8bw5

X-ray diffraction
2.8Å resolution

X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer

Released:

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)
PDBe Complex ID:
PDB-CPX-512513 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 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
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
M08s-1_41mer Chain: F
Molecule details ›
Chain: F
Length: 41 nucleotides
Theoretical weight: 12.99 KDa

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL, SIA
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 11.2C
Unit cell:
a: 68.06Å b: 75.49Å c: 114.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.252