLNHFRRHKTPAVIVLPTGAGKSLVIAELARLARG
RVLVLAHVKELVAQNHAKYQALGLEADIFAAGGKVVFGSVQSVARNLDAF
QGEFSLLIVDECHRIGDDEESQYQQILTHLTKVNPHLRLLGLTATPFRLG
KGWIYQFHYHGMVRGDEKALFRDCIYELPLRYMIKHGYLTPPERLDMPVV
QYDFSRLQAQSNGLFSEADLNRELKKQQRITPHIISQIMEFAATRKGVMI
FAATVEHAKEIVGLLPAEDAALITGDTPGAERDVLIENFKAQRFRYLVNV
AVLTTGFDAPHVDLIAILRPTESVSLYQQIVGRGLRLAPGKTDCLILDYA
GNPHDLYAPEVGTPKGKSDNVPVQVFCPACGFANTFWGKTTADGTLIEHF
GRRCQGWFEDDDGHREQCDFRFRFKNCQCNAENDIAARRCDTVLVDPDDM
LKAALRLKDALVLRCSGMSLQHGHDEKGEWLKITYYDEDGADVSERFRLQ
TPAQRTAFEQLFIRPHTRTPGIPLRWITAADILAQQALLRHPDFVVARMK
GQYWQVREKVFDYE
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 chain8h5y Chain A Residue 602 [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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PDB8h5y Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli.
Resolution2.7001 Å
Binding residue
(original residue number in PDB)		T4 R6 Q9 T33 G34 G36 K37 L39 K68 R343
Binding residue
(residue number reindexed from 1)		T4 R6 Q9 T33 G34 G36 K37 L39 K68 R336
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
Biological Process
GO:0006281 DNA repair
GO:0006301 postreplication repair
GO:0006302 double-strand break repair
GO:0006412 translation
GO:0009410 response to xenobiotic stimulus
GO:0010212 response to ionizing radiation
GO:0051301 cell division

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8h5y, PDBe:8h5y, PDBj:8h5y
PDBsum8h5y
PubMed36614183
UniProtP33919|RADD_ECOLI Putative DNA repair helicase RadD (Gene Name=radD)

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