Structure of PDB 4esv Chain G Binding Site BS02

Receptor Information
>4esv Chain G (length=421) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLR
VADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYAR
IVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSFKNIKD
ILVQTYDNIEMLITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFA
LNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTP
EDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVID
YLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQR
QDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQR
NGPVGTVQLAFIKEYNKFVNL
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 G Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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
Binding residue
(residue number reindexed from 1)		S193 G195 K196 T197 A198 R230 Q241 K413
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
View graph for
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)

[Back to BioLiP]