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- PDB-6d3x: Highly Potent and Selective Plasmin Inhibitors Based on the Sunfl... -

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Basic information

Entry
Database: PDB / ID: 6d3x
TitleHighly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma
Components
  • Plasminogen
  • Trypsin inhibitor 1
KeywordsHYDROLASE / Protease / SFTI / complex
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / negative regulation of endopeptidase activity / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / negative regulation of endopeptidase activity / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / endopeptidase inhibitor activity / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / serine-type endopeptidase inhibitor activity / protein processing / kinase binding / Schaffer collateral - CA1 synapse / 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 / : / protease binding / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / 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 ...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 / 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
Plasminogen / Trypsin inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen
B: Plasminogen
C: Trypsin inhibitor 1
D: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)57,2464
Polymers57,2464
Non-polymers00
Water5,729318
1
A: Plasminogen
C: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)28,6232
Polymers28,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area10700 Å2
MethodPISA
2
B: Plasminogen
D: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)28,6232
Polymers28,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.728, 80.127, 83.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plasminogen / microplasmin


Mass: 27009.055 Da / Num. of mol.: 2 / Fragment: UNP residues 565-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Mass: 1613.921 Da / Num. of mol.: 2 / Fragment: UNP residues 40-53 / Mutation: T4Y, I7K / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
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: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% PEG4000, 0.1 M magnesium chloride, 0.1 M sodium citrate

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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: Nov 21, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→57.724 Å / Num. obs: 49556 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 15.37 Å2 / Rpim(I) all: 0.068 / Rrim(I) all: 0.198 / Rsym value: 0.185 / Net I/av σ(I): 3.4 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.98.21.140.671570.4161.2141.14100
1.9-2.018.20.7140.967430.260.7610.714100
2.01-2.158.20.4671.563680.170.4970.467100
2.15-2.328.20.3282.159340.120.350.328100
2.32-2.558.20.2442.954990.0890.260.244100
2.55-2.858.20.1713.949610.0630.1820.171100
2.85-3.298.10.1244.944340.0460.1330.124100
3.29-4.0280.0856.637600.0310.0910.085100
4.02-5.697.90.0569.429730.0210.060.056100
5.69-46.5527.60.0549.717270.0210.0580.05499.8

