3ARF

Ternary crystal structure of the mouse NKT TCR-CD1d-C20:2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 3ARF

Classification: IMMUNE SYSTEM

Total Structure Weight: 98365.86

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
DB3
Query on DB3

A (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)- 3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide
C44 H83 N O9
WSXMIFGRYXQZQZ-HJCGRHBQSA-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 %)
DB3 N/A in BindingDB
N/A in BindingMoad
Kd: 64 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.225
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 58.95 α = 90.00
b = 87.05 β = 90.00
c = 234.86 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