4F7E

Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide

Structural Biology Knowledgebase: 4F7E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 4F7E

Classification: IMMUNE SYSTEM

Total Structure Weight: 45573.87

Macromolecule Entities
Molecule Chains Length Organism Details
CD1D antigen, d polypeptide A 283 Bos taurus Fragment: UNP residues 129-405
Gene Name(s): CD1D Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B 98 Bos taurus Fragment: UNP residues 21-118
Gene Name(s): B2M Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0SH
Query on 0SH

A N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)- 3,4-dihydroxyoctadecan-2-yl]hexadecanamide
C40 H79 N O9
HRAAKPGXJOTHIU-WVLAUNTOSA-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)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.221
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.78 α = 90.00
b = 74.48 β = 90.00
c = 122.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-15
  • Released Date: 2012-11-14
  • Deposition author(s): Wang, J., Zajonc, D.M.

Revision History

No revisions since initial release