PDBe 2zf0

X-ray diffraction
2.2Å resolution

Exploring Thrombin S1 Pocket

Released:
Source organisms:
Entry authors: Baum B, Heine A, Klebe G

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:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Hirudin variant-1 Chain: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.42 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P01050 (Residues: 54-64; Coverage: 17%)
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: C2
Unit cell:
a: 70Å b: 70.3Å c: 72.5Å
α: 90° β: 101.1° γ: 90°
R-values:
R R work R free
0.174 0.17 0.267
Expression system: Not provided