› 8tqs

X-ray diffraction
2.21Å resolution

Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker.

Released:
DOI: 10.2210/pdb8tqs/pdb
PDB entry 8tqs coloured by chain, front view.
PDB entry 8tqs coloured by chain, side view.
PDB entry 8tqs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors.
Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA
OpenAccess logo Nat Commun 15 3977 (2024)
PMID: 38730234

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-513263 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 41 amino acids
Theoretical weight: 4.82 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 320-360; Coverage: 7%)
Gene name: F2
Sequence domains: Thrombin light chain
DNA (30-MER) Chain: D
Molecule details ›
Chain: D
Length: 30 nucleotides
Theoretical weight: 9.42 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand NA 1 x NA
Ligand MES 1 x MES
Ligand 4CC 1 x 4CC
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: P41212
Unit cell:
a: 81.626Å b: 81.626Å c: 190.514Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.245
Expression system: Homo sapiens

Quick links

Citations

1 review citation

Beyond Anticoagulation: A Comprehensive Review of Non-Vitamin K Oral Anticoagulants (NOACs) in Inflammation and Protease-Activated Receptor Signaling.
Jannati et al. (2024)
1 other article