4APQ

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Type-II Natural Killer T Cell Antigen Receptor Mediated Recognition of Cd1D-Sulfatide

Patel, O.Pellicci, D.G.Gras, S.Clarke, A.J.Sandoval-Romero, M.Le Nours, J.Theodossis, A.Mallevaey, T.Gapin, L.Cardell, S.Godfrey, D.I.Rossjohn, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
A
302Mus musculusGene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B
99Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MOUSE NKT TCR VALPHA14, HUMAN NKT TCR VALPHA14
C
207Homo sapiensGene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6
D
243N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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
CIS
Query on CIS

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Download CCD File 
A
(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE
(2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL; CIS-TETRACOSENOYL SULFATIDE
C48 H91 N O11 S
ZZQWQNAZXFNSEP-JCOQVFCVSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.177 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.110α = 90.00
b = 95.110β = 90.00
c = 291.400γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release