PDBe 3vxf

Hybrid

X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
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
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
Hirudin-2 Chain: J
Molecule details ›
Chain: J
Length: 17 amino acids
Theoretical weight: 1.78 KDa
Source organism: unidentified
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 48-64; Coverage: 26%)
BIVALIRUDIN Chain: I
Molecule details ›
Chain: I
Length: 3 amino acids
Theoretical weight: 419 Da
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Experimental Method: Neutron Diffraction, X-ray diffraction
X-ray source: PHOTON FACTORY BEAMLINE BL-6A, JRR-3M BEAMLINE 1G-C
Spacegroup: P21212
Unit cell:
a: 80.998Å b: 107.8Å c: 45.888Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.161 0.184
Expression system: Not provided