5xx4

A BPTI-[5,55] variant with C14GA38K mutations

Method: X-RAY DIFFRACTION Dmax: 50.1 Å Quality: EXCELLENT

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

Pancreatic trypsin inhibitor

Bos taurus

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 36–93 Mutation:A14G, A38K SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293.15 K;30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCL, pH8.5 Resolution 1.67 Å R-free 0.220
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 36–93 Mutation:A14G, A38K SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293.15 K;30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCL, pH8.5 Resolution 1.67 Å R-free 0.220

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

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 5xx4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xx4
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5xx4
Deposition date deposition_date2017-07-01
Structure title titleA BPTI-[5,55] variant with C14GA38K mutations
Keywords keywordsHYDROLASE INHIBITOR, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.54
Radius of gyration Rg (electron density) rg_electron15.01
Forward intensity I(0) i03687820.00
Molecular weight molecular_weight12940.0 kDa
Excluded volume excluded_volume15879 ų
Envelope volume envelope_volume19044 ų
Hydration-shell volume shell_volume11195 ų
Envelope diameter envelope_diameter49.3
Shell Rg shell_rg19.96
Envelope Rg envelope_rg15.01
Shape Rg shape_rg14.99
Total Rg total_rg16.02
Total atoms total_atoms907
Residues n_residues116
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 dmax50.1
Rg (real space) rg_real15.48
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real3.6880e+06
I(0) uncertainty (real space) i0_real_error4.2420e+04
Rg (reciprocal space) rg_reciprocal15.48
I(0) (reciprocal space) i0_reciprocal3688000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9
Skewness Skewness skewness0.162
Kurtosis Kurtosis kurtosis-0.516
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1133000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5xx4a_
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_idd5xx4b_
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 (2 domains)

Domain ID domain_id5xx4A00
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_id5xx4B00
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)