6BNK

Crystal structure of TCR-MHC-like molecule

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.

Chennamadhavuni, D., Saavedra-Avila, N.A., Carreno, L.J., Guberman-Pfeffer, M.J., Arora, P., Yongqing, T., Koay, H.F., Godfrey, D.I., Keshipeddy, S., Richardson, S.K., Sundararaj, S., Lo, J.H., Wen, X., Gascon, J.A., Yuan, W., Rossjohn, J., Le Nours, J., Porcelli, S.A., Howell, A.R.

(2018) Cell Chem Biol 25: 571


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A, E
302Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Human nkt tcr alpha chain
C, G
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Human nkt tcr beta chain
D, H
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGH
Query on AGH
Download SDF File 
Download CCD File 
A, E
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.970α = 90.00
b = 150.570β = 95.23
c = 101.200γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
SCALAdata scaling
iMOSFLMdata 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: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-05-30
    Type: Data collection, Database references