3TVM

Structure of the mouse CD1d-SMC124-iNKT TCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 3TVM

Classification: IMMUNE SYSTEM

Total Structure Weight: 193240.09

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A, E 285 Mus musculus Fragment: residues 19-298
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
beta-2-microglobulin B, F 99 Mus musculus Mutation: D85A
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Valpha14 (mouse variable domain, human constant domain) C, G 209 Homo sapiens Mus musculus Gene Name(s): TRAC TCRA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Vbeta8.2 (mouse variable domain, human constant domain) D, H 241 Homo sapiens Mus musculus Gene Name(s): TRBC2 TCRBC2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
07P
Query on 07P

A, E N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]- 1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan- 2-yl]hexacosanamide
SMC124 (Synonym)
C55 H107 N O8
BCHXWZQXEKOXKQ-IYKQKVLOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, E 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, E ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

E GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.224
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 78.97 α = 90.00
b = 150.57 β = 96.35
c = 101.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-20
  • Released Date: 2012-02-01
  • Deposition author(s): Girardi, E., Li, Y., Zajonc, D.M.

Revision History

No revisions since initial release