Structure of PDB 8val Chain D Binding Site BS04

Receptor Information
>8val Chain D (length=366) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTR
GVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAAS
RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPP
EHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA
HEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDD
QALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRM
GVEMTLLRALAFHPRM
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 chain8val Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8val Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		A7 W10 R11 P12 V18 V19 G48 V49 G50 K51 T52 S53 L214 R215
Binding residue
(residue number reindexed from 1)		A10 W13 R14 P15 V21 V22 G51 V52 G53 K54 T55 S56 L217 R218
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8val, PDBe:8val, PDBj:8val
PDBsum8val
PubMed38490435
UniProtP06710|DPO3X_ECOLI DNA polymerase III subunit tau (Gene Name=dnaX)

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