3pm3

Bovine trypsin variant X(tripleIle227) in complex with small molecule inhibitor

Method: X-RAY DIFFRACTION Dmax: 55.0 Å Quality: GOOD

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

Cationic trypsin

Bos taurus

UniProt P00760

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 24–246 Fragment:UNP residues 24-246 Mutation:N102E, L104Y, Y175S, P176S, G177F, Q178Y, S195A, V228I CA CALCIUM ION × 1 TFN N-(benzylsulfonyl)-O-tert-butyl-D-seryl-N-(4-carbamimidoylbenzyl)glycinamide × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;30% PEG 8000, 0.1M IMIDAZOLE, 0.2M AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.53 Å R-free 0.181

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.

608 other PDB entries and 770 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–223; UniProt 24–246

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 3pm3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3pm3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3pm3
Deposition date deposition_date2010-11-16
Structure title titleBovine trypsin variant X(tripleIle227) in complex with small molecule inhibitor
Keywords keywordsTrypsin-like serine protease, HYDROLASE, PROTEIN BINDING, NONE, DUODENUM, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.46
Radius of gyration Rg (electron density) rg_electron16.21
Forward intensity I(0) i011634600.00
Molecular weight molecular_weight24379.0 kDa
Excluded volume excluded_volume30042 ų
Envelope volume envelope_volume33223 ų
Hydration-shell volume shell_volume16844 ų
Envelope diameter envelope_diameter54.9
Shell Rg shell_rg22.72
Envelope Rg envelope_rg16.52
Shape Rg shape_rg16.17
Total Rg total_rg17.31
Total atoms total_atoms1696
Residues n_residues220
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax55.0
Rg (real space) rg_real17.33
Rg uncertainty (real space) rg_real_error0.27
I(0) (real space) i0_real1.1630e+07
I(0) uncertainty (real space) i0_real_error1.3660e+05
Rg (reciprocal space) rg_reciprocal17.35
I(0) (reciprocal space) i0_reciprocal11630000.0000
Solution quality estimate total_estimate0.8908
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.7
Skewness Skewness skewness0.144
Kurtosis Kurtosis kurtosis-0.422
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3233000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3pm3a_
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_id3pm3A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3pm3A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases

8. Citations (1)

9. Files and Curves (10)