Structure of PDB 8var Chain B Binding Site BS03

Receptor Information
>8var Chain B (length=362) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVG
KTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTK
VEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHV
KFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEP
RALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQAL
SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPA
ALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVE
MTLLRALAFHPR
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 chain8var Chain B Residue 402 [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]
PDB8var Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		A7 R11 P12 D17 V18 V19 G48 V49 G50 K51 T52 S53 L214
Binding residue
(residue number reindexed from 1)		A7 R11 P12 D17 V18 V19 G48 V49 G50 K51 T52 S53 L214
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006260 DNA replication
Cellular Component
GO:0009360 DNA polymerase III complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8var, PDBe:8var, PDBj:8var
PDBsum8var
PubMed38490435
UniProtP06710|DPO3X_ECOLI DNA polymerase III subunit tau (Gene Name=dnaX)

[Back to BioLiP]