Structure of PDB 4elm Chain A Binding Site BS01

Receptor Information

>4elm Chain A (length=266) Species: 10090 (Mus musculus)

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSA
TVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSRQLVCHVSGF
YPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLAC
RVKHSSLGGQDIILYW

Ligand information

• Ligand ID: SGF
• InChI: InChI=1S/C24H47NO10S/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)18(25)17-33-24-22(29)23(35-36(30,31)32)21(28)20(16-26)34-24/h14-15,18-24,26-29H,2-13,16-17,25H2,1H3,(H,30,31,32)/b15-14+/t18-,19+,20+,21-,22+,23-,24+/m0/s1
• InChIKey: BXSULSOCJNTUJS-YTBMLWRQSA-N
• SMILES:
  ACDLabs 12.01: O=S(=O)(O)OC1C(O)C(OC(OCC(N)C(O)/C=C/CCCCCCCCCCCCC)C1O)CO
  CACTVS 3.370: CCCCCCCCCCCCCC=C[CH](O)[CH](N)CO[CH]1O[CH](CO)[CH](O)[CH](O[S](O)(=O)=O)[CH]1O
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCCC=CC(C(COC1C(C(C(C(O1)CO)O)OS(=O)(=O)O)O)N)O
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCC/C=C/[C@H]([C@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)OS(=O)(=O)O)O)N)O
  CACTVS 3.370: CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](N)CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O[S](O)(=O)=O)[C@H]1O
• Formula: C24 H47 N O10 S
• Name: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside;
  Sphingosine-1-galactoside-3-sulfate
• ZINC: ZINC000064633940
• PDB chain: 4elm Chain A Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4elm Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.
• Resolution: 3.48 Å
• Binding residue (original residue number in PDB): Y73 S76 F77 D80 V118 W142 D153 T156
• Binding residue (residue number reindexed from 1): Y67 S70 F71 D74 V110 W134 D145 T148
• Annotation score: 1

External links

• PDB: RCSB:4elm, PDBe:4elm, PDBj:4elm
• PDBsum: 4elm
• PubMed: 22820602
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)