Structure of PDB 3o9w Chain C Binding Site BS01

Receptor Information

>3o9w Chain C (length=203) Species: 10090 (Mus musculus)

TQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLV
DQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGR
LHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQS
KDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTF
FPS

Ligand information

• Ligand ID: 1O2
• InChI: InChI=1S/C43H80O10/c1-3-5-7-9-11-13-15-17-18-20-21-23-25-27-29-31-38(45)50-34-36(35-51-43-42(49)41(48)40(47)37(33-44)53-43)52-39(46)32-30-28-26-24-22-19-16-14-12-10-8-6-4-2/h17-18,36-37,40-44,47-49H,3-16,19-35H2,1-2H3/b18-17-/t36-,37-,40+,41+,42-,43+/m1/s1
• InChIKey: JBZBYHKCRFIXBI-BNOJPGAFSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)COC(=O)CCCCCCC/C=C\CCCCCCCC
  CACTVS 3.352: CCCCCCCCCCCCCCCC(=O)O[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)COC(=O)CCCCCCCC=CCCCCCCCC
  CACTVS 3.352: CCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)COC(=O)CCCCCCC\C=C/CCCCCCCC
  ACDLabs 11.02: O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COC1OC(C(O)C(O)C1O)CO)CCCCCCC\C=C/CCCCCCCC
  OpenEye OEToolkits 1.7.0: CCCCCCCCCCCCCCCC(=O)OC(COC1C(C(C(C(O1)CO)O)O)O)COC(=O)CCCCCCCC=CCCCCCCCC
• Formula: C43 H80 O10
• Name: (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate;
  1-oleoyl,2-palmitoyl-3-O(alpha-D-galactopyranosyl)-sn-glycerol
• ZINC: ZINC000058650288
• PDB chain: 3o9w Chain A Residue 507

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o9w The V alpha 14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): N30 R95
• Binding residue (residue number reindexed from 1): N30 R94
• Annotation score: 1

External links

• PDB: RCSB:3o9w, PDBe:3o9w, PDBj:3o9w
• PDBsum: 3o9w
• PubMed: 20921281
• UniProt: P01848|TRAC_HUMAN T cell receptor alpha chain constant (Gene Name=TRAC)