2GAZ

Mycobacterial lipoglycan presentation by CD1d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 2GAZ

Classification: IMMUNE SYSTEM

Total Structure Weight: 46853.63

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d1 A 285 Mus musculus Fragment: extracellular domain, residues 19-297
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
beta-2-microglobulin B 99 Mus musculus Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A (2R)-3-[(HYDROXY{[(2R,3R,5S,6R)-3,4,5-TRIHYDROXY- 2,6-BIS(ALPHA-D-MANNOPYRANOSYLOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]PROPANE- 1,2-DIYL DIHEXADECANOATE
2,6-(DI-O-D-MANNOPYRANOSYL)-1-O-(1,2-DI-O- PALMITOYL-SN-GLYCERO-3-PHOSPHORYL)-D-MYO- INOSITOL (Synonym)
C53 H99 O23 P
XGAHMXUNNQXCDP-FKPQOHGQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.212
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 41.83 α = 90.00
b = 110.76 β = 90.00
c = 107.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-09
  • Released Date: 2006-09-26
  • Deposition author(s): Zajonc, D.M.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Advisory, Version format compliance