7b4d

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cellular tumor antigen p53

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	DNA target × 2 ZINC ION × 2 (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 FORMIC ACID × 6 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P53_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 94–293

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7b4d
Deposition date deposition_date	2020-12-02
Structure title title	Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ
Keywords keywords	;P53, TUMOR SUPPRESSOR, DNA BINDING PROTEIN, PROTEIN DNA COMPLEX, MICHAEL ACCEPTOR, MICHAEL REACTION, PROTEIN-DRUG COMPLEX, PROTEIN-DNA-DRUG COMPLEX, loop-sheet-helix motif, DNA TARGET, ACTIVATOR, TRANSCRIPTION, HOOGSTEEN BASE-PAIRING ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7b4d__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7b4d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b4d__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.24 Å
Rg (electron density)	26.56 Å
Total Rg	26.78 Å
Atom count	3512
Residues	418
Excluded volume	60330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b4d__assembly_1__model_1`	tetramer （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Cellular tumor antigen p53
Molecular weight formula_weight	22521.6 kDa
Mutation mutation	R273C S240R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2057

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNRSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRTEEENLRKKG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA target
Molecular weight formula_weight	3664.4 kDa
Mutation mutation	'
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CGGGCATGCCCG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one
Molecular weight formula_weight	139.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	(2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one
Molecular weight formula_weight	139.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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Unit-cell length a length_a	137.587 Å
Unit-cell length b length_b	50.164 Å
Unit-cell length c length_c	34.231 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	18.280 Å
R factor r_factor	0.1721
R_work r_work	0.1684
R_free r_free	0.2043

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cellular tumor antigen p53

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7b4d__assembly_1__model_1

7b4d__assembly_1__model_1 | I(q)

7b4d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cellular tumor antigen p53

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7b4d__assembly_1__model_1

7b4d__assembly_1__model_1 | I(q)

7b4d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)