4APQ

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

Structural Biology Knowledgebase: 4APQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4APQ

Classification: IMMUNE SYSTEM

Total Structure Weight: 99118.75

Macromolecule Entities
Molecule Chains Length Organism Details
ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1 A 302 Mus musculus Fragment: EXTRACELLULAR DOMAIN, RESIDUES 19-297
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
BETA-2-MICROGLOBULIN B 99 Mus musculus Mutation: D85A
Gene Name(s): B2m
MOUSE NKT TCR VALPHA14, HUMAN NKT TCR VALPHA14 C 207 Mus musculus Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-212
Gene Name(s): TRAC TCRA
MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6 D 243 Mus musculus Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-247

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CIS
Query on CIS

A (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO- BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC- 3-ENYL)TETRACOS-15-ENAMIDE
3R, (Synonym)
C48 H91 N O11 S
ZZQWQNAZXFNSEP-JCOQVFCVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.177
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 95.11 α = 90.00
b = 95.11 β = 90.00
c = 291.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-05
  • Released Date: 2013-04-24
  • Deposition author(s): Clarke, A.J., Le Nours, J., Rossjohn, J.

Revision History

No revisions since initial release