Structure of PDB 6vc3 Chain A Binding Site BS01

Receptor Information

>6vc3 Chain A (length=232) Species: 3818 (Arachis hypogaea)

AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAM
PVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGS
IGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKT
VPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPE
RVKFGFSASGSLGGRQIHLIRSWSFTSTLITT

Ligand information

• Ligand ID: QWJ
• InChI: InChI=1S/C15H24O9S2/c1-2-3-25-5-7-9(18)11(20)13(22)15(24-7)26-14-12(21)10(19)8(17)6(4-16)23-14/h1,6-22H,3-5H2/t6-,7-,8+,9-,10+,11+,12-,13-,14+,15+/m1/s1
• InChIKey: VMLLJSJIKUKSIE-PHOFNFIUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C#CCSCC1C(C(C(C(O1)SC2C(C(C(C(O2)CO)O)O)O)O)O)O
  CACTVS 3.385: OC[CH]1O[CH](S[CH]2O[CH](CSCC#C)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 2.0.7: C#CCSC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)S[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O)O)O)O
  ACDLabs 12.01: C1(C(O)C(C(OC1CO)SC2C(C(C(C(CSCC#C)O2)O)O)O)O)O
  CACTVS 3.385: OC[C@H]1O[C@@H](S[C@@H]2O[C@H](CSCC#C)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@H]1O
• Formula: C15 H24 O9 S2
• Name: 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside
• PDB chain: 6vc3 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vc3 Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): D83 G103 Y125 N127 S211 G214
• Binding residue (residue number reindexed from 1): D83 G103 Y125 N127 S211 G214
• Annotation score: 1
• Binding affinity: MOAD: Kd=482uM

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:6vc3, PDBe:6vc3, PDBj:6vc3
• PDBsum: 6vc3
• PubMed: 33135679
• UniProt: P02872|LECG_ARAHY Galactose-binding lectin