› 3kz8

X-ray diffraction
1.91Å resolution

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

Released:
DOI: 10.2210/pdb3kz8/pdb
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
Primary publication:
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.
Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z
Nat Struct Mol Biol 17 423-9 (2010)
PMID: 20364130

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116511 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Cellular tumor antigen p53 Chains: A, B
Molecule details ›
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
Sequence domains: P53 DNA-binding domain
Structure domains: Immunoglobulin-like
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') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand IOD 2 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 138.422Å b: 49.812Å c: 68.056Å
α: 90° β: 93.48° γ: 90°
R-values:
R R work R free
0.223 0.221 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

19 review citations

The multiple mechanisms that regulate p53 activity and cell fate.
Hafner et al. (2019)
18 more

15 mentions without citation

Absence of a simple code: how transcription factors read the genome.
Slattery et al. (2014)
14 more