› 6v7y

X-ray diffraction
2.4Å resolution

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5

Released:
DOI: 10.2210/pdb6v7y/pdb
Model geometry
Data not analysed
Fit model/data
Data not analysed
PDB entry 6v7y coloured by chain, front view.
PDB entry 6v7y coloured by chain, side view.
PDB entry 6v7y coloured by chain, top view.
Source organisms:
Primary publication:
A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Shahine A, Rossjohn J
Nat Cancer (2020)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-231763 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Antigen-presenting glycoprotein CD1d Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 39.47 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 23-296; Coverage: 87%)
Gene name: CD1D
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Nanobody VHH ID5 Chain: F

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
4 bound ligands:
Ligand NAG 2 x NAG
Ligand SO4 5 x SO4
Ligand AGH 1 x AGH
Ligand CL 5 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P3121
Unit cell:
a: 73.27Å b: 73.27Å c: 261.077Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.241 0.276
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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