Structure of PDB 6jon Chain A Binding Site BS01

Receptor Information
>6jon Chain A (length=280) Species: 1230469 (Nitratiruptor phage NrS-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMIMEIPAIKALSRYAQWVIWKKERDTKIPYNPNNGKKASSTDPLAWGDI
DEAQAGLVRYGANGLGFVLTKSDPFVFIDLDHVLDENKRVKCEWARQLLK
EIKSYTEISPSGDGLHVVVSGKLPDYIKHKTKFDDGSALEVYESGRYMTI
TGEVFDGRDDIKELDLSILGEFAEHKILDDEAIIDLMKRKGQWPDAPKDG
DDWSSLDMSFANRLAFWCGKDIERMDRIFRQSPLMRQKWDRPTAGSTYGR
ITLKKACDFVDSVYDPALRNESDCPFEPYN
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain6jon Chain A Residue 401 [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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PDB6jon Crystal structures of phage NrS-1 N300-dNTPs-Mg2+complex provide molecular mechanisms for substrate specificity.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		K27 D78 D80 S108 P109 S110 H115 R145 Y146 M147 T148
Binding residue
(residue number reindexed from 1)		K28 D79 D81 S109 P110 S111 H116 R146 Y147 M148 T149
Annotation score3
Binding affinityMOAD: Kd=13.2uM
PDBbind-CN: -logKd/Ki=4.88,Kd=13.2uM
Enzymatic activity
Enzyme Commision number 2.7.7.-
2.7.7.7: DNA-directed DNA polymerase.
3.6.4.12: DNA helicase.
External links
PDB RCSB:6jon, PDBe:6jon, PDBj:6jon
PDBsum6jon
PubMed31176489
UniProtM5AAG8|POL_BPNNR DNA Primase-polymerase (Gene Name=28)

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