Structure of PDB 3o8x Chain C Binding Site BS01

Receptor Information

>3o8x Chain C (length=203) Species: 10090 (Mus musculus)

TQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLV
DQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGR
LHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQS
KDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTF
FPS

Ligand information

• Ligand ID: GSL
• InChI: InChI=1S/C38H73NO9/c1-3-5-7-9-11-13-15-16-18-19-21-23-25-27-31(40)30(29-47-38-35(44)33(42)34(43)36(48-38)37(45)46)39-32(41)28-26-24-22-20-17-14-12-10-8-6-4-2/h30-31,33-36,38,40,42-44H,3-29H2,1-2H3,(H,39,41)(H,45,46)/t30-,31+,33-,34+,35+,36-,38-/m0/s1
• InChIKey: IRPOZWRRAFKYMQ-LMIAXWKISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCC(C(COC1C(C(C(C(O1)C(=O)O)O)O)O)NC(=O)CCCCCCCCCCCCC)O
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCC[C@H]([C@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)C(=O)O)O)O)O)NC(=O)CCCCCCCCCCCCC)O
  CACTVS 3.341: CCCCCCCCCCCCCCC[CH](O)[CH](CO[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O)NC(=O)CCCCCCCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO[C@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)C(O)=O)NC(=O)CCCCCCCCCCCCC
  ACDLabs 10.04: O=C(O)C1OC(OCC(NC(=O)CCCCCCCCCCCCC)C(O)CCCCCCCCCCCCCCC)C(O)C(O)C1O
• Formula: C38 H73 N O9
• Name: (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID;
  (2S,3R)-N-MYRISTOYL-1-O-(ALPHA-D-GALACTURONOSYL)-2-N-OCTADECANE-3-OL
• ChEMBL: CHEMBL406974
• ZINC: ZINC000024753414
• PDB chain: 3o8x Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o8x The V alpha 14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.
• Resolution: 2.74 Å
• Binding residue (original residue number in PDB): P28 N30 R95 G96
• Binding residue (residue number reindexed from 1): P28 N30 R94 G95
• Annotation score: 1

External links

• PDB: RCSB:3o8x, PDBe:3o8x, PDBj:3o8x
• PDBsum: 3o8x
• PubMed: 20921281
• UniProt: P01848|TRAC_HUMAN T cell receptor alpha chain constant (Gene Name=TRAC)