2AKR

Structural basis of sulfatide presentation by mouse CD1d

Structural Biology Knowledgebase: 2AKR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2AKR

Classification: IMMUNE SYSTEM

Total Structure Weight: 91897.67

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d1 A, C 285 Mus musculus Fragment: extracellular domain, residues 19-297
Mutation: D201H
Gene Name(s): Cd1d1 Cd1.1
Beta-2-microglobulin B, D 99 Mus musculus Fragment: residues 21-119
Gene Name(s): B2m

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

A, C (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO- BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC- 3-ENYL)TETRACOS-15-ENAMIDE
(2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)- GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL; CIS- TETRACOSENOYL SULFATIDE (Synonym)
C48 H91 N O11 S
ZZQWQNAZXFNSEP-JCOQVFCVSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

A, C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.186
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.86 α = 90.00
b = 74.84 β = 102.10
c = 101.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-03
  • Released Date: 2005-12-06
  • Deposition author(s): Zajonc, D.M., Halder, R., Wu, D., Maricic, I., Roy, K., Wong, C.-H., Kumar, V., Wilson, I.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update