SAXSdb — 5fgy

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

Protease

Human adenovirus C serotype 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	pVIC × 1	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

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 5FGY	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 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
4PIE Crystal structure of human adenovirus 2 protease a substrate based 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	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

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

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	5fgy
Deposition date deposition_date	2015-12-21
Structure title title	Structure of human adenovirus 2 protease with cofactor pVIC
Keywords keywords	protease, cofactor, complex, 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	17.70 Å
Radius of gyration Rg (electron density) rg_electron	16.41 Å
Forward intensity I(0) i0	11218700.00
Molecular weight molecular_weight	24316.0 kDa
Excluded volume excluded_volume	30164 Å³
Envelope volume envelope_volume	33388 Å³
Hydration-shell volume shell_volume	16878 Å³
Envelope diameter envelope_diameter	57.7 Å
Shell Rg shell_rg	22.75 Å
Envelope Rg envelope_rg	16.70 Å
Shape Rg shape_rg	16.37 Å
Total Rg total_rg	17.51 Å
Total atoms total_atoms	1707
Residues n_residues	214
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	56.3 Å
Rg (real space) rg_real	17.58 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.1220e+07
I(0) uncertainty (real space) i0_real_error	1.4210e+05
Rg (reciprocal space) rg_reciprocal	17.60 Å
I(0) (reciprocal space) i0_reciprocal	11220000.0000
Solution quality estimate total_estimate	0.6473
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.3 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.341
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2603000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 0.291; 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 (3)

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	1871

MGSSEQELKAIVKDLGCGPYFLGTYDKRFPGFVSPHKLACAIVNTAGRETGGVHWMAFAWNPRSKTCYLFEPFGFSDQRLKQVYQFEYESLLRRSAIASSPDRCITLEKSTQSVQGPNSAACGLFCCMFLHAFANWPQTPMDHNPTMNLITGVPNSMLNSPQVQPTLRRNQEQLYSFLERHSPYFRSHSAQIRSATSFCHLKNM

来源 Source

来源生物 organism	Human adenovirus C serotype 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	pVIC
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	164

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5fgyA00
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	112.420 Å
Unit-cell length b length_b	112.420 Å
Unit-cell length c length_c	49.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	97.360 Å
R factor r_factor	0.1766
R_work r_work	0.1755
R_free r_free	0.1969

fit	/app/data/saxs_computation/fg/5fgy/5fgy.fit
pddf	/app/data/pr_computation/fg/5fgy/5fgy.pr.out
profile	/app/data/saxs_computation/fg/5fgy/5fgy.dat

Structure of human adenovirus 2 protease with cofactor pVIC

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

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 polymer

Polymer Polymer

Entity 3 Entity 3 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)