Structure of PDB 3r52 Chain D Binding Site BS01

Receptor Information

>3r52 Chain D (length=152) Species: 4120 (Ipomoea batatas)

LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISI
TFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRS
IKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYT
AK

Ligand information

• Ligand ID: GYP
• InChI: InChI=1S/C7H14O6/c1-12-7-6(11)5(10)4(9)3(2-8)13-7/h3-11H,2H2,1H3/t3-,4-,5+,6-,7+/m1/s1
• InChIKey: HOVAGTYPODGVJG-ZFYZTMLRSA-N
• SMILES:
  ACDLabs 10.04: OC1C(O)C(O)C(OC1OC)CO
  OpenEye OEToolkits 1.5.0: CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
  CACTVS 3.341: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
  CACTVS 3.341: CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: COC1C(C(C(C(O1)CO)O)O)O
• Formula: C7 H14 O6
• Name: methyl alpha-D-glucopyranoside;
  METHYL-ALPHA-D-GLUCOPYRANOSIDE;
  ALPHA-METHYL-D-GLUCOPYRANOSIDE;
  methyl alpha-D-glucoside;
  methyl D-glucoside;
  methyl glucoside
• ChEMBL: CHEMBL131853
• ZINC: ZINC000003861272
• PDB chain: 3r52 Chain D Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3r52 Ipomoelin, a jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): G21 Y97 G141 W142 Y143 D145
• Binding residue (residue number reindexed from 1): G19 Y95 G139 W140 Y141 D143
• Annotation score: 1
• Binding affinity: MOAD: Kd=498uM

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding

Biological Process

• GO:0002213 defense response to insect
• GO:0009611 response to wounding
• GO:0032874 positive regulation of stress-activated MAPK cascade
• GO:0051289 protein homotetramerization

External links

• PDB: RCSB:3r52, PDBe:3r52, PDBj:3r52
• PDBsum: 3r52
• PubMed: 22808208
• UniProt: P93193|IPO_IPOBA Ipomoelin (Gene Name=IPO)