Structure of PDB 6bbm Chain D Binding Site BS01

Receptor Information
>6bbm Chain D (length=455) Species: 373045 (Escherichia coli O111:NM) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RDPQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHR
HIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSA
ANISAYADIVRERAVVREMISVANEIAEAGFDPQGRTSEDLLDLAESRVF
KIAESRANKDEGPKNIADVLDATVARIEQLFQQPHDGVTGVNTGYDDLNK
KTAGLQPSDLIIVAARPSMGKTTFAMNLVENAAMLQDKPVLIFSLEMPSE
QIMMRSLASLSRVDQTKIRTGQLDDEDWARISGTMGILLEKRNIYIDDSS
GLTPTEVRSRARRIAREHGGIGLIMIDYLQLMRVPALSDNRTLEIAEISR
SLKALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIM
FIYRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGP
QYDDE
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 chain6bbm Chain W 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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PDB6bbm Mechanisms of opening and closing of the bacterial replicative helicase.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		S234 K237 T238 R271
Binding residue
(residue number reindexed from 1)		S218 K221 T222 R255
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0043139 5'-3' DNA helicase activity
Biological Process
GO:0006260 DNA replication
GO:0006268 DNA unwinding involved in DNA replication
GO:0006269 DNA replication, synthesis of primer
GO:0006270 DNA replication initiation
GO:0010212 response to ionizing radiation
GO:0031297 replication fork processing
GO:0032508 DNA duplex unwinding
Cellular Component
GO:0005829 cytosol
GO:0030894 replisome
GO:0033202 DNA helicase complex
GO:1990077 primosome complex
GO:1990100 DnaB-DnaC complex
GO:1990156 DnaB-DnaG complex
GO:1990158 DnaB-DnaC-DnaT-PriA-PriB complex
GO:1990159 DnaB-DnaC-DnaT-PriA-PriC complex
GO:1990160 DnaB-DnaC-Rep-PriC complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bbm, PDBe:6bbm, PDBj:6bbm
PDBsum6bbm
PubMed30582519
UniProtP0ACB0|DNAB_ECOLI Replicative DNA helicase DnaB (Gene Name=dnaB)

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