1z5l

X-ray diffraction
2.2Å resolution

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

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
PDBe Complex ID:
PDB-CPX-135077 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Antigen-presenting glycoprotein CD1d1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 285 amino acids
Theoretical weight: 32.63 KDa
Source organism: Mus musculus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P21
Unit cell:
a: 59.451Å b: 77.045Å c: 111.014Å
α: 90° β: 107.63° γ: 90°
R-values:
R R work R free
0.243 0.242 0.294
Expression system: Drosophila melanogaster