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- PDB-1adz: THE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACT... -

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Entry
Database: PDB / ID: 1adz
TitleTHE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR, NMR, 30 STRUCTURES
ComponentsTISSUE FACTOR PATHWAY INHIBITOR
KeywordsHYDROLASE / INHIBITOR / COAGULATION
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 / DIANA
AuthorsBurgering, M.J.M. / Orbons, L.P.M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The second Kunitz domain of human tissue factor pathway inhibitor: cloning, structure determination and interaction with factor Xa.
Authors: Burgering, M.J. / Orbons, L.P. / van der Doelen, A. / Mulders, J. / Theunissen, H.J. / Grootenhuis, P.D. / Bode, W. / Huber, R. / Stubbs, M.T.
#1: Journal: Curr.Pharm.Des. / Year: 1996
Title: Structural Aspects of Factor Xa Inhibition
Authors: Stubbs II, M.T.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition
Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / Von Der Saal, W. / Wirthensohn, K. / Engh, R.A.
#3: Journal: Embo J. / Year: 1996
Title: The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma?
Authors: Van De Locht, A. / Stubbs, M.T. / Bode, W. / Friedrich, T. / Bollschweiler, C. / Hoffken, W. / Huber, R.
#4: Journal: FEBS Lett. / Year: 1995
Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
Authors: Stubbs, M.T. / Huber, R. / Bode, W.
#5: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W.
#6: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of a High-Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures
Authors: Berndt, K.D. / Guntert, P. / Orbons, L.P. / Wuthrich, K.
History
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TISSUE FACTOR PATHWAY INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,3791
Polymers8,3791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300LOWEST VALUE OF VARIABLE TARGET FUNCTION
Representative

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Components

#1: Protein TISSUE FACTOR PATHWAY INHIBITOR / TFPI / EPI / LACI


Mass: 8379.239 Da / Num. of mol.: 1 / Fragment: FACTOR XA-BINDING DOMAIN (DOMAIN II) / Mutation: N-TERMINAL INS(DYKDDDDKL)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Organ: BLOOD / Plasmid: PFLAG / Production host: Escherichia coli (E. coli) / Strain (production host): JE5505 / 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
111HOMONUCLEAR NOESY
121COSY
131TOCSY

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Sample preparation

Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DIANAGUNTERT,WUTHRICHrefinement
TRIAD NMR FROM TRIPOSTRIPOSstructure solution
RefinementMethod: DIANA / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE DIANA PROGRAM BUT WERE NOT FURTHER REFINED USING A FORCE FIELD AND ENERGY MINIMIZATION AND/OR MOLECULAR DYNAMICS CALCULATIONS
NMR ensembleConformer selection criteria: LOWEST VALUE OF VARIABLE TARGET FUNCTION
Conformers calculated total number: 300 / Conformers submitted total number: 30

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