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Crystal Structure of B*4402 presenting a 10mer EBV epitope

X-ray diffraction
1.701Å resolution
PDB entry 3dx6 coloured by chain, front view.
PDB entry 3dx6 coloured by chain, side view.
PDB entry 3dx6 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 18840.7 Å2
Buried surface area: 6805.82 Å2
Dissociation area: 1,027.48 Å2
Dissociation energy (ΔGdiss): 8.24 kcal/mol
Dissociation entropy (TΔSdiss): 8.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135130

Macromolecules

HLA class I histocompatibility antigen, B alpha chain
Chain: A
Length: 276 amino acids
Theoretical weight: 31.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Pfam:
InterPro:
CATH:
HLA class I histocompatibility antigen, B alpha chain in PDB entry 3dx6, assembly 1, front view.
HLA class I histocompatibility antigen, B alpha chain in PDB entry 3dx6, assembly 1, side view.
HLA class I histocompatibility antigen, B alpha chain in PDB entry 3dx6, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P01889  
127620406080100120140160180200220240260
 
100200
UniProt
P01889
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
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Beta-2-microglobulin
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
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
Beta-2-microglobulin in PDB entry 3dx6, assembly 1, front view.
Beta-2-microglobulin in PDB entry 3dx6, assembly 1, side view.
Beta-2-microglobulin in PDB entry 3dx6, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P61769  
199102030405060708090
 
50100IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
UniProt
P61769
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
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Epstein-Barr nuclear antigen 6
Chain: C
Length: 10 amino acids
Theoretical weight: 1.28 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Not provided
UniProt:
  • Canonical: P03204 (Residues: 281-290; Coverage: 1%)
Gene names: BERF3-BERF4, EBNA6
Epstein-Barr nuclear antigen 6 in PDB entry 3dx6, assembly 1, front view.
Epstein-Barr nuclear antigen 6 in PDB entry 3dx6, assembly 1, side view.
Epstein-Barr nuclear antigen 6 in PDB entry 3dx6, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P03204  
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