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Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer

X-ray diffraction
2.15Å resolution
PDB entry 3kmd coloured by chain, front view.
PDB entry 3kmd coloured by chain, side view.
PDB entry 3kmd 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: 40292.69 Å2
Buried surface area: 9404.09 Å2
Dissociation area: 3,786.6 Å2
Dissociation energy (ΔGdiss): 10.56 kcal/mol
Dissociation entropy (TΔSdiss): 50.89 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116491

Macromolecules

Cellular tumor antigen p53
Chains: A, B, C, D
Length: 200 amino acids
Theoretical weight: 22.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P04637 (Residues: 92-291; Coverage: 51%)
Gene names: P53, TP53
Pfam: P53 DNA-binding domain
InterPro:
CATH: Immunoglobulin-like
Cellular tumor antigen p53 in PDB entry 3kmd, assembly 1, front view.
Cellular tumor antigen p53 in PDB entry 3kmd, assembly 1, side view.
Cellular tumor antigen p53 in PDB entry 3kmd, assembly 1, top view.
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DNA chains E, F
Name: 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3'
Representative chains: E, F
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 19 nucleotides
Theoretical weight: 5.85 KDa
5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' in PDB entry 3kmd, assembly 1, front view.
5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' in PDB entry 3kmd, assembly 1, side view.
5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' in PDB entry 3kmd, assembly 1, top view.
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