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Contents |
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142 a.a.
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254 a.a.
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75 a.a.
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116 a.a.
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* Residue conservation analysis
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PDB id:
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Hydrolase/hydrolase inhibitor
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Title:
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Complex of active site inhibited human blood coagulation factor viia with human recombinant soluble tissue factor
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Structure:
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Blood coagulation factor viia light chain. Chain: l. Engineered: yes. Blood coagulation factor viia heavy chain. Chain: h. Engineered: yes. Soluble tissue factor. Chain: t. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cell_line: baby hamster kidney cells. Organ: blood. Expressed in: mesocricetus auratus. Expression_system_taxid: 10036. Expression_system_cell_line: bhk cells. Expressed in: escherichia coli.
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Resolution:
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2.00Å
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R-factor:
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0.187
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R-free:
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0.218
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Authors:
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D.W.Banner
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Key ref:
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D.W.Banner
et al.
(1996).
The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor.
Nature,
380,
41-46.
PubMed id:
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Date:
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05-Mar-97
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Release date:
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04-Sep-97
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PROCHECK
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Headers
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References
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P08709
(FA7_HUMAN) -
Coagulation factor VII from Homo sapiens
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Seq:
Struc:
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466 a.a.
142 a.a.*
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P08709
(FA7_HUMAN) -
Coagulation factor VII from Homo sapiens
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Seq:
Struc:
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466 a.a.
254 a.a.
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Enzyme class:
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Chains L, H:
E.C.3.4.21.21
- coagulation factor VIIa.
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Reaction:
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Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.
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Nature
380:41-46
(1996)
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PubMed id:
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The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor.
|
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D.W.Banner,
A.D'Arcy,
C.Chène,
F.K.Winkler,
A.Guha,
W.H.Konigsberg,
Y.Nemerson,
D.Kirchhofer.
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ABSTRACT
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Blood coagulation is initiated when tissue factor binds to coagulation factor
VIIa to give an enzymatically active complex which then activates factors IX and
X, leading to thrombin generation and clot formation. We have determined the
crystal structure at 2.0-A degrees resolution of active-site-inhibited factor
VIIa complexed with the cleaved extracellular domain of tissue factor. In the
complex, factor VIIa adopts an extended conformation. This structure provides a
basis for understanding many molecular aspects of the initiation of coagulation.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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|
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B.Plesner,
P.Westh,
S.Hvidt,
and
A.D.Nielsen
(2011).
The molar hydrodynamic volume changes of factor VIIa due to GlycoPEGylation.
|
| |
J Pharm Biomed Anal,
55,
597-602.
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|
|
|
|
|
C.S.Craik,
M.J.Page,
and
E.L.Madison
(2011).
Proteases as therapeutics.
|
| |
Biochem J,
435,
1.
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M.Jiang,
Z.Wang,
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X.Bai,
J.Su,
L.Cao,
W.Zhang,
and
C.Ruan
(2011).
A novel missense mutation close to the charge-stabilizing system in a patient with congenital factor VII deficiency.
|
| |
Blood Coagul Fibrinolysis,
22,
264-270.
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|
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H.D.Downey,
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R.M.Bunte,
and
K.A.High
(2011).
Catalytic domain modification and viral gene delivery of activated factor VII confers hemostasis at reduced expression levels and vector doses in vivo.
|
| |
Blood,
117,
3974-3982.
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|
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and
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(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.
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J Chem Theory Comput,
6,
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|
C.J.Lee,
V.Chandrasekaran,
S.Wu,
R.E.Duke,
and
L.G.Pedersen
(2010).
Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex.
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| |
Thromb Res,
125,
S7.
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|
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|
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|
J.Boles,
and
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(2010).
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| |
Lupus,
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J Med Chem,
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H.R.Stennicke,
and
L.C.Petersen
(2010).
Characterization of canine coagulation factor VII and its complex formation with tissue factor: canine-human cross-species compatibility.
|
| |
J Thromb Haemost,
8,
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|
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|
|
|
|
|
T.Shiraishi,
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K.Esaki,
M.Ohta,
H.Sato,
and
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(2010).
