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- PDB-6d3y: Highly Potent and Selective Plasmin Inhibitors Based on the Sunfl... -

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Basic information

Entry
Database: PDB / ID: 6d3y
TitleHighly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma
Components
  • PlasminogenPlasmin
  • Trypsin inhibitor 1
KeywordsHYDROLASE / proteases / SFTI / complex / fibrinolysis
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / negative regulation of endopeptidase activity ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / negative regulation of endopeptidase activity / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / endopeptidase inhibitor activity / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / serine-type endopeptidase inhibitor activity / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Plasminogen / Trypsin inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å
AuthorsLaw, R.H.P. / Wu, G.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma.
Authors: Swedberg, J.E. / Wu, G. / Mahatmanto, T. / Durek, T. / Caradoc-Davies, T.T. / Whisstock, J.C. / Law, R.H.P. / Craik, D.J.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen
C: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9565
Polymers28,6762
Non-polymers2803
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.905, 41.506, 79.527
Angle α, β, γ (deg.)90.000, 109.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1043-

HOH

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Components

#1: Protein Plasminogen / Plasmin / microplasmin


Mass: 27096.135 Da / Num. of mol.: 1 / Fragment: UNP residues 564-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella pastoris (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide Trypsin inhibitor 1 / / SFTI-1


Mass: 1579.865 Da / Num. of mol.: 1 / Fragment: UNP residues 40-53 / Mutation: I7R / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M 2-ethanesulfonic acid, 0.15 M ammonium sulfate, 13% PEG4000
PH range: 5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.32→74.903 Å / Num. obs: 60637 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.42 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.115 / Rsym value: 0.1 / Net I/av σ(I): 4.1 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.32-1.393.81.0640.682800.631.2411.06492.3
1.39-1.484.20.641182800.3630.7390.64196.8
1.48-1.584.20.3971.678530.2260.4580.39797.5
1.58-1.74.20.2153.273530.1210.2470.21598
1.7-1.874.20.1275.567930.0710.1460.12798.4
1.87-2.094.10.0994.661840.0580.1150.09998.6
2.09-2.414.10.077.254920.0410.0820.0799.4
2.41-2.954.10.05410.946840.030.0620.05499.6
2.95-4.174.10.04810.536500.0260.0550.04899.9
4.17-40.4554.10.067.620680.0320.0680.0699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5UGG & 1SFI

5ugg

1sfi


Resolution: 1.32→40.455 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.39
RfactorNum. reflection% reflection
Rfree0.2132 3040 5.02 %
Rwork0.191 --
obs0.1921 60525 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.23 Å2 / Biso mean: 17.459 Å2 / Biso min: 5.09 Å2
Refinement stepCycle: final / Resolution: 1.32→40.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 17 178 2142
Biso mean--22.59 25.84 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.34060.36271220.27132143226582
1.3406-1.36260.31291530.26882534268795
1.3626-1.38610.29981400.28612521266195
1.3861-1.41130.26371540.23462559271397
1.4113-1.43850.25741400.22962602274297
1.4385-1.46780.2251070.2322592269997
1.4678-1.49970.23071260.22742630275697
1.4997-1.53460.23891410.2252610275196
1.5346-1.5730.21371110.22623273498
1.573-1.61550.20341500.18292582273298
1.6155-1.66310.22271530.1882608276197
1.6631-1.71680.20951460.19022626277299
1.7168-1.77810.22221450.17712622276799
1.7781-1.84930.19841470.18842653280098
1.8493-1.93350.20011460.18752631277798
1.9335-2.03540.20161240.17792672279699
2.0354-2.16290.21861440.1812674281899
2.1629-2.32990.20481280.18242660278899
2.3299-2.56430.18441310.190927192850100
2.5643-2.93530.19131470.189326872834100
2.9353-3.69780.20981470.180827192866100
3.6978-40.47430.19991380.168228182956100
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)
11.3054-0.0416-0.66441.08050.28843.8507-0.0627-0.0215-0.04520.08560.0952-0.09370.42040.2887-0.00540.07360.0264-0.00760.0356-0.01070.0946-3.8972.492322.7093
23.66590.2358-0.68353.4811-1.70627.75630.0071-0.2317-0.00140.3091-0.0320.0644-0.45810.491-0.01180.13780.00390.00960.1177-0.0450.1171-4.117112.3735.191
31.31690.13921.19121.33950.32863.69930.15130.1264-0.0242-0.1567-0.0282-0.11120.38780.3064-0.11190.108-0.03130.02610.1914-0.02040.1204-0.11255.87138.0664
41.2361-0.0564-0.02890.76370.15111.65130.01930.04810.23160.01780.08380.0714-0.1939-0.1804-0.04150.06990.01160.02010.07460.02050.1354-12.321313.568718.2295
51.4897-0.0509-1.12990.20740.34822.09130.14110.19370.4649-0.03350.10630.1193-0.6475-0.4656-0.24880.16380.04840.0430.17430.04970.1945-14.05316.918814.6869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 641 through 791 )A641 - 791
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 14 )C1 - 14
3X-RAY DIFFRACTION3chain 'A' and (resid 545 through 566 )A545 - 566
4X-RAY DIFFRACTION4chain 'A' and (resid 567 through 618 )A567 - 618
5X-RAY DIFFRACTION5chain 'A' and (resid 619 through 640 )A619 - 640

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