SAXSdb — 4zgz

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

Antizyme inhibitor 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–437	Fragment：HUMAN ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR, UNP residues 2-437 Mutation：N21D	Ornithine decarboxylase antizyme 1 × 1 （P54368）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (ADA) PH 6.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 5.81 Å R-free 0.240
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–437	Fragment：HUMAN ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR, UNP residues 2-437 Mutation：N21D	Ornithine decarboxylase antizyme 1 × 1 （P54368）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (ADA) PH 6.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 5.81 Å R-free 0.240

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	AZIN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–438； UniProt 2–437 Author chain C； PDBConstruct 3–438； UniProt 2–437

Ornithine decarboxylase antizyme 1

Homo sapiens

UniProt P54368

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 110–228	Fragment：HUMAN ORNITHINE DECARBOXYLASE ANTIZYME, UNP residues 110-228	Antizyme inhibitor 1 × 1 （O14977）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (ADA) PH 6.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 5.81 Å R-free 0.240
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 110–228	Fragment：HUMAN ORNITHINE DECARBOXYLASE ANTIZYME, UNP residues 110-228	Antizyme inhibitor 1 × 1 （O14977）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (ADA) PH 6.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 5.81 Å R-free 0.240

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 4ZGZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZGY STRUCTURE of HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME Deposited 2015-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 95–219（125 aa） Fragment：UNP RESIDUES 95-219	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100MM MAGNESIUM ACETATE, 50MM MES PH 5.6, 20% 2-METHYL-2, 4-PENTANEDIOL(MPD), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 2.63 Å R-free 0.256
5BWA Crystal structure of ODC-PLP-AZ1 ternary complex Deposited 2015-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 69–228（160 aa） Fragment：UNP residues 69-228	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；288 K；0.2 M di-Ammonium tartrate, 20% PEG 3350	Resolution 3.20 Å R-free 0.289

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

View Construct and Data Evidence

UniProt name	OAZ1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–120； UniProt 110–228 Author chain D； PDBConstruct 2–120； UniProt 110–228

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	4zgz
Deposition date deposition_date	2015-04-24
Structure title title	STRUCTURE OF HUMAN ANTIZYME INHIBITOR IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME
Keywords keywords	TIM BARREL DOMAIN, BETA-SHEET DOMAIN, INHIBITION, ANTIZYME, PLASMA, PROTEIN BINDING; PROTEIN BINDING
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	36.82 Å
Radius of gyration Rg (electron density) rg_electron	36.62 Å
Forward intensity I(0) i0	162444000.00
Molecular weight molecular_weight	105880.0 kDa
Excluded volume excluded_volume	133670 Å³
Envelope volume envelope_volume	189300 Å³
Hydration-shell volume shell_volume	43657 Å³
Envelope diameter envelope_diameter	127.4 Å
Shell Rg shell_rg	42.30 Å
Envelope Rg envelope_rg	36.02 Å
Shape Rg shape_rg	36.66 Å
Total Rg total_rg	36.88 Å
Total atoms total_atoms	7456
Residues n_residues	967
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	121.6 Å
Rg (real space) rg_real	36.93 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.6240e+08
I(0) uncertainty (real space) i0_real_error	3.1100e+06
Rg (reciprocal space) rg_reciprocal	36.87 Å
I(0) (reciprocal space) i0_reciprocal	162400000.0000
Solution quality estimate total_estimate	0.8829
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.8 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.606
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	37690000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.905

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Antizyme inhibitor 1
Molecular weight formula_weight	48470.8 kDa
Mutation mutation	N21D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7456

MGKGFIDDANYSVGLLDEGTDLGNVIDNYVYEHTLTGKNAFFVGDLGKIVKKHSQWQNVVAQIKPFYTVKCNSAPAVLEILAALGTGFACSSKNEMALVQELGVPPENIIYISPCKQVSQIKYAAKVGVNILTCDNEIELKKIARNHPNAKVLLHIATEDNIGGEEGNMKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACKESQVYVHALSDARCVFDMAGEIGFTMNMLDIGGGFTGTEFQLEEVNHVISPLLDIYFPEGSGVKIISEPGSYYVSSAFTLAVNIIAKKVVENDKFPSGVEKTGSDEPAFMYYMNDGVYGSFASKLSEDLNTIPEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYYMMSFSDWYEMQDAGITSDSMMKNFFFVPSCIQ

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Ornithine decarboxylase antizyme 1
Molecular weight formula_weight	14778.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MNDKTRILNVQSRLTDAKRINWRTVLSGGSLYIEIPGGALPEGSKDSFAVLLEFAEEQLRADHVFICFHKNREDRAALLRTFSFLGFEIVRPGHPLVPKRPDACFMAYTFERESSGEEEELEHHHHHH

来源 Source

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

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8. Citations (1)

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Unit-cell length a length_a	166.563 Å
Unit-cell length b length_b	166.563 Å
Unit-cell length c length_c	144.864 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	5.810 Å
Low-resolution limit resolution_low	25.920 Å
R factor r_factor	0.1910
R_work r_work	0.1880
R_free r_free	0.2400

fit	/app/data/saxs_computation/zg/4zgz/4zgz.fit
pddf	/app/data/pr_computation/zg/4zgz/4zgz.pr.out
profile	/app/data/saxs_computation/zg/4zgz/4zgz.dat

STRUCTURE OF HUMAN ANTIZYME INHIBITOR IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME

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

Antizyme inhibitor 1

State in the Current Structure

Other States of the Same Protein in the Database

Ornithine decarboxylase antizyme 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)