Structure of PDB 3dgy Chain B Binding Site BS01

Receptor Information

>3dgy Chain B (length=94) Species: 1894 (Kitasatospora aureofaciens)

ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKG
NGYYHEFTVVTPDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC

Ligand information

• Ligand ID: 2GP
• InChI: InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(23-24(19,20)21)5(17)3(1-16)22-9/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: WTIFIAZWCCBCGE-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O[P](O)(O)=O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)OP(=O)(O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)CO)O)OP(=O)(O)O)N=C(NC2=O)N
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3OP(=O)(O)O)CO
• Formula: C10 H14 N5 O8 P
• Name: GUANOSINE-2'-MONOPHOSPHATE
• DrugBank: DB01937
• ZINC: ZINC000005224737
• PDB chain: 3dgy Chain B Residue 98

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dgy Structure of RNase Sa2 complexes with mononucleotides - new aspects of catalytic reaction and substrate recognition
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): R34 F39 E40 N41 R42 E43 E56 R67 R71 H86 Y87
• Binding residue (residue number reindexed from 1): R34 F39 E40 N41 R42 E43 E56 R64 R68 H83 Y84
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): E56 R67 R71 H86
• Catalytic site (residue number reindexed from 1): E56 R64 R68 H83
• Enzyme Commision number: 3.1.4.8: Transferred entry: 4.6.1.24.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0004521 RNA endonuclease activity
• GO:0004540 RNA nuclease activity

External links

• PDB: RCSB:3dgy, PDBe:3dgy, PDBj:3dgy
• PDBsum: 3dgy
• PubMed: 19558492
• UniProt: Q53752