SAXSdb — 4pie

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

Protease

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–204	Not recorded	Pre-protein VI × 1 （P03274） 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

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 4PIE	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 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 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
4EKF Structure of the Inactive Adenovirus Proteinase at 0.98 Angstrom Resolution Deposited 2012-04-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–204（204 aa）	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
4PID Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor Deposited 2014-05-08	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
5FGY Structure of human adenovirus 2 protease with cofactor pVIC Deposited 2015-12-21	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	PRO_ADE02
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 1–204

Pre-protein VI

OrganismNot specified

UniProt P03274

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 240–250	Fragment：UNP residues 240-250	Protease × 1 （P03252） 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

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 4PIE	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 240–250（11 aa） Fragment：PEPT	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
4PID Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor Deposited 2014-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 240–250（11 aa） Fragment：UNP residues 240-250	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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAP6_ADE02
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 240–250

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	4pie
Deposition date deposition_date	2014-05-08
Structure title title	Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor
Keywords keywords	Adenain, adenovirus, cofactor, pVIc, cysteine protease, Hydrolase-Hydrolase inhibitor complex; Hydrolase/Hydrolase inhibitor
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	17.59 Å
Radius of gyration Rg (electron density) rg_electron	16.30 Å
Forward intensity I(0) i0	11918200.00
Molecular weight molecular_weight	24802.0 kDa
Excluded volume excluded_volume	30563 Å³
Envelope volume envelope_volume	33264 Å³
Hydration-shell volume shell_volume	16895 Å³
Envelope diameter envelope_diameter	54.3 Å
Shell Rg shell_rg	22.67 Å
Envelope Rg envelope_rg	16.55 Å
Shape Rg shape_rg	16.25 Å
Total Rg total_rg	17.38 Å
Total atoms total_atoms	1734
Residues n_residues	213
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	58.2 Å
Rg (real space) rg_real	17.47 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.1920e+07
I(0) uncertainty (real space) i0_real_error	1.4400e+05
Rg (reciprocal space) rg_reciprocal	17.48 Å
I(0) (reciprocal space) i0_reciprocal	11920000.0000
Solution quality estimate total_estimate	0.7889
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.147
Kurtosis Kurtosis kurtosis	-0.352
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2772000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 0.991; 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 (7)

Entity 1 Entity 1 polymer

Description description	Protease
Molecular weight formula_weight	23114.3 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	1771

MGSSEQELKAIVKDLGCGPYFLGTYDKRFPGFVSPHKLACAIVNTAGRETGGVHWMAFAWNPRSKTCYLFEPFGFSDQRLKQVYQFEYESLLRRSAIASSPDRCITLEKSTQSVQGPNSAACGLFCCMFLHAFANWPQTPMDHNPTMNLITGVPNSMLNSPQVQPTLRRNQEQLYSFLERHSPYFRSHSAQIRSATSFCHLKNM

来源 Source

来源生物 organism	Human adenovirus 2
通用名 common_name	HAdV-2
NCBI Class编号 ncbi_taxonomy_id	10515
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	Pre-protein VI
Molecular weight formula_weight	1353.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GVQSLKRRRCF

Entity 3 Entity 3 non-polymer

Description description	N-{(2S)-2-(3-chlorophenyl)-2-[(methylsulfonyl)amino]acetyl}-L-phenylalanyl-N-[(2Z)-2-iminoethyl]glycinamide
Molecular weight formula_weight	508.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4pieA00
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 (1)

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Unit-cell length a length_a	41.312 Å
Unit-cell length b length_b	44.437 Å
Unit-cell length c length_c	98.921 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	40.530 Å
R factor r_factor	0.2096
R_work r_work	0.2069
R_free r_free	0.2603

fit	/app/data/saxs_computation/pi/4pie/4pie.fit
pddf	/app/data/pr_computation/pi/4pie/4pie.pr.out
profile	/app/data/saxs_computation/pi/4pie/4pie.dat

Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor

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

Protease

State in the Current Structure

Other States of the Same Protein in the Database

Pre-protein VI

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 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. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)