Structure of PDB 3gxy Chain B Binding Site BS03

Receptor Information

>3gxy Chain B (length=101) Species: 45916 (Nostoc ellipsosporum)

LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQ
PSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKY
E

Ligand information

• Ligand ID: OPM
• InChI: InChI=1S/C11H22O6/c1-2-3-4-5-16-11-10(15)9(14)8(13)7(6-12)17-11/h7-15H,2-6H2,1H3/t7-,8-,9+,10+,11+/m1/s1
• InChIKey: RYIWDDCNJPSPRA-UVOCVTCTSA-N
• SMILES:
  ACDLabs 10.04: O(CCCCC)C1OC(C(O)C(O)C1O)CO
  CACTVS 3.341: CCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
  CACTVS 3.341: CCCCCO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: CCCCCOC1C(C(C(C(O1)CO)O)O)O
  OpenEye OEToolkits 1.5.0: CCCCCO[C@@H]1[C@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
• Formula: C11 H22 O6
• Name: pentyl alpha-D-mannopyranoside;
  O1-PENTYL-MANNOSE;
  pentyl alpha-D-mannoside;
  pentyl D-mannoside;
  pentyl mannoside
• DrugBank: DB02695
• ZINC: ZINC000005973254
• PDB chain: 3gxy Chain D Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gxy Structures of the complexes of a potent anti-HIV protein cyanovirin-n and high mannose oligosaccharides
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): E23 T25
• Binding residue (residue number reindexed from 1): E23 T25
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.59,Kd=2.6uM

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding

Biological Process

• GO:0050688 regulation of defense response to virus

External links

• PDB: RCSB:3gxy, PDBe:3gxy, PDBj:3gxy
• PDBsum: 3gxy
• PubMed: 12110688
• UniProt: P81180|CVN_NOSEL Cyanovirin-N