Structure of PDB 5of3 Chain C Binding Site BS01

Receptor Information

>5of3 Chain C (length=107) Species: 273057 (Saccharolobus solfataricus P2)

PPQPKKSSDYSWIEKVLEMGLQDSRKRFILYVASRYLVNVKGVNEDEALQ
TLKEFYYKLQSGKVYESWLKSVINGVKKKGLLPWSLKRIEERDKEMYNEI
IRVLKNS

Ligand information

• Ligand ID: APC
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
• InChIKey: CAWZRIXWFRFUQB-IOSLPCCCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
• Formula: C11 H18 N5 O12 P3
• Name: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
  ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL132722
• DrugBank: DB02596
• ZINC: ZINC000008295117
• PDB chain: 5of3 Chain C Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5of3 Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster.
• Resolution: 2.906 Å
• Binding residue (original residue number in PDB): D70 S71 R72 K73 R74 L77 Y103
• Binding residue (residue number reindexed from 1): D23 S24 R25 K26 R27 L30 Y56
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:5of3, PDBe:5of3, PDBj:5of3
• PDBsum: 5of3
• PubMed: 29167441
• UniProt: Q97ZS7