Structure of PDB 4i47 Chain A Binding Site BS01

Receptor Information

>4i47 Chain A (length=246) Species: 3672 (Momordica balsamina)

DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLM
HLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSAR
RKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGA
LLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQ
LAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI

Ligand information

• Ligand ID: MY6
• InChI: InChI=1S/C6H7N5O/c1-11-2-8-4-3(11)5(12)10-6(7)9-4/h2H,1H3,(H3,7,9,10,12)
• InChIKey: FZWGECJQACGGTI-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.370: Cn1cnc2N=C(N)NC(=O)c12
  OpenEye OEToolkits 1.7.0: Cn1cnc2c1C(=O)NC(=N2)N
  ACDLabs 12.01: O=C1c2c(N=C(N1)N)ncn2C
• Formula: C6 H7 N5 O
• Name: 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one
• ZINC: ZINC000008613011
• PDB chain: 4i47 Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4i47 First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): Y70 I71 E85 G109
• Binding residue (residue number reindexed from 1): Y70 I71 E85 G109
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM

Enzymatic activity

• Catalytic site (original residue number in PDB): I71 E160 R163
• Catalytic site (residue number reindexed from 1): I71 E160 R163
• Enzyme Commision number: 3.2.2.22: rRNA N-glycosylase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016787 hydrolase activity
• GO:0030598 rRNA N-glycosylase activity
• GO:0090729 toxin activity

Biological Process

• GO:0017148 negative regulation of translation
• GO:0035821 modulation of process of another organism

External links

• PDB: RCSB:4i47, PDBe:4i47, PDBj:4i47
• PDBsum: 4i47
• PubMed: 23280611
• UniProt: D9J2T9