Structure of PDB 3d5i Chain B Binding Site BS01

Receptor Information

>3d5i Chain B (length=97) Species: 1894 (Kitasatospora aureofaciens)

ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKG
NGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC

Ligand information

• Ligand ID: SGP
• InChI: InChI=1S/C10H12N5O6PS/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-6-5(3(1-16)19-9)20-22(18,23)21-6/h2-3,5-6,9,16H,1H2,(H,18,23)(H3,11,13,14,17)/t3-,5-,6-,9-,22+/m1/s1
• InChIKey: QZEROIIFJLCOOE-FHIGPPGSSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH]4O[P](O)(=S)O[CH]34
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@H]4O[P@](O)(=S)O[C@@H]34
  ACDLabs 10.04: S=P1(OC2C(OC(C2O1)CO)n3c4N=C(N)NC(=O)c4nc3)O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)CO)O[P@](=S)(O4)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C4C(C(O3)CO)OP(=S)(O4)O)N=C(NC2=O)N
• Formula: C10 H12 N5 O6 P S
• Name: GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
• DrugBank: DB03178
• PDB chain: 3d5i Chain B Residue 98

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d5i Structure of RNase Sa2 complexes with mononucleotides - new aspects of catalytic reaction and substrate recognition
• Resolution: 2.2 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 R67 R71 H86 Y87
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E56 R67 R71 H86
• Catalytic site (residue number reindexed from 1): E56 R67 R71 H86
• 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:3d5i, PDBe:3d5i, PDBj:3d5i
• PDBsum: 3d5i
• PubMed: 19558492
• UniProt: Q53752