1Z5L

Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D

Structural Biology Knowledgebase: 1Z5L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Z5L

Classification: IMMUNE SYSTEM

Total Structure Weight: 91763.79

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d antigen A, C 285 Mus musculus Fragment: extracellular domain
Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B, D 99 Mus musculus Fragment: extracellular domain
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
PBS
Query on PBS

A, C (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]- 2-AMINO-OCTADECANE-3,4-DIOL
C32 H63 N O9
PFXOKSFCNLTBGK-YFWOXBOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
R16
Query on R16

A, C HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.242
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.45 α = 90.00
b = 77.04 β = 107.63
c = 111.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-03-18
  • Released Date: 2005-07-19
  • Deposition author(s): Zajonc, D.M., Cantu, C., Mattner, J., Zhou, D., Savage, P.B., Bendelac, A., Wilson, I.A., Teyton, L.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4