3QUX

Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 3QUX

Classification: IMMUNE SYSTEM

Total Structure Weight: 96280.98

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A 285 Mus musculus Fragment: UNP residues 19-297
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2 microglobulin B 99 Mus musculus Fragment: UNP residues 21-119
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Valpha14 (mouse variable domain, human constant domain) C 209 Mus musculus Gene Name(s): TRAC TCRA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Vbeta8.2 (mouse variable domain, human constant domain) D 241 Mus musculus Gene Name(s): TRBC2 TCRBC2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)- 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2- yl]nonadecan-3-yl]hexacosanamide
C51 H101 N O8
BNYLLEHBKIGJHB-XHSUSRKPSA-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)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
QUX N/A in BindingDB
N/A in BindingMoad
Kd: 247 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.208
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 78.50 α = 90.00
b = 189.92 β = 90.00
c = 150.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-24
  • Released Date: 2011-06-29
  • Deposition author(s): Li, Y., Girardi, E., Yu, E.D., Zajonc, D.M.

Revision History

  • 2011-07-13
    Type: Version format compliance