3ldj

Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding

Method: X-RAY DIFFRACTION Dmax: 62.3 Å Quality: GOOD

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

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 36–93 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;20-25% PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.70 Å R-free 0.234
2 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 36–93 Not recorded 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;20-25% PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.70 Å R-free 0.234
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 36–93 Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;20-25% PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.70 Å R-free 0.234

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 263 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

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 3ldj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3ldj
Deposition date deposition_date2010-01-13
Structure title titleCrystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding
Keywords keywordsaprotinin, sucrose octasulfate, Disulfide bond, Protease inhibitor, Secreted, Serine protease inhibitor, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.17
Radius of gyration Rg (electron density) rg_electron17.35
Forward intensity I(0) i09038660.00
Molecular weight molecular_weight20178.0 kDa
Excluded volume excluded_volume24456 ų
Envelope volume envelope_volume29504 ų
Hydration-shell volume shell_volume14835 ų
Envelope diameter envelope_diameter61.5
Shell Rg shell_rg22.49
Envelope Rg envelope_rg17.60
Shape Rg shape_rg17.33
Total Rg total_rg18.25
Total atoms total_atoms1391
Residues n_residues168
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 dmax62.3
Rg (real space) rg_real18.12
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real9.0390e+06
I(0) uncertainty (real space) i0_real_error1.2270e+05
Rg (reciprocal space) rg_reciprocal18.12
I(0) (reciprocal space) i0_reciprocal9039000.0000
Solution quality estimate total_estimate0.8002
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.6
Skewness Skewness skewness0.248
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.4400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1335000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3ldja_
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_idd3ldjb_
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_idd3ldjc_
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_id3ldjA00
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_id3ldjB00
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_id3ldjC00
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)