Structure of PDB 3nx9 Chain A Binding Site BS01

Receptor Information

>3nx9 Chain A (length=246) Species: 3672 (Momordica balsamina)

DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLM
HLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSAR
RKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGA
LLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQ
LAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI

Ligand information

• Ligand ID: GLC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-glucopyranose;
  alpha-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL423707
• ZINC: ZINC000003861213
• PDB chain: 3nx9 Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nx9 Crystal structure of type I ribosome inactivating protein in complex with maltose at 1.7A resolution
• Resolution: 1.7 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: 4

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:3nx9, PDBe:3nx9, PDBj:3nx9
• PDBsum: 3nx9
• UniProt: D9J2T9