Structure of PDB 6jop Chain A Binding Site BS01

Receptor Information
>6jop 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]
MIMEIPAIKALSRYAQWVIWKKERDTKIPYNPNNGKKASSTDPLAWGDID
EAQAGLVRYGANGLGFVLTKSDPFVFIDLDHVLDENKRVKCEWARQLLKE
IKSYTEISPSGDGLHVVVSGKLPDYIKHKTKFDDGSALEVYESGRYMTIT
GEVFDGRDDIKELDLSILGEFAEHKILDDEAIIDLMKRKGQWPDAPKDGD
DWSSLDMSFANRLAFWCGKDIERMDRIFRQSPLMRQKWDRPTAGSTYGRI
TLKKACDFVDSVYDPALRNESDCPFEPYNE
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain6jop 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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PDB6jop Crystal structures of phage NrS-1 N300-dNTPs-Mg2+complex provide molecular mechanisms for substrate specificity.
Resolution2.353 Å
Binding residue
(original residue number in PDB)		K27 D78 D80 S108 P109 S110 H115 R145 Y146 T148
Binding residue
(residue number reindexed from 1)		K27 D78 D80 S108 P109 S110 H115 R145 Y146 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:6jop, PDBe:6jop, PDBj:6jop
PDBsum6jop
PubMed31176489
UniProtM5AAG8|POL_BPNNR DNA Primase-polymerase (Gene Name=28)

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