Structure of PDB 4g0z Chain A Binding Site BS01

Receptor Information

>4g0z Chain A (length=147) Species: 3702 (Arabidopsis thaliana)

SNKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEP
VLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGD
LKRICETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVL

Ligand information

• Ligand ID: 5GP
• InChI: InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: RQFCJASXJCIDSX-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H14 N5 O8 P
• Name: GUANOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL283807
• DrugBank: DB01972
• ZINC: ZINC000002159505
• PDB chain: 4g0z Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4g0z Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): N687 Y691 K695 Q707 C708 L710 K728 K732
• Binding residue (residue number reindexed from 1): N94 Y98 K102 Q114 C115 L117 K135 K139
• Annotation score: 4
• Binding affinity: MOAD: Kd=6.13mM
  PDBbind-CN: -logKd/Ki=2.21,Kd=6.13mM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:4g0z, PDBe:4g0z, PDBj:4g0z
• PDBsum: 4g0z
• PubMed: 22850669
• UniProt: O04379|AGO1_ARATH Protein argonaute 1 (Gene Name=AGO1)