› 5hvf

X-ray diffraction
2.85Å resolution

Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-i83)

Released:
DOI: 10.2210/pdb5hvf/pdb
PDB entry 5hvf coloured by chain, front view.
PDB entry 5hvf coloured by chain, side view.
PDB entry 5hvf coloured by chain, top view.
Source organisms:
Primary publication:
Elucidation of the molecular mechanisms of two nanobodies that inhibit thrombin-activatable fibrinolysis inhibitor activation and activated thrombin-activatable fibrinolysis inhibitor activity.
Zhou X, Weeks SD, Ameloot P, Callewaert N, Strelkov SV, Declerck PJ
J Thromb Haemost 14 1629-38 (2016)
PMID: 27279497

Function and Biology Details

Reaction catalysed: 
Release of C-terminal Arg and Lys from a polypeptide.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212687 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Carboxypeptidase B2 Chain: A
Molecule details ›
Chain: A
Length: 401 amino acids
Theoretical weight: 46.08 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q96IY4 (Residues: 23-423; Coverage: 100%)
Gene name: CPB2
Sequence domains:
Structure domains:
VHH-i83 Chain: B
Molecule details ›
Chain: B
Length: 119 amino acids
Theoretical weight: 12.88 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 3 x NAG
Ligand ZN 1 x ZN
Ligand FLC 1 x FLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 51.29Å b: 69.978Å c: 165.337Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.23
Expression systems:
  • Komagataella pastoris
  • Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Hypofibrinolysis in diabetes: a therapeutic target for the reduction of cardiovascular risk.
Kearney et al. (2017)
5 more

1 mention without citation

Thrombin Activatable Fibrinolysis Inhibitor (TAFI): An Updated Narrative Review.
Sillen et al. (2021)