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- PDB-1irh: The Solution Structure of The Third Kunitz Domain of Tissue Facto... -

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Basic information

Entry
Database: PDB / ID: 1irh
TitleThe Solution Structure of The Third Kunitz Domain of Tissue Factor Pathway Inhibitor
Componentstissue factor pathway inhibitor
KeywordsPROTEIN BINDING / non-protease inhibitor / kunitz domain
Function / homology
Function and homology information


Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / negative regulation of blood coagulation / side of membrane / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / cell surface / endoplasmic reticulum ...Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / negative regulation of blood coagulation / side of membrane / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / cell surface / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tissue factor pathway inhibitor-like / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. ...Tissue factor pathway inhibitor-like / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Tissue factor pathway inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMine, S. / Yamazaki, T. / Miyata, T. / Hara, S. / Kato, H.
CitationJournal: Biochemistry / Year: 2002
Title: Structural mechanism for heparin-binding of the third Kunitz domain of human tissue factor pathway inhibitor.
Authors: Mine, S. / Yamazaki, T. / Miyata, T. / Hara, S. / Kato, H.
History
DepositionOct 2, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tissue factor pathway inhibitor


Theoretical massNumber of molelcules
Total (without water)6,9221
Polymers6,9221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Representative

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Components

#1: Protein tissue factor pathway inhibitor


Mass: 6921.821 Da / Num. of mol.: 1 / Fragment: the third kunitz domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P10646
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2213D 13C-separated NOESY
131HNCO-TROSY
141HMQC-J
151(H)CCH-TOCSY
161HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM the third kunitz domain of tissue factor pathway inhibitor U-15N; 20mM Na-phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21mM the third kunitz domain of tissue factor pathway inhibitor U-15N, 13C; 20mM Na-phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable ...Conformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 40 / Conformers submitted total number: 20

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