5G4N: P53 cancer mutant Y220C

Crystal structure of the p53 cancer mutant Y220C in complex with a difluorinated derivative of the small molecule stabilizer Phikan083. Determined by X-ray diffraction at 1.35 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,647
Mol. weight: 49.83 kDa
Ligands: ZN, O83
Released: 22 Jun 2016

Explore 5G4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5G4N 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	278-290	13

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	221-224	4
β-strand	230-236	7	4
β-strand	251-258	8	3
β-strand	264-274	11	3
α-helix	278-289	12

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

>5G4N_1 CELLULAR TUMOR ANTIGEN P53 (chains A, B)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFR
HSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVR
VCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
O83	1-[9-(2,2-difluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine	C16 H16 F2 N2	2

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

Primary citation

Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions for the Design of P53 Mutant Y220C Rescue Drugs. Bauer, M.R., Jones, R.N., Baud, M.G.J. et al. ACS Chem Biol (2016) 11:2265. DOI 10.1021/ACSCHEMBIO.6B00315 · 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

Browse structure collections

About this viewer

MolViewer shows 5G4N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.