3G08

Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 3G08

Classification: IMMUNE SYSTEM

Total Structure Weight: 46138.30

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d1 A 285 Mus musculus Fragment: UNP residues 19-298
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2 microglobulin B 99 Mus musculus Fragment: UNP residues 21-119
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]- 2,3-dihydroxyoctyl}tetracosanamide
C39 H77 N O9
MPKIDHIOYNMFES-CLTBVUQJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FEE N/A in BindingDB
Kd: 6.843 nM  BindingMOAD
Kd: 6.843 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.195
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 42.24 α = 90.00
b = 107.10 β = 90.00
c = 106.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-27
  • Released Date: 2009-12-08
  • Deposition author(s): Zajonc, D.M.

Revision History

  • 2011-07-13
    Type: Non-polymer description, Version format compliance