Structure of PDB 6k9a Chain A Binding Site BS03

Receptor Information
>6k9a Chain A (length=278) Species: 1230469 (Nitratiruptor phage NrS-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIMEIPAIKALSRYAQWVIWKKERDTKIPYNPNNGKKASSTDPLAWGDID
EAQAGLVRYGANGLGFVLTKSDPFVFIDLDHVLDENKRVKCEWARQLLKE
IKSYTEISPSGDGLHVVVSGKLPDYIKHKTKFDDGSALEVYESGRYMTIT
GEVFDGRDDIKELDLSILGEFAEHKILDDEAIIDLMKRKGQWPDAPKDGD
DWSSLDMSFANRLAFWCGKDIERMDRIFRQSPLMRQKWDRPTAGSTYGRI
TLKKACDFVDSVYDPALRNESDCPFEPY
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[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(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain6k9a Chain A Residue 403 [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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PDB6k9a Structural studies reveal a unique ring-shaped helicase architecture at the C-terminus of deep-sea vent phage DNA polymerase
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K27 D78 S108 P109 S110 H115 Y146 M147 T148
Binding residue
(residue number reindexed from 1)		K27 D78 S108 P109 S110 H115 Y146 M147 T148
Annotation score2
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:6k9a, PDBe:6k9a, PDBj:6k9a
PDBsum6k9a
PubMed
UniProtM5AAG8|POL_BPNNR DNA Primase-polymerase (Gene Name=28)

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