4Y4H

Crystal structure of the mCD1d/GCK152/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.242

Literature

Macromolecules
Sequence Display for 4Y4H

Classification: IMMUNE SYSTEM

Total Structure Weight: 192098.05

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A, E 285 Mus musculus Fragment: Ectodomain, UNP residues 19-297
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B, F 99 Mus musculus Fragment: UNP residues 21-119
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain) C, G 209 Homo sapiens Mus musculus Gene Name(s): Trav11 Trav11d TRAC TCRA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain) D, H 241 Homo sapiens Mus musculus Gene Name(s): TRBC2 TCRBC2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
49X
Query on 49X

A, E (1R)-1,5-anhydro-1-{(1E,3S,4S,5R)-4,5-dihydroxy- 3-[(8-phenyloctanoyl)amino]nonadec-1-en-1- yl}-D-galactitol
GCK152 (Synonym)
C39 H67 N O8
RWGUVAAXYHWJFZ-CSYYKWSVSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.242
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 79.42 α = 90.00
b = 150.38 β = 96.38
c = 102.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-02-10
  • Released Date: 2015-05-27
  • Deposition author(s): Zajonc, D.M., Yu, E.D.

Revision History

  • 2017-09-13
    Type: Author supporting evidence, Derived calculations, Source and taxonomy