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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1p0s
Jmol
Contents
Protein chains
99 a.a. *
235 a.a. *
139 a.a. *
Metals
_MG ×4
_NA
Waters ×51
* Residue conservation analysis
PDB id:
1p0s
Name: Hydrolase
Title: Crystal structure of blood coagulation factor xa in complex ecotin m84r
Structure: Coagulation factor x precursor. Chain: l. Fragment: factor xa light chain. Synonym: stuart factor. Coagulation factor x precursor. Chain: h. Fragment: factor xa heavy chain. Synonym: stuart factor. Ecotin precursor.
Source: Homo sapiens. Human. Organism_taxid: 9606. Escherichia coli. Organism_taxid: 562. Gene: eco or eti or b2209. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.80Å     R-factor:   0.207     R-free:   0.234
Authors: S.X.Wang,E.Hur,C.A.Sousa,L.Brinen,E.J.Slivka,R.J.Fletterick
Key ref:
S.X.Wang et al. (2003). The extended interactions and Gla domain of blood coagulation factor Xa. Biochemistry, 42, 7959-7966. PubMed id: 12834348 DOI: 10.1021/bi027320a
Date:
10-Apr-03     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00742  (FA10_HUMAN) -  Coagulation factor X
Seq:
Struc: 		488 a.a.
99 a.a.*
Protein chain
Pfam   ArchSchema ?
P00742  (FA10_HUMAN) -  Coagulation factor X
Seq:
Struc: 		488 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P23827  (ECOT_ECOLI) -  Ecotin
Seq:
Struc: 		162 a.a.
139 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains L, H: E.C.3.4.21.6  - Coagulation factor Xa.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     proteolysis   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1021/bi027320a Biochemistry 42:7959-7966 (2003)
PubMed id: 12834348  
 
 
The extended interactions and Gla domain of blood coagulation factor Xa.
S.X.Wang, E.Hur, C.A.Sousa, L.Brinen, E.J.Slivka, R.J.Fletterick.
 
  ABSTRACT  
 
The serine protease factor Xa (FXa) is inhibited by ecotin with picomolar affinity. The structure of the tetrameric complex of ecotin variant M84R (M84R) with FXa has been determined to 2.8 A. Substrate directed induced fit of the binding interactions at the S2 and S4 pockets modulates the discrimination of the protease. Specifically, the Tyr at position 99 of FXa changes its conformation with respect to incoming ligand, changing the size of the S2 and S4 pockets. The role of residue 192 in substrate and inhibitor recognition is also examined. Gln 192 from FXa forms a hydrogen bond with the P2 carbonyl group of ecotin. This confirms previous biochemical and structural analyses on thrombin and activated protein C, which suggested that residue 192 may play a more general role in mediating the interactions between coagulation proteases and their inhibitors. The structure of ecotin M84R-FXa (M84R-FXa) also reveals the structure of the Gla domain in the presence of Mg(2+). The first 11 residues of the domain assume a novel conformation and likely represent an intermediate folding state of the domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20419068 B.de Courcy, L.G.Pedersen, O.Parisel, N.Gresh, B.Silvi, J.Pilmé, and J.P.Piquemal (2010).
Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks.
  J Chem Theory Comput, 6, 1048-1063.  
19817987 A.S.Messer, W.H.Velander, and S.P.Bajaj (2009).
Contribution of magnesium in binding of factor IXa to the phospholipid surface: implications for vitamin K-dependent coagulation proteins.
  J Thromb Haemost, 7, 2151-2153.  
19500239 S.Agah, and S.P.Bajaj (2009).
Role of magnesium in factor XIa catalyzed activation of factor IX: calcium binding to factor IX under physiologic magnesium.
  J Thromb Haemost, 7, 1426-1428.  
18680100 N.Singh, and J.M.Briggs (2008).
Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites.
  Biopolymers, 89, 1104-1113.  
18058827 R.E.Saunders, and S.J.Perkins (2008).
CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K-dependent coagulation serine proteases using a text-mining tool.
  Hum Mutat, 29, 333-344.  
16942230 J.P.Piquemal, L.Perera, G.A.Cisneros, P.Ren, L.G.Pedersen, and T.A.Darden (2006).
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.
  J Chem Phys, 125, 054511.  
16757484 S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, and K.Padmanabhan (2006).
High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+, and Zn2+ sites in factor VIIa.
  J Biol Chem, 281, 24873-24888.
PDB codes: 2a2q 2aer 2fir
15545266 L.Jin, P.Pandey, R.E.Babine, J.C.Gorga, K.J.Seidl, E.Gelfand, D.T.Weaver, S.S.Abdel-Meguid, and J.E.Strickler (2005).
Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions.
  J Biol Chem, 280, 4704-4712.
PDB codes: 1xx9 1xxd 1xxf
15219196 H.C.Whinna, E.B.Lesesky, D.M.Monroe, K.A.High, P.J.Larson, and F.C.Church (2004).
Role of the gamma-carboxyglutamic acid domain of activated factor X in the presence of calcium during inhibition by antithrombin-heparin.
  J Thromb Haemost, 2, 1127-1134.  
15314527 M.Schenone, B.C.Furie, and B.Furie (2004).
The blood coagulation cascade.
  Curr Opin Hematol, 11, 272-277.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.