SAXSdb — 4ekf

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

Adenain

Human adenovirus 2

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 1–204	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；293 K；0.3M sodium citrate, pH 5.6, 0.8 M sodium acetate, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 0.98 Å R-free 0.168

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 4EKF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVP STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR Deposited 1996-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–204（204 aa） Fragment：MAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.233
1NLN CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION Deposited 2003-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–204（204 aa） Fragment：adenovirus proteinase	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；cacodylate, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.179
4PID Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor Deposited 2014-05-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–204（204 aa）	Not recorded	ACT ACETATE ION × 1 2UQ N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.8 M sodium/potassium tartrate, 0.1 M HEPES pH 7.5	Resolution 1.59 Å R-free 0.189
4PIE Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor Deposited 2014-05-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–204（204 aa）	Not recorded	3FO N-{(2S)-2-(3-chlorophenyl)-2-[(methylsulfonyl)amino]acetyl}-L-phenylalanyl-N-[(2Z)-2-iminoethyl]glycinamide × 1 SO4 SULFATE ION × 2 ZN ZINC ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1mM peptide-nitrile inhibitor was added to the protein and incubated for 30 minutes. 0.8M lithium sulphate, 0.1 M sodium acetate, pH 4.6	Resolution 1.94 Å R-free 0.260
5FGY Structure of human adenovirus 2 protease with cofactor pVIC Deposited 2015-12-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–204（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277.15 K；Grew over one week at 4 degrees Celsius in 0.1 M sodium citrate pH 6.4, 1.7 M sodium acetate, 1 mM DTT	Resolution 2.10 Å R-free 0.197

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

View Construct and Data Evidence

UniProt name	ADEN_ADE02
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 1–204

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	4ekf
Deposition date deposition_date	2012-04-09
Structure title title	Structure of the Inactive Adenovirus Proteinase at 0.98 Angstrom Resolution
Keywords keywords	alpha and beta protein (a+b), Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.16 Å
Radius of gyration Rg (electron density) rg_electron	15.98 Å
Forward intensity I(0) i0	9023030.00
Molecular weight molecular_weight	21876.0 kDa
Excluded volume excluded_volume	27230 Å³
Envelope volume envelope_volume	30294 Å³
Hydration-shell volume shell_volume	15798 Å³
Envelope diameter envelope_diameter	57.1 Å
Shell Rg shell_rg	22.11 Å
Envelope Rg envelope_rg	16.36 Å
Shape Rg shape_rg	15.96 Å
Total Rg total_rg	17.06 Å
Total atoms total_atoms	2936
Residues n_residues	191
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	57.9 Å
Rg (real space) rg_real	17.06 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	9.0230e+06
I(0) uncertainty (real space) i0_real_error	1.1770e+05
Rg (reciprocal space) rg_reciprocal	17.07 Å
I(0) (reciprocal space) i0_reciprocal	9023000.0000
Solution quality estimate total_estimate	0.7850
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2292000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Adenain
Molecular weight formula_weight	23146.3 kDa
EC 编号 ec_number	3.4.22.39
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	3223

MGSSEQELKAIVKDLGCGPYFLGTYDKRFPGFVSPHKLACAIVNTAGRETGGVHWMAFAWNPRSKTCYLFEPFGFSDQRLKQVYQFEYESLLRRSAIASSPDRCITLEKSTQSVQGPNSAACGLFCCMFLHAFANWPQTPMDHNPTMNLITGVPNSMLNSPQVQPTLRRNQEQLYSFLERHSPYFRSHSAQIRSATSFCHLKNM

来源 Source

来源生物 organism	Human adenovirus 2
NCBI Class编号 ncbi_taxonomy_id	10515
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	258

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ekfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.7 — Adenain-like

CATH v4.4 (1 domains)

Domain ID domain_id	4ekfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

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8. Citations (8)

;Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space: III. ATOMIC RESOLUTION STRUCTURE OF THE NASCENT FORM OF THE ADENOVIRUS PROTEINASE. ;

J.Biol.Chem. (2013)

PMID: 23043139 · DOI: 10.1074/jbc.M112.407429 PRIMARY

;Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. I. binding to DNA and to hexon of the precursor to protein VI, pVI, of human adenovirus. ;

J.Biol.Chem. (2012)

PMID: 23043136 · DOI: 10.1074/jbc.M112.377150

;Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction. ;

J.Biol.Chem. (2012)

PMID: 23043137 · DOI: 10.1074/jbc.M112.407312

;Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. IV. viral proteinase slides along DNA to locate and process its substrates. ;

J.Biol.Chem. (2012)

PMID: 23043138 · DOI: 10.1074/jbc.M112.407460

;Crystallographic structure at 1.6-A resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor: insights on a new fold. ;

Biochim.Biophys.Acta (2003)

PMID: 12758141

Adenovirus proteinase: crystallization and preliminary X-ray diffraction studies to atomic resolution.

Acta Crystallogr.,Sect.D (2002)

PMID: 12198302 · DOI: 10.1107/S0907444902008429

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.

Embo J. (1996)

PMID: 8617222 · DOI: 10.1107/S0907444902008429

Viral DNA and a viral peptide can act as cofactors of adenovirus virion proteinase activity.

Nature (1993)

PMID: 8423855 · DOI: 10.1038/361274a0

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Unit-cell length a length_a	36.270 Å
Unit-cell length b length_b	54.540 Å
Unit-cell length c length_c	42.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	0.980 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1350
R_work r_work	—
R_free r_free	0.1678

fit	/app/data/saxs_computation/ek/4ekf/4ekf.fit
pddf	/app/data/pr_computation/ek/4ekf/4ekf.pr.out
profile	/app/data/saxs_computation/ek/4ekf/4ekf.dat

Structure of the Inactive Adenovirus Proteinase at 0.98 Angstrom Resolution

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

Adenain

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (8)

9. Files and Curves (10)

Files (7)

Curves (3)