1fy8

CRYSTAL STRUCTURE OF THE DELTAILE16VAL17 RAT ANIONIC TRYPSINOGEN-BPTI COMPLEX

Method: X-RAY DIFFRACTION Dmax: 61.6 Å Quality: EXCELLENT

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

TRYPSIN II, ANIONIC

Rattus rattus

UniProt P00763

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 14–246 Not recorded PANCREATIC TRYPSIN INHIBITOR × 1 (P00974) CA CALCIUM ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;PEG 4000, lithium sulfate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.214

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.

35 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY2_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–231; UniProt 14–246

PANCREATIC TRYPSIN INHIBITOR

OrganismNot specified

UniProt P00974

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 I; UniProt 36–93 Not recorded TRYPSIN II, ANIONIC × 1 (P00763) CA CALCIUM ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;PEG 4000, lithium sulfate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.214

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.

123 other PDB entries and 265 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–58; UniProt 36–93

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 1fy8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1fy8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1fy8
Deposition date deposition_date2000-09-28
Structure title titleCRYSTAL STRUCTURE OF THE DELTAILE16VAL17 RAT ANIONIC TRYPSINOGEN-BPTI COMPLEX
Keywords keywordsprotein-protein complex, protease-inhibitor complex, beta barrel, 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_guinier19.39
Radius of gyration Rg (electron density) rg_electron18.46
Forward intensity I(0) i017012200.00
Molecular weight molecular_weight29742.0 kDa
Excluded volume excluded_volume36564 ų
Envelope volume envelope_volume41714 ų
Hydration-shell volume shell_volume19030 ų
Envelope diameter envelope_diameter61.6
Shell Rg shell_rg24.67
Envelope Rg envelope_rg18.75
Shape Rg shape_rg18.45
Total Rg total_rg19.34
Total atoms total_atoms2073
Residues n_residues271
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 dmax61.6
Rg (real space) rg_real19.31
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real1.7010e+07
I(0) uncertainty (real space) i0_real_error2.3360e+05
Rg (reciprocal space) rg_reciprocal19.32
I(0) (reciprocal space) i0_reciprocal17010000.0000
Solution quality estimate total_estimate0.9003
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.376
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5369000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1fy8e_
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
Domain ID domain_idd1fy8i_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

CATH v4.4 (3 domains)

Domain ID domain_id1fy8E01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1fy8E02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1fy8I00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain

8. Citations (1)

9. Files and Curves (10)