4F7C

Crystal structure of bovine CD1d with bound C12-di-sulfatide

Structural Biology Knowledgebase: 4F7C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4F7C

Classification: IMMUNE SYSTEM

Total Structure Weight: 92182.70

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

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

A, C N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]- 3-hydroxyoctadec-4-en-2-yl}dodecanamide
C36 H69 N O14 S2
JBJSVLZKWGLXMO-AZNTWQPMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.222
  • Space Group: P 42
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 168.55 α = 90.00
b = 168.55 β = 90.00
c = 41.53 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