SAXSdb — 1tup

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

PROTEIN (P53 TUMOR SUPPRESSOR )

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 3 DNA 2	;DNA (5'-D(TPTPTPCPCPTPAPGPAPCPTPTPGPCPCPCPA PAPTPTPA)-3') ; × 1 ;DNA (5'-D(APTPAPAPTPTPGPGPGPCPAPAPGPTPCPTPA PGPGPAPA)-3') ; × 1 ZINC ION × 3 water × 5	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	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 94–312 Author chain B； PDBConstruct 1–219； UniProt 94–312 Author chain C； PDBConstruct 1–219； UniProt 94–312

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	1tup
Deposition date deposition_date	1995-07-11
Structure title title	TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA
Keywords keywords	ANTIGEN P53, ANTITUMOR PROTEIN-DNA COMPLEX; ANTITUMOR PROTEIN/DNA
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.

1tup__assembly_1__model_1

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

Download this curve (.dat)

1tup__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tup__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.26 Å
Rg (electron density)	30.10 Å
Total Rg	30.45 Å
Atom count	5444
Residues	627
Excluded volume	93109 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tup__assembly_1__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPTPTPCPCPTPAPGPAPCPTPTPGPCPCPCPA PAPTPTP*A)-3') ;
Molecular weight formula_weight	6348.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	5828

TTTCCTAGACTTGCCCAATTA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APTPAPAPTPTPGPGPGPCPAPAPGPTPCPTPA PGPGPAP*A)-3') ;
Molecular weight formula_weight	6535.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

ATAATTGGGCAAGTCTAGGAA

Entity 3 Entity 3 polymer

Description description	PROTEIN (P53 TUMOR SUPPRESSOR )
Molecular weight formula_weight	24586.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	384

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1tupa_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.2 — p53 DNA-binding domain-like

Domain ID domain_id	d1tupb_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.2 — p53 DNA-binding domain-like

Domain ID domain_id	d1tupc_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.2 — p53 DNA-binding domain-like

CATH v4.4 (3 domains)

Domain ID domain_id	1tupA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	1tupB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	1tupC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

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Unit-cell length a length_a	117.500 Å
Unit-cell length b length_b	67.900 Å
Unit-cell length c length_c	108.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2020
R_work r_work	0.2020
R_free r_free	—

TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA

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

PROTEIN (P53 TUMOR SUPPRESSOR )

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

1tup__assembly_1__model_1

1tup__assembly_1__model_1 | I(q)

1tup__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)

TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA

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

PROTEIN (P53 TUMOR SUPPRESSOR )

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

1tup__assembly_1__model_1

1tup__assembly_1__model_1 | I(q)

1tup__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (3)