› 5lgy

X-ray diffraction
2.92Å resolution

Lysine 120-acetylated P53 DNA binding domain in a complex with the BAX response element.

Released:
DOI: 10.2210/pdb5lgy/pdb
PDB entry 5lgy coloured by chain, front view.
PDB entry 5lgy coloured by chain, side view.
PDB entry 5lgy coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.
Vainer R, Cohen S, Shahar A, Zarivach R, Arbely E
J Mol Biol 428 3013-25 (2016)
PMID: 27338200

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-118990 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Cellular tumor antigen p53 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 198 amino acids
Theoretical weight: 22.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04637 (Residues: 94-291; Coverage: 50%)
Gene names: P53, TP53
Sequence domains: P53 DNA-binding domain
Structure domains: Immunoglobulin-like
DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand ALY 4 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 67.703Å b: 70.344Å c: 104.995Å
α: 90° β: 95.83° γ: 90°
R-values:
R R work R free
0.24 0.238 0.277
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

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

3 mentions without citation

Identifying Functional Cysteine Residues in the Mitochondria.
Bak et al. (2017)
2 more