› 2bvr

X-ray diffraction
1.25Å resolution

Human thrombin complexed with fragment-based small molecules occupying the S1 pocket

Released:
DOI: 10.2210/pdb2bvr/pdb
PDB entry 2bvr coloured by chain, front view.
PDB entry 2bvr coloured by chain, side view.
PDB entry 2bvr coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening
Neumann T, Junker H-D, Keil O, Burkert K, Ottleben H, Gamer J, Sekul R, Deppe H, Feurer A, Tomandl D, Metz G
Lett Drug Des Discov 2 590- (2005)

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-133076 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 252 amino acids
Theoretical weight: 29.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 42%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.38 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 61-71; Coverage: 17%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain

Ligands and Environments

1 bound ligand:
Ligand 4CP 1 x 4CP
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS
Spacegroup: C2
Unit cell:
a: 70.322Å b: 71.702Å c: 72.539Å
α: 90° β: 100.28° γ: 90°
R-values:
R R work R free
0.21 0.21 0.229
Expression systems:
  • Escherichia coli
  • Not provided

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