› 5vz5

X-ray diffraction
2.59Å resolution

Crystal structure of an anaplastic lymphoma kinase-derived neuroblastoma tumor antigen bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501

Released:
DOI: 10.2210/pdb5vz5/pdb
PDB entry 5vz5 coloured by chain, front view.
PDB entry 5vz5 coloured by chain, side view.
PDB entry 5vz5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.
Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG
Front Immunol 9 99 (2018)
PMID: 29441070

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135262 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 280 amino acids
Theoretical weight: 32.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01889 (Residues: 25-304; Coverage: 83%)
Gene names: HLA-B, HLAB
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 BL21
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
ALK tyrosine kinase receptor Chain: C
Molecule details ›
Chain: C
Length: 10 amino acids
Theoretical weight: 1.25 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9UM73 (Residues: 1274-1283; Coverage: 1%)
Gene name: ALK

Ligands and Environments

2 bound ligands:
Ligand GOL 7 x GOL
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P6122
Unit cell:
a: 112.89Å b: 112.89Å c: 177.38Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.216 0.265
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

4 review citations

Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman et al. (2020)
3 more

1 mention without citation

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.
Toor et al. (2018)