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Human p53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA

X-ray diffraction
1.8Å resolution
PDB entry 3d0a coloured by chain, front view.
PDB entry 3d0a coloured by chain, side view.
PDB entry 3d0a coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Cellular tumor antigen p53 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 21117.74 Å2
Buried surface area: 3734.06 Å2
Dissociation area: 792.66 Å2
Dissociation energy (ΔGdiss): 3.51 kcal/mol
Dissociation entropy (TΔSdiss): 12.32 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116165
Assembly 2
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Assembly Name: Cellular tumor antigen p53 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 20985.85 Å2
Buried surface area: 4002.64 Å2
Dissociation area: 1,399.14 Å2
Dissociation energy (ΔGdiss): 2.49 kcal/mol
Dissociation entropy (TΔSdiss): 23.04 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116165

Macromolecules

Cellular tumor antigen p53
Chains: A, B, C, D
Length: 200 amino acids
Theoretical weight: 22.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04637 (Residues: 94-293; Coverage: 51%)
Gene names: P53, TP53
Pfam: P53 DNA-binding domain
InterPro:
CATH: Immunoglobulin-like
Cellular tumor antigen p53 in PDB entry 3d0a, assembly 1, front view.
Cellular tumor antigen p53 in PDB entry 3d0a, assembly 1, side view.
Cellular tumor antigen p53 in PDB entry 3d0a, assembly 1, top view.
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DNA chains E, F, G, H
Name: DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3')
Representative chains: E, F, G, H
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') in PDB entry 3d0a, assembly 1, front view.
DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') in PDB entry 3d0a, assembly 1, side view.
DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') in PDB entry 3d0a, assembly 1, top view.
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