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Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution

Source organism: Homo sapiens
Biochemical function: copper ion binding
Biological process: proteolysis
Cellular component: extracellular region

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EC 3.4.21.6: Coagulation factor Xa

Reaction catalysed:
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Systematic name:
-
Alternative Name(s):
  • Activated Stuart-Prower factor
  • Activated blood-coagulation factor X
  • Activated factor X
  • Autoprothrombin C
  • Factor Xa
  • Plasma thromboplastin
  • Prothrombase
  • Prothrombinase
  • Stuart factor
  • Thrombokinase
  • Thromboplastin

EC 3.4.21.5: Thrombin

Reaction catalysed:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Systematic name:
-
Alternative Name(s):
  • Activated blood-coagulation factor II
  • Beta-thrombin
  • Blood-coagulation factor IIa
  • E thrombin
  • Factor IIa
  • Fibrinogenase
  • Gamma-thrombin
  • Thrombase
  • Thrombin-C
  • Thrombofort
  • Topical
  • Tropostasin

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00051
Domain description: Kringle domain
Occurring in:
  1. Prothrombin
The deposited structure of PDB entry 7tpp contains 2 copies of Pfam domain PF00051 (Kringle domain) in Prothrombin. Showing 2 copies in chain A [auth E].

PF00754
Domain description: F5/8 type C domain
Occurring in:
  1. Coagulation factor V light chain
The deposited structure of PDB entry 7tpp contains 2 copies of Pfam domain PF00754 (F5/8 type C domain) in Coagulation factor V light chain. Showing 2 copies in chain D.

PF07732
Domain description: Multicopper oxidase
Occurring in:
  1. Coagulation factor V heavy chain
  2. Coagulation factor V light chain
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF07732 (Multicopper oxidase) in Coagulation factor V heavy chain. Showing 1 copy in chain C.
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF07732 (Multicopper oxidase) in Coagulation factor V light chain. Showing 1 copy in chain D.

PF00089
Domain description: Trypsin
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF00089 (Trypsin) in Prothrombin. Showing 1 copy in chain A [auth E].
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF00089 (Trypsin) in Activated factor Xa heavy chain. Showing 1 copy in chain E [auth B].

PF00594
Domain description: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain
Occurring in:
  1. Factor X light chain
  2. Prothrombin
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF00594 (Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain) in Prothrombin. Showing 1 copy in chain A [auth E].
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF00594 (Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain) in Factor X light chain. Showing 1 copy in chain B [auth A].

PF09396
Domain description: Thrombin light chain
Occurring in:
  1. Prothrombin
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF09396 (Thrombin light chain) in Prothrombin. Showing 1 copy in chain A [auth E].

PF14670
Domain description: Coagulation Factor Xa inhibitory site
Occurring in:
  1. Factor X light chain
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF14670 (Coagulation Factor Xa inhibitory site) in Factor X light chain. Showing 1 copy in chain B [auth A].

PF00008
Domain description: EGF-like domain
Occurring in:
  1. Factor X light chain
The deposited structure of PDB entry 7tpp contains 1 copy of Pfam domain PF00008 (EGF-like domain) in Factor X light chain. Showing 1 copy in chain B [auth A].

InterPro InterPro annotations
IPR000294
Domain description: Gamma-carboxyglutamic acid-rich (GLA) domain
Occurring in:
  1. Factor X light chain
  2. Prothrombin
IPR000421
Domain description: Coagulation factor 5/8, C-terminal domain
Occurring in:
  1. Coagulation factor V light chain
IPR008972
Domain description: Cupredoxin
Occurring in:
  1. Coagulation factor V heavy chain
  2. Coagulation factor V light chain
IPR000001
Domain description: Kringle
Occurring in:
  1. Prothrombin
IPR001254
Domain description: Serine proteases, trypsin domain
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
IPR001314
Domain description: Peptidase S1A, chymotrypsin family
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
IPR003966
Domain description: Prothrombin/thrombin
Occurring in:
  1. Prothrombin
IPR000742
Domain description: EGF-like domain
Occurring in:
  1. Factor X light chain
IPR043504
Domain description: Peptidase S1, PA clan, chymotrypsin-like fold
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
IPR011707
Domain description: Multicopper oxidase-like, N-terminal
Occurring in:
  1. Coagulation factor V heavy chain
  2. Coagulation factor V light chain
IPR018056
Domain description: Kringle, conserved site
Occurring in:
  1. Prothrombin
IPR013806
Domain description: Kringle-like fold
Occurring in:
  1. Prothrombin
IPR038178
Domain description: Kringle superfamily
Occurring in:
  1. Prothrombin
IPR008979
Domain description: Galactose-binding-like domain superfamily
Occurring in:
  1. Coagulation factor V light chain
IPR018114
Domain description: Serine proteases, trypsin family, histidine active site
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
IPR009003
Domain description: Peptidase S1, PA clan
Occurring in:
  1. Activated factor Xa heavy chain
  2. Prothrombin
IPR035972
Domain description: Gamma-carboxyglutamic acid-rich (GLA) domain superfamily
Occurring in:
  1. Factor X light chain
  2. Prothrombin
IPR018992
Domain description: Thrombin light chain
Occurring in:
  1. Prothrombin
IPR037111
Domain description: Thrombin light chain domain superfamily
Occurring in:
  1. Prothrombin
IPR033138
Domain description: Multicopper oxidases, conserved site
Occurring in:
  1. Coagulation factor V light chain
IPR045087
Domain description: Multicopper oxidase
Occurring in:
  1. Coagulation factor V heavy chain
IPR000152
Domain description: EGF-type aspartate/asparagine hydroxylation site
Occurring in:
  1. Factor X light chain
IPR018097
Domain description: EGF-like calcium-binding, conserved site
Occurring in:
  1. Factor X light chain
IPR001881
Domain description: EGF-like calcium-binding domain
Occurring in:
  1. Factor X light chain
IPR017857
Domain description: Coagulation factor-like, Gla domain superfamily
Occurring in:
  1. Factor X light chain

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