› 2ody

X-ray diffraction
2.35Å resolution

Thrombin-bound boophilin displays a functional and accessible reactive-site loop

Released:
DOI: 10.2210/pdb2ody/pdb
PDB entry 2ody coloured by chain, front view.
PDB entry 2ody coloured by chain, side view.
PDB entry 2ody coloured by chain, top view.
Source organisms:
Primary publication:
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
Macedo-Ribeiro S, Almeida C, Calisto BM, Friedrich T, Mentele R, Stürzebecher J, Fuentes-Prior P, Pereira PJ
PLoS One 3 e1624 (2008)
PMID: 18286181

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133175 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 49 amino acids
Theoretical weight: 5.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 318-366; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Structure domains: Thrombin light chain domain
Thrombin heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 259 amino acids
Theoretical weight: 29.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 367-625; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Boophilin-H2 Chains: E, F
Molecule details ›
Chains: E, F
Length: 127 amino acids
Theoretical weight: 14 KDa
Source organism: Rhipicephalus microplus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WPI2 (Residues: 16-142; Coverage: 100%)
Sequence domains: Kunitz/Bovine pancreatic trypsin inhibitor domain
Structure domains: Pancreatic trypsin inhibitor Kunitz domain

Ligands and Environments

3 bound ligands:
Ligand PO4 4 x PO4
Ligand NA 2 x NA
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P212121
Unit cell:
a: 92.5Å b: 104.2Å c: 129.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.23
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Tick salivary compounds: their role in modulation of host defences and pathogen transmission.
Kazimírová et al. (2013)
11 more

8 mentions without citation

Miniproteins as phage display-scaffolds for clinical applications.
Zoller et al. (2011)
7 more