Design and synthesis of peptidomimetic factor VIIa inhibitors.
|
| |
Chem Pharm Bull (Tokyo),
58,
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|
PDB code:
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Y.Z.Ohkubo,
J.H.Morrissey,
and
E.Tajkhorshid
(2010).
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor.
|
| |
J Thromb Haemost,
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|
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|
|
|
|
|
A.S.Minazzo,
R.C.Darlington,
and
J.B.Ross
(2009).
Loop dynamics of the extracellular domain of human tissue factor and activation of factor VIIa.
|
| |
Biophys J,
96,
681-692.
|
|
|
|
|
|
|
E.Persson,
and
O.H.Olsen
(2009).
Activation loop 3 and the 170 loop interact in the active conformation of coagulation factor VIIa.
|
| |
FEBS J,
276,
3099-3109.
|
|
|
|
|
|
|
M.Maly,
I.Hrachovinova,
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P.Salaj,
P.Hajek,
and
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(2009).
Patients with acute coronary syndromes have low tissue factor activity and microparticle count, but normal concentration of tissue factor antigen in platelet free plasma: a pilot study.
|
| |
Eur J Haematol,
82,
148-153.
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|
|
|
|
|
M.Sen,
M.Herzik,
J.W.Craft,
A.L.Creath,
S.Agrawal,
W.Ruf,
and
G.B.Legge
(2009).
Spectroscopic Characterization of Successive Phosphorylation of the Tissue Factor Cytoplasmic Region.
|
| |
Open Spectrosc J,
3,
58-64.
|
|
|
PDB codes:
|
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|
|
|
|
|
N.Mackman,
and
M.Taubman
(2009).
Tissue factor: past, present, and future.
|
| |
Arterioscler Thromb Vasc Biol,
29,
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|
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|
|
|
|
|
Q.Zhang,
H.H.Petersen,
H.Ostergaard,
W.Ruf,
and
A.J.Olson
(2009).
Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa.
|
| |
Proteins,
77,
559-569.
|
|
|
|
|
|
|
R.Bieker,
T.Kessler,
C.Schwöppe,
T.Padró,
T.Persigehl,
C.Bremer,
J.Dreischalück,
A.Kolkmeyer,
W.Heindel,
R.M.Mesters,
and
W.E.Berdel
(2009).
Infarction of tumor vessels by NGR-peptide-directed targeting of tissue factor: experimental results and first-in-man experience.
|
| |
Blood,
113,
5019-5027.
|
|
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|
|
|
|
R.Chattopadhyay,
R.Iacob,
S.Sen,
R.Majumder,
K.B.Tomer,
and
B.R.Lentz
(2009).
Functional and structural characterization of factor Xa dimer in solution.
|
| |
Biophys J,
96,
974-986.
|
|
|
|
|
|
|
C.Reinhardt,
M.L.von Brühl,
D.Manukyan,
L.Grahl,
M.Lorenz,
B.Altmann,
S.Dlugai,
S.Hess,
I.Konrad,
L.Orschiedt,
N.Mackman,
L.Ruddock,
S.Massberg,
and
B.Engelmann
(2008).
Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation.
|
| |
J Clin Invest,
118,
1110-1122.
|
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|
|
|
|
J.R.Bjelke,
O.H.Olsen,
M.Fodje,
L.A.Svensson,
S.Bang,
G.Bolt,
B.B.Kragelund,
and
E.Persson
(2008).
Mechanism of the Ca2+-induced enhancement of the intrinsic factor VIIa activity.
|
| |
J Biol Chem,
283,
25863-25870.
|
|
|
PDB code:
|
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|
|
|
|
|
|
K.D.Rand,
M.D.Andersen,
O.H.Olsen,
T.J.Jørgensen,
H.Ostergaard,
O.N.Jensen,
H.R.Stennicke,
and
E.Persson
(2008).
The origins of enhanced activity in factor VIIa analogs and the interplay between key allosteric sites revealed by hydrogen exchange mass spectrometry.
|
| |
J Biol Chem,
283,
13378-13387.
|
|
|
|
|
|
|
P.Hauske,
C.Ottmann,
M.Meltzer,
M.Ehrmann,
and
M.Kaiser
(2008).
