SAXSdb — 1trn

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

TRYPSIN

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–247 Chain B； UniProt 24–247	Non-standard monomer：Yes (specific site not provided by mmCIF)	ISP PHOSPHORYLISOPROPANE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å

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 1TRN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FXY COAGULATION FACTOR XA-TRYPSIN CHIMERA INHIBITED WITH D-PHE-PRO-ARG-CHLOROMETHYLKETONE Deposited 1998-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 127–247（121 aa）	Mutation：Q20Y, E21N, C27V	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6K, 100 MM HEPES, PH 7.8.	Resolution 2.15 Å R-free 0.245
2RA3 Human cationic trypsin complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2007-09-14	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 24–247（224 aa） Chain B 24–247（224 aa）	Mutation：R117H, S195A Mutation：R117H, S195A	CA CALCIUM ION × 2 SO4 SULFATE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1M Tris hydrochloride pH 8.5, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.46 Å R-free 0.178
2RA3 Human cationic trypsin complexed with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2007-09-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 24–247（224 aa） Chain B 24–247（224 aa）	Mutation：R117H, S195A Mutation：R117H, S195A	CA CALCIUM ION × 4 SO4 SULFATE ION × 48	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1M Tris hydrochloride pH 8.5, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.46 Å R-free 0.178
4WWY human cationic trypsin G193R mutant in complex with bovine pancreatic trypsin inhibitor Deposited 2014-11-12	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 24–247（224 aa） Fragment：UNP residues 24-247	Mutation：G193R, R117H	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M ammonium sulfate, 0.1M sodium cacodylate trihydrate, 30% PEG-8000	Resolution 1.70 Å R-free 0.207
4WWY human cationic trypsin G193R mutant in complex with bovine pancreatic trypsin inhibitor Deposited 2014-11-12	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 24–247（224 aa） Fragment：UNP residues 24-247	Mutation：G193R, R117H	SO4 SULFATE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M ammonium sulfate, 0.1M sodium cacodylate trihydrate, 30% PEG-8000	Resolution 1.70 Å R-free 0.207
4WXV Human cationic trypsin K97D mutant in complex with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2014-11-14	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 24–247（224 aa） Fragment：UNP residues 24-247	Mutation：K97D, R117H, S195A	CA CALCIUM ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M ammonium sulfate, 0.1 sodium cacodylate trihydrate, 30% PEG-8000	Resolution 2.10 Å R-free 0.281
4WXV Human cationic trypsin K97D mutant in complex with bovine pancreatic trypsin inhibitor (BPTI) Deposited 2014-11-14	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 24–247（224 aa） Fragment：UNP residues 24-247	Mutation：K97D, R117H, S195A	CA CALCIUM ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M ammonium sulfate, 0.1 sodium cacodylate trihydrate, 30% PEG-8000	Resolution 2.10 Å R-free 0.281
7QE8 Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 (SPINK1) Deposited 2021-12-01	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 24–247（224 aa）	Mutation：S200A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；1 ul protein solution (20 mg/mL in 20 mM HEPES, pH 7.4, 150 mM NaCl) + 1 ul well solution (15% PEG 4000, 0.3 M AS), cryo 15% PEG 4000, 0.3 M AS, 8% PEG 400	Resolution 2.90 Å R-free 0.243
7QE8 Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 (SPINK1) Deposited 2021-12-01	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 24–247（224 aa）	Mutation：S200A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；1 ul protein solution (20 mg/mL in 20 mM HEPES, pH 7.4, 150 mM NaCl) + 1 ul well solution (15% PEG 4000, 0.3 M AS), cryo 15% PEG 4000, 0.3 M AS, 8% PEG 400	Resolution 2.90 Å R-free 0.243
7QE9 Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 N34S (SPINK1 N34S) Deposited 2021-12-01	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 24–247（224 aa）	Mutation：S200A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；1 uL protein solution (20 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl) + 1 uL well solution (15% PEG 4000, 0.3 M AS), cryo: 15% PEG 4000, 0.3 M AS, 8% PEG 400	Resolution 2.10 Å R-free 0.234
7QE9 Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 N34S (SPINK1 N34S) Deposited 2021-12-01	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 24–247（224 aa）	Mutation：S200A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；1 uL protein solution (20 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl) + 1 uL well solution (15% PEG 4000, 0.3 M AS), cryo: 15% PEG 4000, 0.3 M AS, 8% PEG 400	Resolution 2.10 Å R-free 0.234
8H3S Substrate-bound EP, polyA model Deposited 2022-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 16–247（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
8ZI4 Cryo-EM structure of wtEP-trypsinogen Deposited 2024-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 16–247（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8ZIV wtEP-trypsinogen in Tryp-1 Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 16–247（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8ZIY trypsinogen-EP-E574A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 16–247（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
8ZJ4 trypsinogen-EP-N619A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 16–247（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRY1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 24–247 Author chain B； PDBConstruct 1–224； UniProt 24–247

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	1trn
Deposition date deposition_date	1995-03-16
Structure title title	CRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION OF TYROSINE 151
Keywords keywords	HUMAN TRYPSIN, DFP INHIBITED, HYDROLASE (SERINE PROTEINASE); HYDROLASE (SERINE PROTEINASE)
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	26.52 Å
Radius of gyration Rg (electron density) rg_electron	26.11 Å
Forward intensity I(0) i0	42531800.00
Molecular weight molecular_weight	48641.0 kDa
Excluded volume excluded_volume	60075 Å³
Envelope volume envelope_volume	72405 Å³
Hydration-shell volume shell_volume	23977 Å³
Envelope diameter envelope_diameter	88.6 Å
Shell Rg shell_rg	32.31 Å
Envelope Rg envelope_rg	26.07 Å
Shape Rg shape_rg	26.13 Å
Total Rg total_rg	26.73 Å
Total atoms total_atoms	3404
Residues n_residues	440
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	85.6 Å
Rg (real space) rg_real	26.67 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	4.2530e+07
I(0) uncertainty (real space) i0_real_error	6.4980e+05
Rg (reciprocal space) rg_reciprocal	26.63 Å
I(0) (reciprocal space) i0_reciprocal	42530000.0000
Solution quality estimate total_estimate	0.8658
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.571
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11000000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TRYPSIN
Molecular weight formula_weight	24217.2 kDa
EC 编号 ec_number	3.4.21.4
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	3705

IVGGYNCEENSVPYQVSLNSGYHFCGGSLINEQWVVSAGHCYKSRIQVRLGEHNIEVLEGNEQFINAAKIIRHPQYDRKTLNNDIMLIKLSSRAVINARVSTISLPTAPPATGTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDSCQGDSGGPVVCNGQLQGVVSWGDGCAQKNKPGVYTKVYNYVKWIKNTIAANS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	PHOSPHORYLISOPROPANE
Molecular weight formula_weight	140.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	301

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1trna_
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	d1trnb_
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 (4 domains)

Domain ID domain_id	1trnA01
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	1trnA02
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	1trnB01
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	1trnB02
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	107.120 Å
Unit-cell length b length_b	107.120 Å
Unit-cell length c length_c	39.920 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	8

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	—

fit	/app/data/saxs_computation/tr/1trn/1trn.fit
pddf	/app/data/pr_computation/tr/1trn/1trn.pr.out
profile	/app/data/saxs_computation/tr/1trn/1trn.dat

CRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION OF TYROSINE 151

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

TRYPSIN

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