SAXSdb — 6har

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

PRSS3 protein

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 28–251	Not recorded	Amyloid-beta A4 protein × 1 （H7C0V9） EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES pH 6.8, 16% PEG 20, 000	Resolution 1.50 Å R-free 0.193

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 6HAR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3L3T Human mesotrypsin complexed with amyloid precursor protein inhibitor variant (APPIR15K) Deposited 2009-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–251（224 aa） Fragment：UNP residues 28-251	Mutation：S195A	FMT FORMIC ACID × 7 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4M sodium formate solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.38 Å R-free 0.237
3L3T Human mesotrypsin complexed with amyloid precursor protein inhibitor variant (APPIR15K) Deposited 2009-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–251（224 aa） Fragment：UNP residues 28-251	Mutation：S195A	FMT FORMIC ACID × 5 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4M sodium formate solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.38 Å R-free 0.237
3L3T Human mesotrypsin complexed with amyloid precursor protein inhibitor variant (APPIR15K) Deposited 2009-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–251（224 aa） Fragment：UNP residues 28-251	Mutation：S195A	FMT FORMIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4M sodium formate solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.38 Å R-free 0.237
3L3T Human mesotrypsin complexed with amyloid precursor protein inhibitor variant (APPIR15K) Deposited 2009-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–251（224 aa） Fragment：UNP residues 28-251	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4M sodium formate solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.38 Å R-free 0.237
3P92 Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17G) Deposited 2010-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–251（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25% PEG4000, 0.2M Na acetate and 100mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.159
3P92 Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17G) Deposited 2010-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–251（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25% PEG4000, 0.2M Na acetate and 100mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.159
3P95 Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17D) Deposited 2010-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–251（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25% PEG4000, 0.2M Na acetate and 100mM Tris pH 8.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.30 Å R-free 0.132
4DG4 Human mesotrypsin-S39Y complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2012-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–251（224 aa） Fragment：unp residues 28-251	Mutation：S195A, S39Y	SO4 SULFATE ION × 5 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.211
4DG4 Human mesotrypsin-S39Y complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2012-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–251（224 aa） Fragment：unp residues 28-251	Mutation：S195A, S39Y	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.211
4DG4 Human mesotrypsin-S39Y complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2012-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–251（224 aa） Fragment：unp residues 28-251	Mutation：S195A, S39Y	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.211
4DG4 Human mesotrypsin-S39Y complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2012-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 28–251（224 aa） Fragment：unp residues 28-251	Mutation：S195A, S39Y	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.211
5JBT Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2) Deposited 2016-04-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–251（224 aa）	Mutation：S195A	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Ammonium Sulfate 0.1 M Sodium Cacodylate Trihydrate 30% PEG 8000	Resolution 1.40 Å R-free 0.199
6GFI Structure of Human Mesotrypsin in complex with APPI variant T11V/M17R/I18F/F34V Deposited 2018-04-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–251（224 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium Chloride, 0.1M Bis-Tris pH 6.8 , 1.42M Ammonium Sulfate	Resolution 2.30 Å R-free 0.301
6GFI Structure of Human Mesotrypsin in complex with APPI variant T11V/M17R/I18F/F34V Deposited 2018-04-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–251（224 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium Chloride, 0.1M Bis-Tris pH 6.8 , 1.42M Ammonium Sulfate	Resolution 2.30 Å R-free 0.301

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8N2U3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 28–251

Amyloid-beta A4 protein

Homo sapiens

UniProt H7C0V9

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 E； UniProt 216–268	Not recorded	PRSS3 protein × 1 （Q8N2U3） EDO 1,2-ETHANEDIOL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES pH 6.8, 16% PEG 20, 000	Resolution 1.50 Å R-free 0.193

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	H7C0V9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 18–70； UniProt 216–268

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	6har
Deposition date deposition_date	2018-08-08
Structure title title	Crystal structure of Mesotrypsin in complex with APPI-M17C/I18F/F34C
Keywords keywords	PRSS3, Mesotrypsin, Serine protease, Kunitz type inhibitor, APPI, protein fibril; PROTEIN FIBRIL
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	19.00 Å
Radius of gyration Rg (electron density) rg_electron	18.10 Å
Forward intensity I(0) i0	17247900.00
Molecular weight molecular_weight	30260.0 kDa
Excluded volume excluded_volume	37318 Å³
Envelope volume envelope_volume	42244 Å³
Hydration-shell volume shell_volume	19310 Å³
Envelope diameter envelope_diameter	61.2 Å
Shell Rg shell_rg	24.59 Å
Envelope Rg envelope_rg	18.53 Å
Shape Rg shape_rg	18.09 Å
Total Rg total_rg	19.02 Å
Total atoms total_atoms	2116
Residues n_residues	275
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	60.7 Å
Rg (real space) rg_real	18.91 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.7250e+07
I(0) uncertainty (real space) i0_real_error	2.0110e+05
Rg (reciprocal space) rg_reciprocal	18.93 Å
I(0) (reciprocal space) i0_reciprocal	17250000.0000
Solution quality estimate total_estimate	0.8964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.219
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	4932000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PRSS3 protein
Molecular weight formula_weight	24257.5 kDa
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	2437

IVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTAPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVGFLEGGKDSCQRDAGGPVVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTIAANS

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	Amyloid-beta A4 protein
Molecular weight formula_weight	9070.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

YVDYKDDDDKEFEVCSEQAETGPCRACFSRWYFDVTEGKCAPFCYGGCGGNRNNFDTEEYCMAVCGSAIPRHHHHHHAAA

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	Komagataella phaffii GS115

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6hara_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6hare1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

Domain ID domain_id	d6hare2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6harA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6harE00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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8. Citations (1)

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Unit-cell length a length_a	34.091 Å
Unit-cell length b length_b	82.781 Å
Unit-cell length c length_c	46.559 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.497 Å
Low-resolution limit resolution_low	46.466 Å
R factor r_factor	0.1703
R_work r_work	0.1690
R_free r_free	0.1928

fit	/app/data/saxs_computation/ha/6har/6har.fit
pddf	/app/data/pr_computation/ha/6har/6har.pr.out
profile	/app/data/saxs_computation/ha/6har/6har.dat

Crystal structure of Mesotrypsin in complex with APPI-M17C/I18F/F34C

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

PRSS3 protein

State in the Current Structure

Other States of the Same Protein in the Database

Amyloid-beta A4 protein

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)