Structure of PDB 8dvi Chain B Binding Site BS02

Receptor Information
>8dvi Chain B (length=432) Species: 2681598 (Escherichia phage T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVEIILSHLIFDQAYFSKVWPYMDSEYFESGPAKNTFKLIKSHVNEYHSV
PSINALNVALENSSFTETEYSGVKTLISKLADSPEDHSWLVKETEKYVQQ
RAMFNATSKIIEIQTNAELPPEKRNKKMPDVGAIPDIMRQALSISFDSYV
GHDWMDDYEARWLSYMNKARKVPFKLRILNKITKGGAETGTLNVLMAGVN
VGKSLGLCSLAADYLQLGHNVLYISMEMAEEVCAKRIDANMLDVSLDDID
DGHISYAEYKGKMEKWREKSTLGRLIVKQYPTGGADANTFRSLLNELKLK
KNFVPTIIIVDYLGICKSCRIRVYSENSYTTVKAIAEELRALAVETETVL
WTAAQVGKQAWDSSDVNMSDIAESAGLPATADFMLAVIETEELAAAEQQL
IKQIKSRYGDKNKWNKFLMGVQKGNQKWVEIE
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain8dvi Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dvi Structural basis of the T4 bacteriophage primosome assembly and primer synthesis.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		V199 N200 G202 K203 S204 R236 L246 K423
Binding residue
(residue number reindexed from 1)		V199 N200 G202 K203 S204 R236 L246 K423
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0017116 single-stranded 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:0032508 DNA duplex unwinding
GO:0039686 bidirectional double-stranded viral DNA replication
GO:0039693 viral DNA genome replication
Cellular Component
GO:0005829 cytosol
GO:1990077 primosome complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dvi, PDBe:8dvi, PDBj:8dvi
PDBsum8dvi
PubMed37474605
UniProtP04530|HELIC_BPT4 DnaB-like replicative helicase (Gene Name=41)

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