› 3ln5

X-ray diffraction
1.9Å resolution

Crystal structure of HLA-B*4104 in complex with a 11mer self-peptide derived from S-methyl-5-thioadenosine phosphorylase

Released:
DOI: 10.2210/pdb3ln5/pdb
PDB entry 3ln5 coloured by chain, front view.
PDB entry 3ln5 coloured by chain, side view.
PDB entry 3ln5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family.
Bade-Döding C, Theodossis A, Gras S, Kjer-Nielsen L, Eiz-Vesper B, Seltsam A, Huyton T, Rossjohn J, McCluskey J, Blasczyk R
Haematologica 96 110-8 (2011)
PMID: 20934997

Function and Biology Details

Reaction catalysed: 
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135243 (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: 274 amino acids
Theoretical weight: 31.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01889 (Residues: 25-298; Coverage: 81%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 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
S-methyl-5'-thioadenosine phosphorylase Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.26 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q13126 (Residues: 227-237; Coverage: 4%)
Gene names: MSAP, MTAP

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 50.95Å b: 82.12Å c: 110.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.191 0.241
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation.
Wieczorek et al. (2017)
4 more

3 mentions without citation

The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family.
Bade-Döding et al. (2011)
2 more