Structure of PDB 6bbm Chain C Binding Site BS01

Receptor Information
>6bbm Chain C (length=453) Species: 373045 (Escherichia coli O111:NM) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHI
FTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAAN
ISAYADIVRERAVVREMISVANEIAEAGFDPQGRTSEDLLDLAESRVFKI
AESRANKDEGPKNIADVLDATVARIEQLFQQPHDGVTGVNTGYDDLNKKT
AGLQPSDLIIVAARPSMGKTTFAMNLVENAAMLQDKPVLIFSLEMPSEQI
MMRSLASLSRVDQTKIRTGQLDDEDWARISGTMGILLEKRNIYIDDSSGL
TPTEVRSRARRIAREHGGIGLIMIDYLQLMRVPALSDNRTLEIAEISRSL
KALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFI
YRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGPQY
DDE
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 C 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)		P233 S234 M235 G236 K237 T238 T239 E262
Binding residue
(residue number reindexed from 1)		P215 S216 M217 G218 K219 T220 T221 E244
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

View graph for
Molecular Function
View graph for
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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