SAXSdb — 6ntt

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

Trypsin inhibitor A

Glycine max

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 1–216	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–216	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

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 6NTT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVU TRYPSIN INHIBITOR FROM SOYBEAN (STI) Deposited 1997-09-20	Different construct Different ligand/ion 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 7.5；pH 7.5	Resolution 2.30 Å R-free 0.269
1AVW COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, ORTHORHOMBIC 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 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 construct Different ligand/ion 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 construct Different ligand/ion 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
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 6 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 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216

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	6ntt
Deposition date deposition_date	2019-01-30
Structure title title	X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene
Keywords keywords	silver bullets, ligands, symmetry, oligomer, crystallization, buffer, PLANT PROTEIN; PLANT PROTEIN
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	24.91 Å
Radius of gyration Rg (electron density) rg_electron	24.04 Å
Forward intensity I(0) i0	28851400.00
Molecular weight molecular_weight	40327.0 kDa
Excluded volume excluded_volume	50155 Å³
Envelope volume envelope_volume	65358 Å³
Hydration-shell volume shell_volume	23261 Å³
Envelope diameter envelope_diameter	92.1 Å
Shell Rg shell_rg	30.33 Å
Envelope Rg envelope_rg	24.49 Å
Shape Rg shape_rg	24.05 Å
Total Rg total_rg	24.80 Å
Total atoms total_atoms	2828
Residues n_residues	351
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	86.9 Å
Rg (real space) rg_real	25.05 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.8850e+07
I(0) uncertainty (real space) i0_real_error	4.0910e+05
Rg (reciprocal space) rg_reciprocal	25.02 Å
I(0) (reciprocal space) i0_reciprocal	28850000.0000
Solution quality estimate total_estimate	0.7631
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.487
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7900000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.826; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Trypsin inhibitor A
Molecular weight formula_weight	24031.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3130

MKSTIFFLFLFCAFTTSYLPSAIADFVLDNEGNPLENGGTYYILSDITAFGGIRAAPTGNERCPLTVVQSRNELDKGIGTIISSPYRIRFIAEGHPLSLKFDSFAVIMLCVGIPTEWSVVEDLPEGPAVKIGENKDAMDGWFRLERVSDDEFNNYKLVFCPQQAEDDKCGDIGISIDHDDGTRRLVVSKNKPLVVQFQKLDKESLAKKNHGLSRSE

来源 Source

来源生物 organism	Glycine max
通用名 common_name	Soybean
NCBI Class编号 ncbi_taxonomy_id	3847
宿主生物 host_organism	Glycine max

Entity 2 Entity 2 non-polymer

Description description	naphthalene-1,5-disulfonic acid
Molecular weight formula_weight	288.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6nttA00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	6nttB00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	41.880 Å
Unit-cell length b length_b	64.680 Å
Unit-cell length c length_c	69.080 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	32.610 Å
R factor r_factor	0.2138
R_work r_work	0.2092
R_free r_free	0.3059

fit	/app/data/saxs_computation/nt/6ntt/6ntt.fit
pddf	/app/data/pr_computation/nt/6ntt/6ntt.pr.out
profile	/app/data/saxs_computation/nt/6ntt/6ntt.dat

X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene

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

Trypsin inhibitor A

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