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1utk

Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements

Method: X-RAY DIFFRACTION Dmax: 52.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRYPSIN I

OrganismNot specified

UniProt P35031

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 1–242 Not recorded SO4 SULFATE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.00 Resolution 1.53 Å R-free 0.229

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 1UTK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BZX THE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR Deposited 1998-11-05 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 E 21–242（222 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 0.8-1.2 M POTASSIUM SODIUM TARTRATE
Resolution 2.10 Å R-free 0.238
1HJ8 1.00 AA Trypsin from Atlantic Salmon Deposited 2001-01-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–242（222 aa） Fragment：RESIDUES 21-242
Not recorded BEN BENZAMIDINE × 2 SO4 SULFATE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；pH 5.80
Resolution 1.00 Å R-free 0.149
1UTJ Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements Deposited 2003-12-09 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–242（242 aa）
Not recorded ABN BENZYLAMINE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.00
Resolution 1.83 Å R-free 0.207
1UTL Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements Deposited 2003-12-09 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain M 1–242（242 aa）
Not recorded PRA 3-PHENYLPROPYLAMINE × 1 CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.00
Resolution 1.70 Å R-free 0.216
1UTM Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements Deposited 2003-12-09 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–242（242 aa）
Not recorded PEA 2-PHENYLETHYLAMINE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.00
Resolution 1.50 Å R-free 0.217
2STA ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA MAXIMA TRYPSIN INHIBITOR I) Deposited 1998-12-10 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 E 21–242（222 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.80 Å R-free 0.233
2STB ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA PEPO TRYPSIN INHIBITOR II) Deposited 1998-12-11 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 E 21–242（222 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.80 Å R-free 0.201
2TBS COLD-ADAPTION OF ENZYMES: STRUCTURAL COMPARISON BETWEEN SALMON AND BOVINE TRYPSINS Deposited 1994-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–242（222 aa）
Not recorded CA CALCIUM ION × 1 BEN BENZAMIDINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY1_SALSA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–242； UniProt 1–242

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1utk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1utk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1utk
Deposition date deposition_date2003-12-09
Structure title titleTrypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements
Keywords keywordsHYDROLASE, TRYPSIN, INHIBITOR SPECIFICITY, ELECTROSTATIC INTERACTIONS, COLD-ADAPTATION, MOLECULAR DYNAMICS, BINDING FREE ENERGY; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.19 Å
Radius of gyration Rg (electron density) rg_electron16.18 Å
Forward intensity I(0) i011563400.00
Molecular weight molecular_weight24073.0 kDa
Excluded volume excluded_volume29493 ų
Envelope volume envelope_volume32378 ų
Hydration-shell volume shell_volume16538 ų
Envelope diameter envelope_diameter53.2 Å
Shell Rg shell_rg22.48 Å
Envelope Rg envelope_rg16.42 Å
Shape Rg shape_rg16.18 Å
Total Rg total_rg17.10 Å
Total atoms total_atoms1677
Residues n_residues219
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax52.8 Å
Rg (real space) rg_real17.07 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.1560e+07
I(0) uncertainty (real space) i0_real_error1.2680e+05
Rg (reciprocal space) rg_reciprocal17.08 Å
I(0) (reciprocal space) i0_reciprocal11560000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.2 Å
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2910000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1utka_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

Domain ID domain_id1utkA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1utkA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
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8. Citations (1)

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9. Files and Curves (10)