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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: 1.8→46.552 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2161 2468 5 %
Rwork0.1888 --
obs0.1902 49405 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.74 Å2 / Biso mean: 20.8373 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 1.8→46.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 0 327 4221
Biso mean---28.96 -
Num. residues----516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83470.30341440.277325822726
1.8347-1.87210.29161260.246525692695
1.8721-1.91280.26081390.231625792718
1.9128-1.95730.24571380.225125522690
1.9573-2.00630.27321450.207725822727
2.0063-2.06050.25851240.201925722696
2.0605-2.12110.22121150.192826152730
2.1211-2.18960.22171350.189125702705
2.1896-2.26790.24961170.186426042721
2.2679-2.35860.22451670.183325622729
2.3586-2.4660.23011420.182725822724
2.466-2.5960.19951410.185626042745
2.596-2.75860.24571510.182625882739
2.7586-2.97160.21711370.180226292766
2.9716-3.27060.1861100.179526322742
3.2706-3.74360.18321440.166426532797
3.7436-4.71590.17341580.16126502808
4.7159-46.56730.20041350.197528122947
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)
14.9655-0.69090.40634.4582-1.04431.2964-0.0487-0.01230.09070.04270.04990.3341-0.0979-0.269-0.14370.08630.00320.01460.1725-0.00150.1492-31.9215-6.100729.0649
23.1312-1.5234-1.24982.69991.20983.4494-0.0178-0.0001-0.3316-0.04070.0724-0.08540.3513-0.1047-0.00670.144-0.0136-0.01240.08260.0220.16-22.8512-13.673723.6003
33.45130.3645-0.81221.6057-0.32642.8935-0.09010.1266-0.3415-0.09040.0943-0.0570.23640.073-0.00190.16610.0087-0.010.1377-0.01020.1501-16.4459-12.419917.7727
41.84930.3435-0.14620.4896-0.34721.32010.03320.00110.15660.007-0.00180.0814-0.0186-0.0056-0.03310.12940.0049-0.00090.1133-0.00770.1305-20.1276-4.081725.0053
51.56011.25960.24741.88680.56131.54660.0777-0.28160.12340.047-0.02390.0725-0.05620.0711-0.03450.11160.00060.00340.1947-0.02070.1139-13.55540.727238.6203
61.64440.6163-0.58431.70040.28543.22040.0599-0.03310.12990.0232-0.03630.0483-0.0280.11410.01950.1057-0.00550.00340.0985-0.01490.1087-18.5717-0.66433.5927
72.02090.3117-0.70251.8343-0.06634.488-0.01840.27520.1586-0.1779-0.04290.009-0.31010.0168-0.02040.1088-0.0104-0.00380.11230.01060.1071-14.15314.089618.4011
83.8210.3598-0.58463.91260.03630.0937-0.10070.23050.1281-0.04810.0547-0.4952-0.12610.4206-0.02180.11750.0018-0.00240.23580.03060.179531.8468-6.526422.078
92.2133-0.7591-0.30860.9123-0.25172.45-0.0286-0.1163-0.2310.04520.09560.06870.1228-0.0699-0.04110.11950.0043-0.00430.09430.01870.122718.8907-13.020931.199
103.4671-2.05021.00091.7478-0.48231.7421-0.1454-0.2524-0.14430.20950.14430.108-0.0323-0.0397-0.00090.1398-0.01080.00820.16810.02590.11913.4234-6.545837.5695
111.6514-0.95890.20231.0122-0.09381.79020.10210.22520.1469-0.085-0.0833-0.1296-0.06470.0552-0.00770.1099-0.01870.02170.16760.02930.123322.4168-2.897519.923
121.2469-0.97710.19831.5138-0.71282.20520.09820.2830.0275-0.1052-0.03980.00860.0004-0.0395-0.03570.1248-0.00490.00920.17470.02750.103714.8945-0.734815.425
131.6137-0.2129-0.40831.52240.10275.4704-0.1016-0.19810.20470.13770.0089-0.0386-0.4590.18950.09440.09990.001-0.00860.1095-0.02170.098714.3234.069533.1379
148.4111-2.74952.24971.6043-0.08777.17970.0475-0.36290.17980.2963-0.2902-0.405-0.0960.51930.10470.141-0.0121-0.02640.21820.05690.2296-4.3335-9.438233.6677
152.74261.72521.87421.64980.8077.50030.18340.24480.1962-0.0582-0.22090.5623-0.0417-0.39390.04850.1418-0.0275-0.00880.2284-0.03520.27814.3928-9.790918.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 546 through 567 )A546 - 567
2X-RAY DIFFRACTION2chain 'A' and (resid 568 through 585 )A568 - 585
3X-RAY DIFFRACTION3chain 'A' and (resid 586 through 640 )A586 - 640
4X-RAY DIFFRACTION4chain 'A' and (resid 641 through 697 )A641 - 697
5X-RAY DIFFRACTION5chain 'A' and (resid 698 through 743 )A698 - 743
6X-RAY DIFFRACTION6chain 'A' and (resid 744 through 771 )A744 - 771
7X-RAY DIFFRACTION7chain 'A' and (resid 772 through 791 )A772 - 791
8X-RAY DIFFRACTION8chain 'B' and (resid 546 through 567 )B546 - 567
9X-RAY DIFFRACTION9chain 'B' and (resid 568 through 630 )B568 - 630
10X-RAY DIFFRACTION10chain 'B' and (resid 631 through 657 )B631 - 657
11X-RAY DIFFRACTION11chain 'B' and (resid 658 through 710 )B658 - 710
12X-RAY DIFFRACTION12chain 'B' and (resid 711 through 771 )B711 - 771
13X-RAY DIFFRACTION13chain 'B' and (resid 772 through 791 )B772 - 791
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 14 )C1 - 14
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 14 )D1 - 14

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