3ARD

Ternary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha-galactosylceramide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3ARD

Classification: IMMUNE SYSTEM

Total Structure Weight: 98422.05

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A 302 Mus musculus Fragment: heavy chain
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
NKT Valpha14-Jalpha18 C 207 Homo sapiens Mus musculus Details: Chimera of mouse variable domain and human constant domain
Gene Name(s): TRAC TCRA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Vbeta8.2 D 244 Homo sapiens Mus musculus Details: Chimera of mouse variable domain and human constant domain
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
3GH
Query on 3GH

A N-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]- 3-hydroxyoctadecan-2-yl}hexacosanamide
C50 H99 N O7
XFTWWKOPEFGPIP-AYIWZJAFSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3GH N/A in BindingDB
N/A in BindingMoad
Kd: 175 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.213
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 58.99 α = 90.00
b = 86.73 β = 90.00
c = 235.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-27
  • Released Date: 2011-03-30
  • Deposition author(s): Wun, K.S., Rossjohn, J.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2014-01-29
    Type: Database references