› 6c6f

X-ray diffraction
1.67Å resolution

Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d

Released:
DOI: 10.2210/pdb6c6f/pdb
PDB entry 6c6f coloured by chain, front view.
PDB entry 6c6f coloured by chain, side view.
PDB entry 6c6f coloured by chain, top view.
Source organism: Mus musculus
Entry authors: Zajonc DM, Wang J

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135077 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.63 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
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, BMA, MAN, FUC
Carbohydrate polymer
3 bound ligands:
Ligand NAG 2 x NAG
Ligand ELS 1 x ELS
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 41.627Å b: 98.476Å c: 55.431Å
α: 90° β: 106.21° γ: 90°
R-values:
R R work R free
0.196 0.196 0.222
Expression system: Spodoptera frugiperda

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