3D06: Cellular tumor antigen p53

Human p53 core domain with hot spot mutation R249S (I). Determined by X-ray diffraction at 1.2 Å resolution. Released 20 Jan 2009.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,687
Mol. weight: 22.5 kDa
Ligands: ZN
Released: 20 Jan 2009

Explore 3D06 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D06 contains 6 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	1
β-strand	110-112	3	2
β-strand	124-127	4	1
β-strand	132-135	4	1
β-strand	141-146	6	2
α-helix	150-152	3
β-strand	156-163	8	1
α-helix	166-168	3
α-helix	172-173	2
α-helix	177-180	4
β-strand	195-198	4	2
β-strand	204-207	4	1
β-strand	214-219	6	1
α-helix	222-224	3
β-strand	230-236	7	2
β-strand	251-258	8	1
β-strand	264-274	11	1
α-helix	278-287	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cellular tumor antigen p53	A	protein	200	Homo sapiens	P04637 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3D06_1 Cellular tumor antigen p53 (chains A)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRSPILTIITLEDSSGNLLGRNSFEVR
VCACPGRDRRTEEENLRKKG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations. Suad, O., Rozenberg, H., Brosh, R. et al. J Mol Biol (2009) 385:249-265. DOI 10.1016/j.jmb.2008.10.063 · PubMed

Other PDB entries of the same protein (UniProt P04637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C5S 1.01 Å, Disulfide-linked, antiparallel p53-derived peptide dimer (CV1)
5MHC 1.2 Å, Crystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide
8UQR 1.22 Å, Crystal structure of the human p53 tetramerization domain
6GGC 1.24 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320
6SHZ 1.24 Å, p53 cancer mutant Y220C
4MZI 1.25 Å, Crystal structure of a human mutant p53
6GGE 1.25 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327
3LW1 1.28 Å, Binary complex of 14-3-3 sigma and p53 pT387-peptide
5O1E 1.3 Å, p53 cancer mutant Y220C im complex with compound MB577
6RL3 1.3 Å, Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface
8E7A 1.3 Å, Crystal structure of the p53 (Y107H) core domain orthorhombic P form
5O1C 1.32 Å, p53 cancer mutant Y220C in complex with compound MB184

Browse structure collections

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