4ZAK

Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 4ZAK

Classification: IMMUNE SYSTEM

Total Structure Weight: 96134.86

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A 285 Mus musculus 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
Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain C 209 Homo sapiens Mus musculus Mutation: T98A, Y103H, R106A, T111I
Gene Name(s): Trav11 Trav11d Traj18 B2M Gene View HDCMA22P
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region D 241 Homo sapiens Mus musculus Mutation: S168C, C186S
Gene Name(s): TRBC2 TCRBC2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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
4LX
Query on 4LX

A N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)- 3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide
C50 H99 N O8 S
MSKBSPRYFRAUPB-BYSUZVQFSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.216
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 78.92 α = 90.00
b = 190.54 β = 90.00
c = 150.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-04-13
  • Released Date: 2015-07-01
  • Deposition author(s): Zajonc, D.M., Birkholz, A.M.

Revision History

  • 2015-07-29
    Type: Database references
  • 2017-09-06
    Type: Author supporting evidence, Derived calculations, Source and taxonomy