6MJI

Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.

Janssens, J., Bitra, A., Wang, J., Decruy, T., Venken, K., van der Eycken, J., Elewaut, D., Zajonc, D.M., van Calenbergh, S.

(2019) ChemMedChem 14: 147-168


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
C
209Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Trav11 (Trav11d), B2M
Find proteins for A0A0B4J1J9 (Mus musculus)
Go to UniProtKB:  A0A0B4J1J9
Find proteins for K7N5M3 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  K7N5M3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-chain,Tcell receptor chain,T cell receptor beta constant 2
D
241Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: TRBC2 (TCRBC2),
Find proteins for A2NTY6 (Mus musculus)
Go to UniProtKB:  A2NTY6
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Find proteins for A0N8J3 (Mus musculus)
Go to UniProtKB:  A0N8J3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A
285Mus musculusMutation(s): 0 
Gene Names: Cd1d1
Find proteins for A0A0R4J090 (Mus musculus)
Go to UniProtKB:  A0A0R4J090
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
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Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC
Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA
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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
JTD
Query on JTD
Download SDF File 
Download CCD File 
A
N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide
C54 H105 N O9
CVKVQMALSPWMOL-KGOGAPLFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.216α = 90.00
b = 191.161β = 90.00
c = 151.095γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references