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- PDB-4bqd: KD1 of human TFPI in complex with a synthetic peptide -

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Basic information

Entry
Database: PDB / ID: 4bqd
TitleKD1 of human TFPI in complex with a synthetic peptide
Components
  • PEPTIDE
  • TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT
KeywordsBLOOD CLOTTING
Function / homology
Function and homology information


negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / side of membrane / caveola / serine-type endopeptidase inhibitor activity / blood coagulation / cell surface / endoplasmic reticulum ...negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / side of membrane / caveola / serine-type endopeptidase inhibitor activity / 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. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...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 / Tissue factor pathway inhibitor (Lipoprotein-associated coagulation inhibitor) variant
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.48 Å
AuthorsGriessner, A. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Small Peptides Blocking Inhibition of Factor Xa and Tissue Factor-Factor Viia by Tissue Factor Pathway Inhibitor (Tfpi)
Authors: Dockal, M. / Hartman, R. / Fries, M. / Christella, M. / Thomassen, L.G.D. / Heizman, A. / Ehrlich, H. / Rosing, J. / Osterkamp, F. / Polakowski, T. / Reineke, U. / Griessner, A. / ...Authors: Dockal, M. / Hartman, R. / Fries, M. / Christella, M. / Thomassen, L.G.D. / Heizman, A. / Ehrlich, H. / Rosing, J. / Osterkamp, F. / Polakowski, T. / Reineke, U. / Griessner, A. / Brandstetter, H. / Scheiflinger, F.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Jul 17, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT
B: TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT
C: PEPTIDE
D: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4696
Polymers23,2844
Non-polymers1842
Water1,29772
1
A: TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT
C: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)11,6422
Polymers11,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10.5 kcal/mol
Surface area6190 Å2
MethodPISA
2
B: TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT
D: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8264
Polymers11,6422
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10.2 kcal/mol
Surface area5590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.670, 69.320, 42.370
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

21C-2008-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 78
2010B15 - 78
1020C1 - 20
2020D1 - 20

NCS ensembles :
ID
1
2

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Components

#1: Protein TISSUE FACTOR PATHWAY INHIBITOR (LIPOPROTEIN-ASSOCIATED COAGULATION INHIBITOR) VARIANT


Mass: 9278.473 Da / Num. of mol.: 2 / Fragment: RESIDUES 40-118 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q59EE5, UniProt: P10646*PLUS
#2: Protein/peptide PEPTIDE


Mass: 2363.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 12168 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.12

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.48→42.35 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.855 / SU B: 17.82 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26207 514 4.7 %RANDOM
Rwork0.22664 ---
obs0.2283 10318 92.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-1.6 Å2
2--5.2 Å20 Å2
3----4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.48→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 12 72 1591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191536
X-RAY DIFFRACTIONr_bond_other_d0.0020.021446
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9682051
X-RAY DIFFRACTIONr_angle_other_deg2.1263.0073326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9165177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87423.95181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41115279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3011510
X-RAY DIFFRACTIONr_chiral_restr0.5230.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211709
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02375
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A34390.09
12B34390.09
21C9590.14
22D9590.14
LS refinement shellResolution: 2.482→2.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 29 -
Rwork0.305 692 -
obs--86.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.0311-2.52062.32286.0316-1.88184.7404-0.2079-0.17710.87640.02170.0096-0.081-0.8999-0.5480.19830.22620.13230.04220.1216-0.03050.3969-13.6806-16.27089.9339
27.0881-3.52341.14937.6496-0.84034.89660.0695-0.1288-0.7769-0.06410.12570.23310.8170.4608-0.19530.16570.09660.02430.11240.0010.260114.8306-41.88894.6813
30.16-0.1141.08762.0262-1.83768.306-0.0279-0.2095-0.01830.12610.29710.3653-0.3724-1.3738-0.26920.13630.02050.04230.34660.02390.4034-15.6987-25.472118.4789
412.9509-8.6428-2.932110.4821.080.8376-0.2456-0.52120.3030.49550.3052-0.22550.00360.1765-0.05950.09280.0666-0.00120.2692-0.02510.178815.8854-32.045412.2564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 79
2X-RAY DIFFRACTION2B15 - 79
3X-RAY DIFFRACTION3C0 - 20
4X-RAY DIFFRACTION4D0 - 20

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