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INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX

X-ray diffraction
2Å resolution
PDB entry 1de7 coloured by chain, front view.
PDB entry 1de7 coloured by chain, side view.
PDB entry 1de7 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: alpha-thrombin complex and peptide
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Multimeric state: hetero trimer
Accessible surface area: 12670.51 Å2
Buried surface area: 3724.58 Å2
Dissociation area: 641.9 Å2
Dissociation energy (ΔGdiss): 2.46 kcal/mol
Dissociation entropy (TΔSdiss): 7.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133099
Assembly 2
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Assembly Name: alpha-thrombin complex and peptide
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Multimeric state: hetero trimer
Accessible surface area: 12256.45 Å2
Buried surface area: 3643.22 Å2
Dissociation area: 679.48 Å2
Dissociation energy (ΔGdiss): 2.05 kcal/mol
Dissociation entropy (TΔSdiss): 7.2 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133099

Macromolecules

Thrombin light chain
Chains: J, 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:
SCOP: Eukaryotic proteases
Thrombin light chain in PDB entry 1de7, assembly 1, front view.
Thrombin light chain in PDB entry 1de7, assembly 1, side view.
Thrombin light chain in PDB entry 1de7, assembly 1, top view.
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Thrombin heavy chain
Chains: H, K
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
SCOP: Eukaryotic proteases
Thrombin heavy chain in PDB entry 1de7, assembly 1, front view.
Thrombin heavy chain in PDB entry 1de7, assembly 1, side view.
Thrombin heavy chain in PDB entry 1de7, assembly 1, top view.
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FACTOR XIII ACTIVATION PEPTIDE (28-37)
Chains: A, B
Length: 11 amino acids
Theoretical weight: 1.13 KDa
FACTOR XIII ACTIVATION PEPTIDE (28-37) in PDB entry 1de7, assembly 1, front view.
FACTOR XIII ACTIVATION PEPTIDE (28-37) in PDB entry 1de7, assembly 1, side view.
FACTOR XIII ACTIVATION PEPTIDE (28-37) in PDB entry 1de7, assembly 1, top view.
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