Structure of PDB 4xba Chain A Binding Site BS01

Receptor Information

>4xba Chain A (length=199) Species: 284812 (Schizosaccharomyces pombe 972h-)

SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLT
HVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNY
IKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTS
NLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVS

Ligand information

• Ligand ID: GMP
• InChI: InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m1/s1
• InChIKey: NYHBQMYGNKIUIF-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: c1nc2c(n1C3C(C(C(O3)CO)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)CO
  OpenEye OEToolkits 1.7.5: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O
• Formula: C10 H13 N5 O5
• Name: GUANOSINE
• ChEMBL: CHEMBL375655
• DrugBank: DB02857
• ZINC: ZINC000001550030
• PDB chain: 4xba Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xba DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): Y41 D63 M64 F65 M143 H147
• Binding residue (residue number reindexed from 1): Y9 D31 M32 F33 M111 H115
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.6.1.71: adenosine-5'-diphospho-5'-[DNA] diphosphatase.
  3.6.1.72: DNA-3'-diphospho-5'-guanosine diphosphatase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

External links

• PDB: RCSB:4xba, PDBe:4xba, PDBj:4xba
• PDBsum: 4xba
• PubMed: 26007660
• UniProt: O74859|APTX_SCHPO Aprataxin-like protein (Gene Name=hnt3)