Structure of PDB 3ca5 Chain A Binding Site BS01

Receptor Information

>3ca5 Chain A (length=257) Species: 4202 (Sambucus nigra)

TSFTRNIVGRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQRWTFDSDDTIR
SMGKCMTANGLNNGSNIVIFNCSTAAENAIKWEVPIDGSIINPSSGLVMT
APRAASRTILLLEDNIYAASQGWTVTNNVKPIVASIVGYKEMCLQSNGEN
NGVWMEDCEATSLQQQWALYGDRTIRVNSTRGLCVTTNGYNSKDLIIILK
CQGLPSQRWFFNSDGAIVNPKSRLVMDVRASNVSLREIIIFPATGNPNQQ
WVTQVLP

Ligand information

• Ligand ID: AMG
• 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-PZRMXXKTSA-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[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: COC1C(C(C(C(O1)CO)O)O)O
  CACTVS 3.341: CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
• Formula: C7 H14 O6
• Name: methyl alpha-D-galactopyranoside;
  ALPHA-METHYL-D-GALACTOSIDE;
  methyl alpha-D-galactoside;
  methyl D-galactoside;
  methyl galactoside
• ChEMBL: CHEMBL467773
• DrugBank: DB02100
• ZINC: ZINC000004262102
• PDB chain: 3ca5 Chain A Residue 267

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ca5 Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): D16 N19 Q29 W31 Q36 N38
• Binding residue (residue number reindexed from 1): D16 N19 Q29 W31 Q36 N38
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.2.22: rRNA N-glycosylase.

External links

• PDB: RCSB:3ca5, PDBe:3ca5, PDBj:3ca5
• PDBsum: 3ca5
• PubMed: 18798567
• UniProt: P33183|NIGB_SAMNI Nigrin b