› 6hsx

X-ray diffraction
1.56Å resolution

Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative

Released:
DOI: 10.2210/pdb6hsx/pdb
PDB entry 6hsx coloured by chain, front view.
PDB entry 6hsx coloured by chain, side view.
PDB entry 6hsx coloured by chain, top view.
Source organisms:
Primary publication:
Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Ngo K, Collins-Kautz C, Gerstenecker S, Wagner B, Heine A, Klebe G
J Med Chem 63 3274-3289 (2020)
PMID: 32011145

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 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
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 62-72; Coverage: 17%)

Ligands and Environments

6 bound ligands:
Ligand DMS 2 x DMS
Ligand GOL 2 x GOL
Ligand NA 2 x NA
Ligand NAG 1 x NAG
Ligand PO4 1 x PO4
Ligand GOZ 1 x GOZ
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 69.997Å b: 71.726Å c: 72.634Å
α: 90° β: 100.353° γ: 90°
R-values:
R R work R free
0.163 0.162 0.184
Expression system: Not provided

Quick links

Citations

1 citations in other articles

Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
Wienen-Schmidt et al. (2021)

1 mention without citation

Machine learning assessment of the binding region as a tool for more efficient computational receptor-ligand docking.
Simončič et al. (2022)