2hex

DECAMERS OBSERVED IN THE CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR

Method: X-RAY DIFFRACTION Dmax: 68.7 Å Quality: EXCELLENT

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

PROTEIN (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 homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 36–93 Chain B; UniProt 36–93 Chain C; UniProt 36–93 Chain D; UniProt 36–93 Chain E; UniProt 36–93 Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;USING SOLUTION #32 IN CRYSTAL SCREEN I (HAMPTON RESEARCH), pH 6.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.288
2 Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 36–93 Chain B; UniProt 36–93 Chain C; UniProt 36–93 Chain D; UniProt 36–93 Chain E; UniProt 36–93 Not recorded SO4 SULFATE ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;USING SOLUTION #32 IN CRYSTAL SCREEN I (HAMPTON RESEARCH), pH 6.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.288

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 264 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–58; UniProt 36–93 Author chain B; PDBConstruct 1–58; UniProt 36–93 Author chain C; PDBConstruct 1–58; UniProt 36–93 Author chain D; PDBConstruct 1–58; UniProt 36–93 Author chain E; 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 2hex

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hex
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hex
Deposition date deposition_date1998-08-01
Structure title titleDECAMERS OBSERVED IN THE CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR
Keywords keywordsBOVINE PANCREATIC TRYPSIN INHIBITOR, PENTAMERIC MOLECULE, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.16
Radius of gyration Rg (electron density) rg_electron21.21
Forward intensity I(0) i021613700.00
Molecular weight molecular_weight32718.0 kDa
Excluded volume excluded_volume39836 ų
Envelope volume envelope_volume50689 ų
Hydration-shell volume shell_volume20321 ų
Envelope diameter envelope_diameter68.3
Shell Rg shell_rg27.14
Envelope Rg envelope_rg20.98
Shape Rg shape_rg21.19
Total Rg total_rg22.03
Total atoms total_atoms2264
Residues n_residues281
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 dmax68.7
Rg (real space) rg_real22.03
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real2.1610e+07
I(0) uncertainty (real space) i0_real_error2.4230e+05
Rg (reciprocal space) rg_reciprocal22.06
I(0) (reciprocal space) i0_reciprocal21610000.0000
Solution quality estimate total_estimate0.9111
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.536
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1316000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2hexa_
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
Domain ID domain_idd2hexb_
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
Domain ID domain_idd2hexc_
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
Domain ID domain_idd2hexd_
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
Domain ID domain_idd2hexe_
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 (5 domains)

Domain ID domain_id2hexA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id2hexB00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id2hexC00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id2hexD00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id2hexE00
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)