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- PDB-7ths: Macrocyclic plasmin inhibitor -

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Basic information

Entry
Database: PDB / ID: 7ths
TitleMacrocyclic plasmin inhibitor
ComponentsPlasminogen
KeywordsBLOOD CLOTTING / Hydrolase/Inhibitor / protease / inhibitor / Hydrolase-Inhibitor complex
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / 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 ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / 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 / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
(2S)-butane-1,2-diol / Chem-I5Y / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuojie, W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1127593 Australia
CitationJournal: Chemmedchem / Year: 2023
Title: Synthesis and Structural Characterization of Macrocyclic Plasmin Inhibitors.
Authors: Wiedemeyer, S.J.A. / Wu, G. / Pham, T.L.P. / Lang-Henkel, H. / Perez Urzua, B. / Whisstock, J.C. / Law, R.H.P. / Steinmetzer, T.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,01912
Polymers54,6392
Non-polymers2,38110
Water6,395355
1
A: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5136
Polymers27,3191
Non-polymers1,1935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5076
Polymers27,3191
Non-polymers1,1875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.723, 50.598, 92.757
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasminogen


Mass: 27319.402 Da / Num. of mol.: 2 / Mutation: S760A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Homo sapiens (human) / References: UniProt: P00747, plasmin
#2: Chemical ChemComp-I5Y / (6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3,13,21-trioxo-2,6,9,14,22-pentaazatetracyclo[23.2.2.2~6,9~.2~15,18~]tritriaconta-1(27),15,17,25,28,30-hexaene-23-carboxamide


Mass: 808.988 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H52N8O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-I5Q / (2S)-butane-1,2-diol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→92.627 Å / Num. obs: 42073 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.49 Å2 / Rpim(I) all: 0.068 / Rrim(I) all: 0.162 / Rsym value: 0.146 / Net I/av σ(I): 4 / Net I/σ(I): 8.7 / Num. measured all: 227640
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.95.20.8530.73154260830.410.9490.8532.3100
1.9-2.015.40.5661.13108757830.2650.6260.5663.4100
2.01-2.155.60.3921.73035454230.1790.4310.3924.7100
2.15-2.325.50.2672.52801750720.1230.2940.2676.3100
2.32-2.555.40.2063.42503646620.0960.2280.2067.5100
2.55-2.855.20.1512.32187042170.0740.1690.1519.7100
2.85-3.295.70.09972145437630.0450.1090.09914.1100
3.29-4.025.60.0698.41782231770.0320.0760.06919.7100
4.02-5.695.20.05311.91288024850.0250.0580.05322.3100
5.69-48.6555.40.0512.6757814080.0230.0560.0521.199.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UGG

5ugg


Resolution: 1.8→46.31 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 2097 4.99 %
Rwork0.1852 39941 -
obs0.1863 42038 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.45 Å2 / Biso mean: 22.2901 Å2 / Biso min: 6.27 Å2
Refinement stepCycle: final / Resolution: 1.8→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3751 0 271 355 4377
Biso mean--29.12 27.63 -
Num. residues----491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.840.28831310.25526182749
1.84-1.890.28531370.241326472784
1.89-1.940.25851510.219726422793
1.94-20.22781600.200526022762
2-2.060.2141410.199426502791
2.06-2.130.19551410.198326602801
2.13-2.220.22371540.192426262780
2.22-2.320.20511360.184726702806
2.32-2.440.20111270.18626772804
2.44-2.60.19851630.188826222785
2.6-2.80.22231470.184126582805
2.8-3.080.21781120.184826792791
3.08-3.520.18991450.171127062851
3.52-4.440.17021270.15327132840
4.44-46.310.20331250.181127712896
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)
11.9174-0.31820.33381.9470.53971.7290.0527-0.0654-0.0298-0.0526-0.0313-0.538-0.14190.4724-0.01230.1147-0.0390.01410.22970.01370.237142.0146-26.231933.9173
21.89180.2815-0.60111.23560.19142.1636-0.08560.2490.0887-0.64160.0343-0.4718-0.30040.32070.11640.3573-0.02030.12110.23920.01610.28440.613-27.833722.1529
31.31420.0981-0.1421.633-0.03461.20730.0378-0.0317-0.0137-0.0849-0.0424-0.2876-0.17180.24890.02390.1453-0.01790.01890.120.00580.168335.1029-27.936234.7587
44.8812-0.826-0.99811.99790.95181.3071-0.0187-0.14510.10530.0128-0.01660.046-0.11450.01770.03460.1440.001-0.01760.08650.00160.063923.7778-19.331339.9704
51.4983-0.0599-0.05021.67290.73791.92670.063-0.1088-0.06990.0416-0.0335-0.1007-0.01010.0809-0.02510.0598-0.0137-0.00710.08330.01720.070929.312-29.867836.8695
60.85010.08830.0251.74430.47560.9359-0.0146-0.04970.02440.06770.01660.03690.03370.01950.00280.0410.0185-0.0160.0780.00070.072819.2374-4.020713.0425
71.8888-1.90110.04054.70461.39212.5089-0.0713-0.19350.03650.1490.1901-0.20750.35450.3618-0.02340.10950.0292-0.04290.1414-0.00930.115425.1785-5.198520.2208
81.26750.30350.34080.95660.2670.77330.0217-0.00510.01090.0428-0.03310.05850.0003-0.040.01510.06440.01440.00440.0771-0.0020.06849.2064-4.21659.7327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 547 through 600 )A547 - 600
2X-RAY DIFFRACTION2chain 'A' and (resid 601 through 640 )A601 - 640
3X-RAY DIFFRACTION3chain 'A' and (resid 641 through 697 )A641 - 697
4X-RAY DIFFRACTION4chain 'A' and (resid 698 through 743 )A698 - 743
5X-RAY DIFFRACTION5chain 'A' and (resid 744 through 791 )A744 - 791
6X-RAY DIFFRACTION6chain 'B' and (resid 542 through 610 )B542 - 610
7X-RAY DIFFRACTION7chain 'B' and (resid 611 through 630 )B611 - 630
8X-RAY DIFFRACTION8chain 'B' and (resid 631 through 791 )B631 - 791

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