Structure of PDB 4g0y Chain A Binding Site BS01

Receptor Information

>4g0y Chain A (length=147) Species: 3702 (Arabidopsis thaliana)

SNKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEP
VLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGD
LKRICETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVL

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 4g0y Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4g0y Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.
• Resolution: 1.65 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=4.99mM
  PDBbind-CN: -logKd/Ki=2.30,Kd=4.99mM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:4g0y, PDBe:4g0y, PDBj:4g0y
• PDBsum: 4g0y
• PubMed: 22850669
• UniProt: O04379|AGO1_ARATH Protein argonaute 1 (Gene Name=AGO1)