1d0d

CRYSTAL STRUCTURE OF TICK ANTICOAGULANT PROTEIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR

Method: X-RAY DIFFRACTION Dmax: 68.8 Å Quality: GOOD

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

ANTICOAGULANT PROTEIN

OrganismNot specified

UniProt P17726

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 A; UniProt 1–60 Not recorded PANCREATIC TRYPSIN INHIBITOR × 1 (P00974) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;ammonium sulfate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 1.62 Å R-free 0.211

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAP_ORNMO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–60; UniProt 1–60

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 B; UniProt 36–93 Not recorded ANTICOAGULANT PROTEIN × 1 (P17726) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;ammonium sulfate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 1.62 Å R-free 0.211

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 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 1d0d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d0d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d0d
Deposition date deposition_date1999-09-09
Structure title titleCRYSTAL STRUCTURE OF TICK ANTICOAGULANT PROTEIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
Keywords keywordsFACTOR XA INHIBITOR, KUNITZ INHIBITOR, BLOOD CLOTTING INHIBITOR; BLOOD CLOTTING INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.97
Radius of gyration Rg (electron density) rg_electron19.38
Forward intensity I(0) i04416060.00
Molecular weight molecular_weight13792.0 kDa
Excluded volume excluded_volume16564 ų
Envelope volume envelope_volume21940 ų
Hydration-shell volume shell_volume10580 ų
Envelope diameter envelope_diameter69.2
Shell Rg shell_rg23.09
Envelope Rg envelope_rg19.14
Shape Rg shape_rg19.30
Total Rg total_rg20.17
Total atoms total_atoms958
Residues n_residues118
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 dmax68.8
Rg (real space) rg_real20.15
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real4.4160e+06
I(0) uncertainty (real space) i0_real_error6.0310e+04
Rg (reciprocal space) rg_reciprocal20.12
I(0) (reciprocal space) i0_reciprocal4416000.0000
Solution quality estimate total_estimate0.8142
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.5
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha610000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.412; Smooth: 0.930

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d0da_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.2 — Soft tick anticoagulant proteins
Domain ID domain_idd1d0db_
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_id1d0dA00
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_id1d0dB00
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)