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- PDB-1tfx: COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHI... -

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Basic information

Entry
Database: PDB / ID: 1tfx
TitleCOMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN
Components
  • TISSUE FACTOR PATHWAY INHIBITOR
  • TRYPSIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) / HYDROLASE / INHIBITOR / BLOOD COAGULATION / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
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 / trypsin / side of membrane / digestion / serine-type endopeptidase inhibitor activity / caveola / blood coagulation ...Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / negative regulation of blood coagulation / trypsin / side of membrane / digestion / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / metal ion binding / 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 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Trypsin / Tissue factor pathway inhibitor
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStubbs, M.T. / Huber, R.
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: J.Biol.Chem. / Year: 1997
Title: The Three-Dimensional Structure of Recombinant Leech-Derived Tryptase Inhibitor in Complex with Trypsin. Implications for the Structure of Human Mast Cell Tryptase and its Inhibition
Authors: Stubbs, M.T. / Morenweiser, R. / Sturzebecher, J. / Bauer, M. / Bode, W. / Huber, R. / Piechottka, G.P. / Matschiner, G. / Sommerhoff, C.P. / Fritz, H. / Auerswald, E.A.
#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: Curr.Pharm.Des. / Year: 1996
Title: Structural Aspects of Factor Xa Inhibition
Authors: Stubbs II, M.T.
#4: 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.
#5: 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.
#6: 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.
History
DepositionJan 21, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: TRYPSIN
C: TISSUE FACTOR PATHWAY INHIBITOR
D: TISSUE FACTOR PATHWAY INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7746
Polymers60,6944
Non-polymers802
Water2,576143
1
A: TRYPSIN
C: TISSUE FACTOR PATHWAY INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3873
Polymers30,3472
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-21 kcal/mol
Surface area12100 Å2
MethodPISA
2
B: TRYPSIN
D: TISSUE FACTOR PATHWAY INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3873
Polymers30,3472
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-21 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.900, 96.200, 137.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, -0.0114, 0.0008), (0.0113, 0.9755, -0.2199), (0.0017, 0.2199, 0.9755)
Vector: 6.3181, -39.9006, -7.8059)

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Components

#1: Protein TRYPSIN


Mass: 23493.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: BLOOD / Plasmid: PFLAG / Production host: Escherichia coli (E. coli) / Strain (production host): JE5505 / References: UniProt: P00761, trypsin
#2: Protein TISSUE FACTOR PATHWAY INHIBITOR / TFPI / EPI / LACI


Mass: 6853.665 Da / Num. of mol.: 2 / Fragment: FACTOR XA-BINDING DOMAIN, DOMAIN II
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE IS PART OF A MULTIDISCIPLINARY STUDY INTO THE STRUCTURE AND FUNCTION OF THE SECOND ...THIS STRUCTURE IS PART OF A MULTIDISCIPLINARY STUDY INTO THE STRUCTURE AND FUNCTION OF THE SECOND DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR, WHICH IS RESPONSIBLE FOR SWITCHING OFF THE EARLY STAGES OF BLOOD COAGULATION. COORDINATES FOR THE NMR SOLUTION STRUCTURE HAVE ALSO BEEN DEPOSITED AS PDB ENTRY 1ADZ.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1 M / Common name: Na/K phosphate

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. obs: 17364 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / Rsym value: 0.3 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 32380
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PORCINE TRYPSIN MODEL FROM LDTI TRYPSIN (PDB ENTRY 1LDT)

1ldt


Resolution: 2.6→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.162 --
obs0.162 13757 84.5 %
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 0 142 4381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.212 558 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor obs: 0.212

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