PDBe 2zhw

X-ray diffraction
2.02Å resolution

Exploring thrombin S3 pocket

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

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 12 amino acids
Theoretical weight: 1.53 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 60-71; Coverage: 19%)
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: RIGAKU RUH3R
Spacegroup: C2
Unit cell:
a: 68.9Å b: 71.5Å c: 71.3Å
α: 90° β: 99.1° γ: 90°
R-values:
R R work R free
0.206 0.188 0.292
Expression system: Not provided