Allosteric regulation of proteases.
|
| |
Chembiochem,
9,
2920-2928.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
S.M.Lee,
Y.S.Heo,
E.Y.Lee,
C.L.Chang,
H.J.Shin,
J.S.Chung,
and
S.H.Hwang
(2008).
Compound heterozygous mutations in severe factor VII deficiency including a novel nonsense mutation.
|
| |
Blood Coagul Fibrinolysis,
19,
92-94.
|
|
|
|
|
|
|
V.Chandrasekaran,
C.J.Lee,
R.E.Duke,
L.Perera,
and
L.G.Pedersen
(2008).
Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling.
|
| |
Protein Sci,
17,
1354-1361.
|
|
|
|
|
|
|
Y.Z.Ohkubo,
and
E.Tajkhorshid
(2008).
Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors.
|
| |
Structure,
16,
72-81.
|
|
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|
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A.W.Shaw,
V.S.Pureza,
S.G.Sligar,
and
J.H.Morrissey
(2007).
The local phospholipid environment modulates the activation of blood clotting.
|
| |
J Biol Chem,
282,
6556-6563.
|
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|
C.J.Lee,
V.Chandrasekaran,
R.E.Duke,
L.Perera,
and
L.G.Pedersen
(2007).
A proposed structural model of human protein Z.
|
| |
J Thromb Haemost,
5,
1558-1561.
|
|
|
|
|
|
|
C.Manithody,
L.Yang,
and
A.R.Rezaie
(2007).
Identification of a basic region on tissue factor that interacts with the first epidermal growth factor-like domain of factor X.
|
| |
Biochemistry,
46,
3193-3199.
|
|
|
|
|
|
|
D.M.Monroe,
and
N.S.Key
(2007).
The tissue factor-factor VIIa complex: procoagulant activity, regulation, and multitasking.
|
| |
J Thromb Haemost,
5,
1097-1105.
|
|
|
|
|
|
|
E.Persson,
and
A.Ostergaard
(2007).
Mg(2+) binding to the Gla domain of factor X influences the interaction with tissue factor.
|
| |
J Thromb Haemost,
5,
1977-1978.
|
|
|
|
|
|
|
H.H.Versteeg,
and
W.Ruf
(2007).
Tissue factor coagulant function is enhanced by protein-disulfide isomerase independent of oxidoreductase activity.
|
| |
J Biol Chem,
282,
25416-25424.
|
|
|
|
|
|
|
J.López-Sagaseta,
R.Montes,
C.Puy,
N.Díez,
K.Fukudome,
and
J.Hermida
(2007).
Binding of factor VIIa to the endothelial cell protein C receptor reduces its coagulant activity.
|
| |
J Thromb Haemost,
5,
1817-1824.
|
|
|
|
|
|
|
K.S.Sakariassen,
and
L.Orning
(2007).
Validation of the human tissue factor/FVIIa complex as an antithrombotic target and the discovery of a synthetic peptide.
|
| |
Future Cardiol,
3,
249-262.
|
|
|
|
|
|
|
L.Yang,
J.S.Bae,
C.Manithody,
and
A.R.Rezaie
(2007).
Identification of a specific exosite on activated protein C for interaction with protease-activated receptor 1.
|
| |
J Biol Chem,
282,
25493-25500.
|
|
|
|
|
|
|
M.Giansily-Blaizot,
D.Thorel,
P.Khau Van Kien,
C.Behar,
M.C.Romey,
F.Mugneret,
J.F.Schved,
and
M.Claustres
(2007).
Characterisation of a large complex intragenic re-arrangement in the FVII gene (F7) avoiding misdiagnosis in inherited factor VII deficiency.
|
| |
Br J Haematol,
138,
359-365.
|
|
|
|
|
|
|
M.Hoffman,
C.M.Colina,
A.G.McDonald,
G.M.Arepally,
L.Pedersen,
and
D.M.Monroe
(2007).
Tissue factor around dermal vessels has bound factor VII in the absence of injury.
|
| |
J Thromb Haemost,
5,
1403-1408.
|
|
|
|
|
|
|
M.Ndonwi,
G.J.Broze,
S.Agah,
A.E.Schmidt,
and
S.P.Bajaj
(2007).
