4ELM

Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 4ELM

Classification: IMMUNE SYSTEM

Total Structure Weight: 194702.55

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A, C 285 Mus musculus Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2 microglobulin B, D 99 Mus musculus Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain) E, G 208 Mus musculus
Hy19.3 TCR beta chain (mouse variable domain, human constant domain) F, H 244 Mus musculus

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SGF
Query on SGF

A, C (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en- 1-yl 3-O-sulfo-beta-D-galactopyranoside
Sphingosine-1-galactoside-3-sulfate (Synonym)
C24 H47 N O10 S
BXSULSOCJNTUJS-YTBMLWRQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A, C PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

C ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.209
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 98.51 α = 90.00
b = 127.00 β = 110.53
c = 104.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-11
  • Released Date: 2012-07-25
  • Deposition author(s): Girardi, E., Maricic, I., Wang, J., Mac, T.T., Iyer, P., Kumar, V., Zajonc, D.M.

Revision History

  • 2013-01-09
    Type: Database references
  • 2013-02-06
    Type: Non-polymer description
  • 2015-08-12
    Type: Refinement description