SAXSdb — 1avu

▼

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

TRYPSIN INHIBITOR

OrganismNot specified

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 25–205	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.269

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 1AVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVW COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, ORTHORHOMBIC CRYSTAL FORM Deposited 1997-09-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–201（177 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.75 Å R-free 0.214
1AVX COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, TETRAGONAL CRYSTAL FORM Deposited 1997-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–201（177 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.90 Å R-free 0.280
1BA7 SOYBEAN TRYPSIN INHIBITOR Deposited 1998-04-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–205（181 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å R-free 0.223
1BA7 SOYBEAN TRYPSIN INHIBITOR Deposited 1998-04-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–205（181 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å R-free 0.223
6NTT X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene Deposited 2019-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–216（216 aa）	Not recorded	21D naphthalene-1,5-disulfonic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of protein stock solution and reservoir supplemented with 0.10 M 1,5-Disulfonyl Naphthalene. Crystallization time about 2 weeks.	Resolution 2.40 Å R-free 0.306
6NTT X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene Deposited 2019-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–216（216 aa）	Not recorded	21D naphthalene-1,5-disulfonic acid × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of protein stock solution and reservoir supplemented with 0.10 M 1,5-Disulfonyl Naphthalene. Crystallization time about 2 weeks.	Resolution 2.40 Å R-free 0.306
6O1F Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab Deposited 2019-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 25–216（192 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；5% PEG 4000 0.1M lithium sulfate 0.1M Tris pH 7.5	Resolution 2.15 Å R-free 0.233

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITRA_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–181； UniProt 25–205

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1avu
Deposition date deposition_date	1997-09-20
Structure title title	TRYPSIN INHIBITOR FROM SOYBEAN (STI)
Keywords keywords	SERINE PROTEASE INHIBITOR, TRYPSIN INHIBITOR, KUNITZ-TYPE, BETA-TREFOIL FOLD; SERINE PROTEASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.59 Å
Radius of gyration Rg (electron density) rg_electron	15.15 Å
Forward intensity I(0) i0	6363370.00
Molecular weight molecular_weight	18184.0 kDa
Excluded volume excluded_volume	22740 Å³
Envelope volume envelope_volume	26017 Å³
Hydration-shell volume shell_volume	14408 Å³
Envelope diameter envelope_diameter	51.6 Å
Shell Rg shell_rg	21.12 Å
Envelope Rg envelope_rg	15.46 Å
Shape Rg shape_rg	15.13 Å
Total Rg total_rg	16.35 Å
Total atoms total_atoms	1282
Residues n_residues	172
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

▼

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

Maximum dimension Dmax dmax	52.8 Å
Rg (real space) rg_real	16.45 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	6.3630e+06
I(0) uncertainty (real space) i0_real_error	6.5850e+04
Rg (reciprocal space) rg_reciprocal	16.47 Å
I(0) (reciprocal space) i0_reciprocal	6363000.0000
Solution quality estimate total_estimate	0.8852
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.070
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1153000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.991

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1avua_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.1 — Kunitz (STI) inhibitors

CATH v4.4 (1 domains)

Domain ID domain_id	1avuA00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

▶

8. Citations (4)

▶

Unit-cell length a length_a	39.420 Å
Unit-cell length b length_b	58.080 Å
Unit-cell length c length_c	96.350 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	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2690

Description description	TRYPSIN INHIBITOR
Molecular weight formula_weight	20115.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1326

TRYPSIN INHIBITOR FROM SOYBEAN (STI)

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

TRYPSIN INHIBITOR

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

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

fit	/app/data/saxs_computation/av/1avu/1avu.fit
pddf	/app/data/pr_computation/av/1avu/1avu.pr.out
profile	/app/data/saxs_computation/av/1avu/1avu.dat