4l8c

X-ray diffraction
2.8Å resolution

Crystal structure of the H2Db in complex with the NP-N3D peptide

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135008 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 280 amino acids
Theoretical weight: 32.47 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01899 (Residues: 25-304; Coverage: 83%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
NP-N3D peptide Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 9 amino acids
Theoretical weight: 1.03 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21
Unit cell:
a: 81.567Å b: 85.464Å c: 138.506Å
α: 90° β: 90.18° γ: 90°
R-values:
R R work R free
0.189 0.186 0.258
Expression system: Escherichia coli BL21(DE3)