› 3bgm

X-ray diffraction
1.6Å resolution

Crystal Structure of PKD2 Phosphopeptide Bound to Human Class I MHC HLA-A2

Released:
DOI: 10.2210/pdb3bgm/pdb
PDB entry 3bgm coloured by chain, front view.
PDB entry 3bgm coloured by chain, side view.
PDB entry 3bgm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self.
Mohammed F, Cobbold M, Zarling AL, Salim M, Barrett-Wilt GA, Shabanowitz J, Hunt DF, Engelhard VH, Willcox BE
Nat Immunol 9 1236-43 (2008)
PMID: 18836451

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-137825 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, A alpha chain Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04439 (Residues: 25-298; Coverage: 80%)
Gene names: HLA-A, HLAA
Sequence domains:
Structure 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: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Serine/threonine-protein kinase D2 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9BZL6 (Residues: 526-534; Coverage: 1%)
Gene names: HSPC187, PKD2, PRKD2

Ligands and Environments

1 bound ligand:
Ligand EDO 4 x EDO
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 117.8Å b: 54.8Å c: 75.8Å
α: 90° β: 105° γ: 90°
R-values:
R R work R free
0.203 0.202 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

35 review citations

α-Enolase: a promising therapeutic and diagnostic tumor target.
Capello et al. (2011)
34 more

5 mentions without citation

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self.
Mohammed et al. (2008)
4 more