3HE6

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.234

Literature

Macromolecules
Sequence Display for 3HE6

Classification: IMMUNE SYSTEM

Total Structure Weight: 98011.64

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d1 A 302 Mus musculus Fragment: extracellular domain
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2 microglobulin B 99 Mus musculus Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Valpha14(mouse variable domain, human constant domain) C 207 Homo sapiens Mus musculus
Vbeta8.2(mouse variable domain, human constant domain) D 244 Homo sapiens Mus musculus Gene Name(s): TRBC1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AGH
Query on AGH

A N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- 2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.234
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.11 α = 90.00
b = 81.51 β = 90.00
c = 233.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-05-07
  • Released Date: 2009-07-28
  • Deposition author(s): Patel, O., Rossjohn, J.

Revision History

  • 2011-07-13
    Type: Non-polymer description, Version format compliance