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X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer

X-ray diffraction
2.98Å resolution
PDB entry 5cmx coloured by chain, front view.
PDB entry 5cmx coloured by chain, side view.
PDB entry 5cmx coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 2 distinct polypeptide molecules
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: alpha-thrombin complex and DNA
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Multimeric state: hetero trimer
Accessible surface area: 16893.75 Å2
Buried surface area: 3399.95 Å2
Dissociation area: 551.66 Å2
Dissociation energy (ΔGdiss): -0.39 kcal/mol
Dissociation entropy (TΔSdiss): 11.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118503

Macromolecules

Thrombin light chain
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
Pfam: Thrombin light chain
InterPro:
Thrombin light chain in PDB entry 5cmx, assembly 1, front view.
Thrombin light chain in PDB entry 5cmx, assembly 1, side view.
Thrombin light chain in PDB entry 5cmx, assembly 1, top view.
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Thrombin heavy chain
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
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
Thrombin heavy chain in PDB entry 5cmx, assembly 1, front view.
Thrombin heavy chain in PDB entry 5cmx, assembly 1, side view.
Thrombin heavy chain in PDB entry 5cmx, assembly 1, top view.
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DNA chain A
Name: RE31
Representative chains: A
Length: 31 nucleotides
Theoretical weight: 9.73 KDa
RE31 in PDB entry 5cmx, assembly 1, front view.
RE31 in PDB entry 5cmx, assembly 1, side view.
RE31 in PDB entry 5cmx, assembly 1, top view.
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