Structure of PDB 7rr3 Chain A Binding Site BS04

Receptor Information

>7rr3 Chain A (length=275) Species: 1230469 (Nitratiruptor phage NrS-1)

MIMEIPAIKALSRYAQWVIWKKERDTKIPYNPNNGKKASSTDPLAWGDID
EAQAGLVRYGANGLGFVLTKSDPFVFIDLDHVLDENKRVKCEWARQLLKE
IKSYTEISPSGDGLHVVVSGKLPDYIKHKTKFDDGSALEVYESGRYMTIT
GEVFDGRDDIKELDLSILGEFAEHKILDDEAIIDLMKRKGQWPDAPADGD
DWSSLDMSFANRLAFWCGKDIERMDRIFRQSPLMRQKWDRPTAGSTYGRI
TLKKACDFVDSVYDPALRNESDCPF

Ligand information

• Ligand ID: DCT
• InChI: InChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
• InChIKey: ARLKCWCREKRROD-POYBYMJQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1CC(OC1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
  OpenEye OEToolkits 1.5.0: C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2
• Formula: C9 H16 N3 O12 P3
• Name: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL1201384
• ZINC: ZINC000013516800
• PDB chain: 7rr3 Chain A Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rr3 Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage NrS-1 Primase-Polymerase.
• Resolution: 2.24 Å
• Binding residue (original residue number in PDB): K27 F76 D78 D80 S108 P109 S110 H115 R145 Y146 T148
• Binding residue (residue number reindexed from 1): K27 F76 D78 D80 S108 P109 S110 H115 R145 Y146 T148
• Annotation score: 1

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:7rr3, PDBe:7rr3, PDBj:7rr3
• PDBsum: 7rr3
• PubMed: 34975792
• UniProt: M5AAG8|POL_BPNNR DNA Primase-polymerase (Gene Name=28)