SAXSdb — 5tp0

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

Trypsin-3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 81–304	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 4 BRN BERENIL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES 2 M Ammonium Sulfate 2 % PEG-400	Resolution 1.25 Å R-free 0.137

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 5TP0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H4W Structure of human trypsin IV (brain trypsin) Deposited 2001-05-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–304（224 aa）	Not recorded	BEN BENZAMIDINE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；HANGING DROP VAPOUR DIFFUSION 3.3 MG/ML PROTEIN, 2% PEG 4000, 0.05M TRIS PH7.7, 2.5MM CACL2, 2.5 MG/ML BENZAMIDINE/HCL, 25 C, pH 7.70	Resolution 1.70 Å R-free 0.203
2R9P Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor(BPTI) Deposited 2007-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 81–304（224 aa） Chain C 81–304（224 aa）	Mutation：S195A Mutation：S195A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.40 Å R-free 0.224
2R9P Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor(BPTI) Deposited 2007-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 81–304（224 aa） Chain D 81–304（224 aa）	Mutation：S195A Mutation：S195A	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.40 Å R-free 0.224
3L33 Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) Deposited 2009-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 81–304（224 aa） Fragment：Trypsin-3	Mutation：S195A	FMT FORMIC ACID × 9 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 298.0K	Resolution 2.48 Å R-free 0.256
3L33 Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) Deposited 2009-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 81–304（224 aa） Fragment：Trypsin-3	Mutation：S195A	FMT FORMIC ACID × 6 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 298.0K	Resolution 2.48 Å R-free 0.256
3L33 Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) Deposited 2009-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 81–304（224 aa） Fragment：Trypsin-3	Mutation：S195A	FMT FORMIC ACID × 3 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 298.0K	Resolution 2.48 Å R-free 0.256
3L33 Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) Deposited 2009-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 81–304（224 aa） Fragment：Trypsin-3	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 298.0K	Resolution 2.48 Å R-free 0.256
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 81–304（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 81–304（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 81–304（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 81–304（224 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U32 Human mesotrypsin complexed with HAI-2 Kunitz domain 1 Deposited 2014-07-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 81–304（224 aa）	Mutation：S195A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；0.1 M trisodium citrate pH 5.5, 10% (w/v) PEG 4000, and 0.2 M sodium acetate	Resolution 1.65 Å R-free 0.213
5C67 Human Mesotrypsin in complex with amyloid precursor protein inhibitor variant APPI-M17G/I18F/F34V Deposited 2015-06-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 81–304（224 aa）	Mutation：S257A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M ammonium sulfate, 0.1 M Tris pH 7.5, and 20% PEG-1000	Resolution 1.83 Å R-free 0.267
5C67 Human Mesotrypsin in complex with amyloid precursor protein inhibitor variant APPI-M17G/I18F/F34V Deposited 2015-06-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 81–304（224 aa）	Mutation：S257A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M ammonium sulfate, 0.1 M Tris pH 7.5, and 20% PEG-1000	Resolution 1.83 Å R-free 0.267
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 81–304（224 aa）	Mutation：S257A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 81–304（224 aa）	Mutation：S257A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 81–304（224 aa）	Mutation：S257A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 81–304（224 aa）	Mutation：S257A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
9BOS Human mesotrypsin (PRSS3) unliganded and in an active (E) conformation Deposited 2024-05-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–304（224 aa）	Mutation：S195A	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 2F2 dimethyl ether × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES pH 6.5, 15% PEG 20000	Resolution 1.70 Å R-free 0.262
9BOT Human mesotrypsin (PRSS3) unliganded and in autoinhibited (E*) conformation Deposited 2024-05-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–304（224 aa）	Mutation：S195A	SO4 SULFATE ION × 2 CA CALCIUM ION × 1 ACT ACETATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.8M ammonium sulfate, 0.1M Bis-Tris pH 5.5	Resolution 1.60 Å R-free 0.195

9 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRY3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 81–304

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	5tp0
Deposition date deposition_date	2016-10-19
Structure title title	Human mesotrypsin in complex with diminazene
Keywords keywords	trypsin, serine-type endopeptidase, serine hydrolase, complex with small molecule drug, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
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	17.30 Å
Radius of gyration Rg (electron density) rg_electron	16.22 Å
Forward intensity I(0) i0	11916700.00
Molecular weight molecular_weight	24790.0 kDa
Excluded volume excluded_volume	30535 Å³
Envelope volume envelope_volume	33681 Å³
Hydration-shell volume shell_volume	17007 Å³
Envelope diameter envelope_diameter	55.0 Å
Shell Rg shell_rg	22.68 Å
Envelope Rg envelope_rg	16.51 Å
Shape Rg shape_rg	16.21 Å
Total Rg total_rg	17.20 Å
Total atoms total_atoms	1732
Residues n_residues	221
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	53.4 Å
Rg (real space) rg_real	17.17 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.1920e+07
I(0) uncertainty (real space) i0_real_error	1.2040e+05
Rg (reciprocal space) rg_reciprocal	17.19 Å
I(0) (reciprocal space) i0_reciprocal	11920000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.103
Kurtosis Kurtosis kurtosis	-0.480
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3185000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.992

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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	Trypsin-3
Molecular weight formula_weight	24273.5 kDa
EC 编号 ec_number	3.4.21.4
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	2028

IVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTAPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVGFLEGGKDSCQRDSGGPVVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTIAANS

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	BERENIL
Molecular weight formula_weight	281.3 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	224

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5tp0a_
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

CATH v4.4 (2 domains)

Domain ID domain_id	5tp0A01
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	5tp0A02
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

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8. Citations (1)

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Unit-cell length a length_a	40.916 Å
Unit-cell length b length_b	64.443 Å
Unit-cell length c length_c	80.675 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	1.250 Å
Low-resolution limit resolution_low	32.240 Å
R factor r_factor	0.1188
R_work r_work	0.1178
R_free r_free	0.1372

fit	/app/data/saxs_computation/tp/5tp0/5tp0.fit
pddf	/app/data/pr_computation/tp/5tp0/5tp0.pr.out
profile	/app/data/saxs_computation/tp/5tp0/5tp0.dat

Human mesotrypsin in complex with diminazene

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

Trypsin-3

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