› 6v5t

X-ray diffraction
2.1Å resolution

Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan

Released:
DOI: 10.2210/pdb6v5t/pdb
PDB entry 6v5t coloured by chain, front view.
PDB entry 6v5t coloured by chain, side view.
PDB entry 6v5t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2.
Ruben EA, Gandhi PS, Chen Z, Koester SK, DeKoster GT, Frieden C, Di Cera E
OpenAccess logo J Biol Chem 295 8227-8235 (2020)
PMID: 32358061

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133054 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thrombin heavy chain Chain: E
Molecule details ›
Chain: E
Length: 290 amino acids
Theoretical weight: 33.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 333-622; Coverage: 49%)
Gene name: F2
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 1 x SO4
1 modified residue:
Ligand FTR 9 x FTR

Experiments and Validation Details

Entry percentile scores
X-ray source: Cu FINE FOCUS
Spacegroup: P21
Unit cell:
a: 44.545Å b: 58.887Å c: 52.455Å
α: 90° β: 98.42° γ: 90°
R-values:
R R work R free
0.18 0.177 0.23
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Small, but powerful and attractive: 19F in biomolecular NMR.
Gronenborn AM. (2022)
1 more

1 mention without citation

19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2.
Ruben et al. (2020)