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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3)

X-ray diffraction
1.91Å resolution
PDB entry 3kz8 coloured by chain, front view.
PDB entry 3kz8 coloured by chain, side view.
PDB entry 3kz8 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero hexamer (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 hexamer
Accessible surface area: 40250.76 Å2
Buried surface area: 9788.9 Å2
Dissociation area: 3,556.68 Å2
Dissociation energy (ΔGdiss): 7.16 kcal/mol
Dissociation entropy (TΔSdiss): 50.66 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116511

Macromolecules

Cellular tumor antigen p53
Chains: A, B
Length: 200 amino acids
Theoretical weight: 22.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 3kz8, assembly 1, front view.
Cellular tumor antigen p53 in PDB entry 3kz8, assembly 1, side view.
Cellular tumor antigen p53 in PDB entry 3kz8, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')
Representative chains: C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') in PDB entry 3kz8, assembly 1, front view.
DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') in PDB entry 3kz8, assembly 1, side view.
DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') in PDB entry 3kz8, assembly 1, top view.
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