4l8b

X-ray diffraction
2.2Å resolution

Crystal structure of the H2Db in complex with the NP-N5H peptide

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135007 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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-N5H peptide Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.05 KDa

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21212
Unit cell:
a: 90.99Å b: 132.138Å c: 47.038Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.198 0.232
Expression system: Escherichia coli BL21(DE3)