› 4ufg

X-ray diffraction
1.65Å resolution

Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-((1S)-2-((4- carbamimidoylphenyl)methylamino)-1-methyl-2-oxo-ethyl)-N-methyl-3- phenyl-propanamide ethane

Released:
DOI: 10.2210/pdb4ufg/pdb
PDB entry 4ufg coloured by chain, front view.
PDB entry 4ufg coloured by chain, side view.
PDB entry 4ufg coloured by chain, top view.
Source organisms:
Primary publication:
Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
Rühmann EH, Rupp M, Betz M, Heine A, Klebe G
ChemMedChem 11 309-19 (2016)
PMID: 26762840

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: 258 amino acids
Theoretical weight: 29.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-621; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 61-72; Coverage: 19%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 29 amino acids
Theoretical weight: 3.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 333-361; Coverage: 5%)
Gene name: F2
Sequence domains: Thrombin light chain

Ligands and Environments

4 bound ligands:
Ligand NA 2 x NA
Ligand D6J 1 x D6J
Ligand PO4 1 x PO4
Ligand NAG 1 x NAG
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: C2
Unit cell:
a: 70.092Å b: 71.249Å c: 72.587Å
α: 90° β: 100.53° γ: 90°
R-values:
R R work R free
0.163 0.162 0.186
Expression system: Not provided

Quick links

Citations

2 review citations

Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization.
Minetti et al. (2022)
1 more

1 mention without citation

Plumage redness signals mitochondrial function in the house finch.
Hill et al. (2019)