Substitution of the Gla domain in factor X with that of protein C impairs its interaction with factor VIIa/tissue factor: lack of comparable effect by similar substitution in factor IX.
|
| |
J Biol Chem,
282,
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|
|
|
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|
|
N.S.Key,
J.G.Geng,
and
R.R.Bach
(2007).
Tissue factor; from Morawitz to microparticles.
|
| |
Trans Am Clin Climatol Assoc,
118,
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|
|
|
|
|
|
|
O.H.Olsen,
K.D.Rand,
H.Østergaard,
and
E.Persson
(2007).
A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation.
|
| |
Protein Sci,
16,
671-682.
|
|
|
|
|
|
|
O.Taboureau,
and
O.H.Olsen
(2007).
Computational study of coagulation factor VIIa's affinity for phospholipid membranes.
|
| |
Eur Biophys J,
36,
133-144.
|
|
|
|
|
|
|
R.K.Pruthi,
V.Rodriguez,
C.Allen,
J.A.Slaby,
K.A.Schmidt,
and
E.A.Plumhoff
(2007).
Molecular analysis in a patient with severe factor VII deficiency and an inhibitor: report of a novel mutation (S103G).
|
| |
Eur J Haematol,
79,
354-359.
|
|
|
|
|
|
|
R.Krishnan,
P.L.Kotian,
P.Chand,
S.Bantia,
S.Rowland,
and
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(2007).
Probing the S2 site of factor VIIa to generate potent and selective inhibitors: the structure of BCX-3607 in complex with tissue factor-factor VIIa.
|
| |
Acta Crystallogr D Biol Crystallogr,
63,
689-697.
|
|
|
PDB code:
|
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|
|
|
|
|
C.M.Colina,
D.Venkateswarlu,
R.Duke,
L.Perera,
and
L.G.Pedersen
(2006).
What causes the enhancement of activity of factor VIIa by tissue factor?
|
| |
J Thromb Haemost,
4,
2726-2729.
|
|
|
|
|
|
|
E.K.Waters,
S.Yegneswaran,
and
J.H.Morrissey
(2006).
Raising the active site of factor VIIa above the membrane surface reduces its procoagulant activity but not factor VII autoactivation.
|
| |
J Biol Chem,
281,
26062-26068.
|
|
|
|
|
|
|
K.D.Rand,
T.J.Jørgensen,
O.H.Olsen,
E.Persson,
O.N.Jensen,
H.R.Stennicke,
and
M.D.Andersen
(2006).
Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange.
|
| |
J Biol Chem,
281,
23018-23024.
|
|
|
|
|
|
|
K.E.Persson,
J.Stenflo,
S.Linse,
Y.Stenberg,
R.J.Preston,
D.A.Lane,
and
S.M.Rezende
(2006).
Binding of calcium to anticoagulant protein S: role of the fourth EGF module.
|
| |
Biochemistry,
45,
10682-10689.
|
|
|
|
|
|
|
M.Pinotti,
L.Rizzotto,
P.Pinton,
P.Ferraresi,
A.Chuansumrit,
P.Charoenkwan,
G.Marchetti,
R.Rizzuto,
G.Mariani,
and
F.Bernardi
(2006).
Intracellular readthrough of nonsense mutations by aminoglycosides in coagulation factor VII.
|
| |
J Thromb Haemost,
4,
1308-1314.
|
|
|
|
|
|
|
S.M.Bates,
and
J.I.Weitz
(2006).
The status of new anticoagulants.
|
| |
Br J Haematol,
134,
3.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
V.M.Chen,
and
P.J.Hogg
(2006).
Allosteric disulfide bonds in thrombosis and thrombolysis.
|
| |
J Thromb Haemost,
4,
2533-2541.
|
|
|
|
|
|
|
A.E.Johnson
(2005).
Fluorescence approaches for determining protein conformations, interactions and mechanisms at membranes.
|
| |
Traffic,
6,
1078-1092.
|
|
|
|
|
|
|
A.E.Schmidt,
H.S.Chand,
D.Cascio,
W.Kisiel,
and
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Where a reference describes a PDB structure, the PDB
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