PDBe 3dd2

X-ray diffraction
1.9Å resolution

Crystal structure of an RNA aptamer bound to human thrombin

Released:
Source organism: Homo sapiens
Primary publication:
Crystal structure of an RNA aptamer bound to thrombin.
RNA 14 2504-12 (2008)
PMID: 18971322

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 30 amino acids
Theoretical weight: 3.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 332-361; Coverage: 5%)
Gene name: F2
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
RNA (26-MER) Chain: B
Molecule details ›
Chain: B
Length: 26 nucleotides
Theoretical weight: 8.37 KDa

Ligands and Environments


2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P21212
Unit cell:
a: 83.766Å b: 134.017Å c: 44.033Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.254