Structure of PDB 5nnw Chain D Binding Site BS02

Receptor Information

>5nnw Chain D (length=206) Species: 65070 (Pythium aphanidermatum)

AVINHDAVPVWPQPEPADATQALAVRFKPQLDVVNGCQPYPAVDPQGNTS
GGLKPSAAACRDMSKAQVYSRSGTYNGYYAIMYSWYMPKDSIGHRHDWEN
VVVWLDNAASANIVALSASAHSGYKKSFPADKSYLDGITAKISYKSTWPL
DHELGFTTSAGKQQPLIQWEQMTQAARDALESTDFGNANVPFKSNFQDKL
VKAFFQ

Ligand information

• Ligand ID: GCS
• InChI: InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6-/m1/s1
• InChIKey: MSWZFWKMSRAUBD-QZABAPFNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)N)O)O)O
  CACTVS 3.341: N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)N)O)O)O
  CACTVS 3.341: N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1N)CO
• Formula: C6 H13 N O5
• Name: 2-amino-2-deoxy-beta-D-glucopyranose;
  beta-D-glucosamine;
  2-amino-2-deoxy-beta-D-glucose;
  2-amino-2-deoxy-D-glucose;
  2-amino-2-deoxy-glucose;
  D-GLUCOSAMINE
• ChEMBL: CHEMBL234432
• ZINC: ZINC000003860468
• PDB chain: 5nnw Chain D Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nnw Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins.
• Resolution: 1.54 Å
• Binding residue (original residue number in PDB): D93 G100 H101 D158
• Binding residue (residue number reindexed from 1): D90 G93 H94 D151
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

Biological Process

• GO:0031640 killing of cells of another organism

External links

• PDB: RCSB:5nnw, PDBe:5nnw, PDBj:5nnw
• PDBsum: 5nnw
• PubMed: 29242345
• UniProt: Q9SPD4