5VCJ

Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycolipid recognition by iNKT cells

Wang, J.Zajonc, D.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A
285Mus musculusMutation(s): 1 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
C
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
D
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBS
Query on PBS

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Download CCD File 
A
(2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
C32 H63 N O9
PFXOKSFCNLTBGK-YFWOXBOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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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

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

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Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.261α = 90.00
b = 191.611β = 90.00
c = 151.249γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKLdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-31 
  • Released Date: 2018-04-04 
  • Deposition Author(s): Wang, J., Zajonc, D.M.

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release