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- PDB-1bf9: N-TERMINAL EGF-LIKE DOMAIN FROM HUMAN FACTOR VII, NMR, 23 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bf9
TitleN-TERMINAL EGF-LIKE DOMAIN FROM HUMAN FACTOR VII, NMR, 23 STRUCTURES
ComponentsFACTOR VII
KeywordsBLOOD COAGULATION / EGF / HYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / response to genistein / serine-type peptidase complex / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / response to genistein / serine-type peptidase complex / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of blood coagulation / animal organ regeneration / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / circadian rhythm / protein processing / Golgi lumen / response to estrogen / blood coagulation / response to estradiol / : / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY EMBEDDING WITHOUT METRIZATION, RESTRAINED SIMULATED ANNEALING, SIMULATED ANNEALING REFINEMENT
AuthorsMuranyi, A. / Finn, B.E. / Gippert, G.P. / Forsen, S. / Stenflo, J. / Drakenberg, T.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure of the N-terminal EGF-like domain from human factor VII.
Authors: Muranyi, A. / Finn, B.E. / Gippert, G.P. / Forsen, S. / Stenflo, J. / Drakenberg, T.
#1: Journal: Nature / Year: 1996
Title: The Crystal Structure of the Complex of Blood Coagulation Factor Viia with Soluble Tissue Factor
Authors: Banner, D.W. / D'Arcy, A. / Chene, C. / Winkler, F.K. / Guha, A. / Konigsberg, W.H. / Nemerson, Y. / Kirchhofer, D.
#2: Journal: Protein Sci. / Year: 1992
Title: The Three-Dimensional Structure of the First Egf-Like Module of Human Factor Ix: Comparison with Egf and Tgf-Alpha
Authors: Baron, M. / Norman, D.G. / Harvey, T.S. / Handford, P.A. / Mayhew, M. / Tse, A.G. / Brownlee, G.G. / Campbell, I.D.
#3: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding
Authors: Ullner, M. / Selander, M. / Persson, E. / Stenflo, J. / Drakenberg, T. / Teleman, O.
History
DepositionMay 28, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACTOR VII


Theoretical massNumber of molelcules
Total (without water)4,4331
Polymers4,4331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100NO DISTANCE RESTRAINT VIOLATED BY MORE THAN 0.2 ANGSTROM AND NO DIHEDRAL ANGLE RESTRAINTS VIOLATED BY MORE THAN 2 DEGREES
Representative

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Components

#1: Protein/peptide FACTOR VII


Mass: 4432.865 Da / Num. of mol.: 1 / Fragment: N-TERMINAL EGF-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / References: UniProt: P08709, coagulation factor VIIa
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
1212Q
131TOCSY
141NOESY

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: NO SALT ADDED / pH: 5.6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY EMBEDDING WITHOUT METRIZATION, RESTRAINED SIMULATED ANNEALING, SIMULATED ANNEALING REFINEMENT
Software ordinal: 1
NMR ensembleConformer selection criteria: NO DISTANCE RESTRAINT VIOLATED BY MORE THAN 0.2 ANGSTROM AND NO DIHEDRAL ANGLE RESTRAINTS VIOLATED BY MORE THAN 2 DEGREES
Conformers calculated total number: 100 / Conformers submitted total number: 23

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