Structure of PDB 4esv Chain E Binding Site BS03

Receptor Information
>4esv Chain E (length=418) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRG
EPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEK
SVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEGAFKNIKDILVQT
YDNIEMLHNITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNI
AQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDW
GKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQ
LIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDK
RPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGP
VGTVQLAFIKEYNKFVNL
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4esv Chain E Residue 501 [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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PDB4esv The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S213 G215 K216 T217 A218 R250 Q261 K433 N436
Binding residue
(residue number reindexed from 1)		S190 G192 K193 T194 A195 R227 Q238 K410 N413
Annotation score3
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
Biological Process
GO:0006260 DNA replication
GO:0006268 DNA unwinding involved in DNA replication
GO:0006269 DNA replication, synthesis of primer
Cellular Component
GO:0005829 cytosol
GO:1990077 primosome complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4esv, PDBe:4esv, PDBj:4esv
PDBsum4esv
PubMed23022319
UniProtQ9X4C9|DNAB_GEOSE Replicative DNA helicase DnaB (Gene Name=dnaB)

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