5AOK: Cellular tumor antigen P53

Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan7099. Determined by X-ray diffraction at 1.35 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,797
Mol. weight: 49.97 kDa
Ligands: ZN, GOH
Released: 16 Dec 2015

Explore 5AOK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AOK contains 12 α-helices and 24 β-strands across 2 chains. 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	179-181	3
β-strand	195-197	3	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	278-289	12

Chain B: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	96-99	4
β-strand	103	1	3
β-strand	110-112	3	4
β-strand	124-127	4	3
β-strand	132-135	4	3
β-strand	141-146	6	4
α-helix	150-152	3
β-strand	156-163	8	3
α-helix	172-173	2
α-helix	179-181	3
β-strand	195-197	3	4
β-strand	204-207	4	3
β-strand	214-219	6	3
α-helix	222-224	3
β-strand	230-236	7	4
β-strand	251-258	8	3
β-strand	264-274	11	3
α-helix	278-290	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cellular tumor antigen P53	A, B	protein	219	HOMO SAPIENS	P04637 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5AOK_1 CELLULAR TUMOR ANTIGEN P53 (chains A, B)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFR
HSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVR
VCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
GOH	5-[2-cyclopropyl-5-(1H-pyrrol-1-yl)-1,3-oxazol-4-yl]-1H-1,2,3,4-tetrazole	C11 H10 N6 O	2

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

Exploiting Transient Protein States for the Design of Small-Molecule Stabilizers of Mutant P53. Joerger, A.C., Bauer, M.R., Wilcken, R. et al. Structure (2015) 23:2246. DOI 10.1016/J.STR.2015.10.016 · 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)
3D06 1.2 Å, Human p53 core domain with hot spot mutation R249S (I)
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

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