3ZME: P53 core domain mutant Y220C

Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242. Determined by X-ray diffraction at 1.35 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,764
Mol. weight: 49.79 kDa
Ligands: QC5, ZN
Released: 8 May 2013

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

Secondary structure: helices and β-sheets

3ZME contains 11 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: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
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

>3ZME_1 Cellular tumor antigen p53 (chains A, B)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFR
HSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVR
VCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Ligands and cofactors

ID	Name	Formula	Copies
QC5	2-(4-(4-fluorophenyl)-5-(1H-pyrrol-1-yl)-1H-pyrazol-1-yl)-N,N-dimethylethanamine	C17 H19 F N4	2
ZN	Zinc ion	Zn	2

Primary citation

Small molecule induced reactivation of mutant p53 in cancer cells. Liu, X., Wilcken, R., Joerger, A.C. et al. Nucleic Acids Res (2013) 41:6034-6044. DOI 10.1093/nar/gkt305 · 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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