4y16

X-ray diffraction
2.6Å resolution

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-100913 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 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
Ig-like domain-containing protein; T cell receptor alpha chain constant Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0B4J1J9 (Residues: 22-114; Coverage: 100%)
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC, Trav11, Trav11d
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein; T cell receptor beta constant 2 Chain: D
Molecule details ›
Chain: D
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A2NTY6 (Residues: 29-144; Coverage: 97%)
  • Canonical: A0A5B9 (Residues: 1-128; Coverage: 72%)
Gene names: TCRBC2, TRBC2
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, FUL
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2221
Unit cell:
a: 79.64Å b: 191.914Å c: 151.92Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.244
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)