› 7zkn

X-ray diffraction
3.03Å resolution

X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form gamma

Released:
DOI: 10.2210/pdb7zkn/pdb
PDB entry 7zkn coloured by chain, front view.
PDB entry 7zkn coloured by chain, side view.
PDB entry 7zkn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers.
Troisi R, Riccardi C, Pérez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F
OpenAccess logo Mol Ther Nucleic Acids 30 585-594 (2022)
PMID: 36457701

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270282 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 distinct):
Thrombin light chain Chains: A, C
Molecule details ›
Chains: A, C
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 Chains: B, D
Molecule details ›
Chains: B, D
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
TBA-NNp/DDp Chains: E, F, G, I
Molecule details ›
Chains: E, F, G, I
Length: 15 nucleotides
Theoretical weight: 4.74 KDa

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand 0G6 2 x 0G6
Ligand JL0 4 x JL0
Ligand JKR 4 x JKR
Ligand K 4 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 11.2C
Spacegroup: P21
Unit cell:
a: 76.62Å b: 114.86Å c: 83.44Å
α: 90° β: 117.25° γ: 90°
R-values:
R R work R free
0.203 0.201 0.243

Quick links

Citations

4 citation in other articles

New insight into the traditional model of the coagulation cascade and its regulation: illustrated review of a three-dimensional view.
Troisi et al. (2023)
3 more

2 mentions without citation

Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.
Troisi et al. (2023)
1 more