SAXSdb — 2fej

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 94–297	Fragment：DNA binding domain	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 7.1；298 K；Ionic strength (raw mmCIF value) 150 mM；Pressure ambient NMR sample composition：0.4 mM p53 core U-15N,13C, 2H; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 + reverse Tyr ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O \| 100% D2O NMR sample composition：0.3 mM p53 core U-15N,13C, 2H + Met and Phe (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3 mM p53 core U-15N,13C, 2H + Met and Arg (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.4 mM p53 core U-15N,13C, 2H (50%); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2FEJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YC5 Sir2-p53 peptide-nicotinamide Deposited 2004-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–389（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 NCA NICOTINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, nicotinamide, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.202
2H1L The Structure of the Oncoprotein SV40 Large T Antigen and p53 Tumor Suppressor Complex Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain M 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain N 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain O 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain P 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain Q 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain R 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；5.4% PEG 4000, 73mM Mops Buffer, 22mM Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.16 Å R-free 0.308
2H1L The Structure of the Oncoprotein SV40 Large T Antigen and p53 Tumor Suppressor Complex Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain S 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain T 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain U 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain V 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain W 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain X 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；5.4% PEG 4000, 73mM Mops Buffer, 22mM Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.16 Å R-free 0.308
2H4F Sir2-p53 peptide-NAD+ Deposited 2006-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 372–389（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, NAD, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
2H4H Sir2 H116Y mutant-p53 peptide-NAD Deposited 2006-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–389（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG 3350, pH9.6, NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.99 Å R-free 0.237
2H59 Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose Deposited 2006-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 372–389（18 aa） Chain E 372–389（18 aa）	Not recorded	ZN ZINC ION × 2 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 3OD (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-4,5-DIHYDROXYTETRAHYDROFURAN-3-YL ACETATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PEG 8000, Na-Tartrate:K-Phosphate, NaCl, NAD, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.247

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P53_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 94–297

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	2fej
Deposition date deposition_date	2005-12-16
Structure title title	Solution structure of human p53 DNA binding domain.
Keywords keywords	BETA SANDWICH, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.86 Å
Radius of gyration Rg (electron density) rg_electron	17.38 Å
Forward intensity I(0) i0	10900300000.00
Molecular weight molecular_weight	829600.0 kDa
Excluded volume excluded_volume	1013400 Å³
Envelope volume envelope_volume	65599 Å³
Hydration-shell volume shell_volume	25258 Å³
Envelope diameter envelope_diameter	71.9 Å
Shell Rg shell_rg	28.91 Å
Envelope Rg envelope_rg	22.00 Å
Shape Rg shape_rg	17.38 Å
Total Rg total_rg	17.45 Å
Total atoms total_atoms	114444
Residues n_residues	7344
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	62.5 Å
Rg (real space) rg_real	17.76 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.0900e+10
I(0) uncertainty (real space) i0_real_error	1.2270e+08
Rg (reciprocal space) rg_reciprocal	17.78 Å
I(0) (reciprocal space) i0_reciprocal	10900000000.0000
Solution quality estimate total_estimate	0.7861
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.308
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1397000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2feja_
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 (1 domains)

Domain ID domain_id	2fejA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

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8. Citations (1)

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Description description	Cellular tumor antigen p53
Molecular weight formula_weight	23008.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	114444

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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

fit	/app/data/saxs_computation/fe/2fej/2fej.fit
pddf	/app/data/pr_computation/fe/2fej/2fej.pr.out
profile	/app/data/saxs_computation/fe/2fej/2fej.dat

Solution structure of human p53 DNA binding domain.

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)