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Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein

X-ray diffraction
2.8Å resolution
PDB entry 3it8 coloured by chain, front view.
PDB entry 3it8 coloured by chain, side view.
PDB entry 3it8 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexamer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Transmembrane tumor necrosis factor complex and Ig-like domain-containing protein
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Multimeric state: hetero hexamer
Accessible surface area: 59529.8 Å2
Buried surface area: 14991.27 Å2
Dissociation area: 2,973.93 Å2
Dissociation energy (ΔGdiss): -18.33 kcal/mol
Dissociation entropy (TΔSdiss): 42.07 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-134288
Assembly 2
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Assembly Name: Transmembrane tumor necrosis factor complex and Ig-like domain-containing protein
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Multimeric state: hetero hexamer
Accessible surface area: 59555.0 Å2
Buried surface area: 14945.03 Å2
Dissociation area: 2,948.19 Å2
Dissociation energy (ΔGdiss): -20.22 kcal/mol
Dissociation entropy (TΔSdiss): 42.07 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-134288

Macromolecules

Tumor necrosis factor, soluble form
Chains: A, B, C, G, H, I
Length: 161 amino acids
Theoretical weight: 17.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01375 (Residues: 82-233; Coverage: 65%)
Gene names: TNF, TNFA, TNFSF2
Pfam: TNF(Tumour Necrosis Factor) family
InterPro:
CATH: Jelly Rolls
Tumor necrosis factor, soluble form in PDB entry 3it8, assembly 1, front view.
Tumor necrosis factor, soluble form in PDB entry 3it8, assembly 1, side view.
Tumor necrosis factor, soluble form in PDB entry 3it8, assembly 1, top view.
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Ig-like domain-containing protein
Chains: D, E, F, J, K, L
Length: 324 amino acids
Theoretical weight: 37.33 KDa
Source organism: Yaba-like disease virus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9DHW0 (Residues: 17-332; Coverage: 94%)
Gene name: 2L
Pfam: Poxvirus, 2L, N-terminal domain
InterPro:
CATH:
Ig-like domain-containing protein in PDB entry 3it8, assembly 1, front view.
Ig-like domain-containing protein in PDB entry 3it8, assembly 1, side view.
Ig-like domain-containing protein in PDB entry 3it8, assembly 1, top view.
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