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- PDB-8f7u: Macrocyclic Plasmin Inhibitor -

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Basic information

Entry
Database: PDB / ID: 8f7u
TitleMacrocyclic Plasmin Inhibitor
ComponentsActivation peptide
KeywordsHydrolase/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 / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / 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 / 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 / protease binding / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-GGI / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 new macrocyclicplasmin inhibitors
Authors: Guojie, W.
History
DepositionNov 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activation peptide
B: Activation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86911
Polymers54,6392
Non-polymers2,2309
Water8,377465
1
A: Activation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2924
Polymers27,3191
Non-polymers9733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5777
Polymers27,3191
Non-polymers1,2576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.710, 50.305, 92.456
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Activation peptide


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
#2: Chemical ChemComp-GGI / (5S,8R,18S,21R)-N-{[4-(aminomethyl)phenyl]methyl}-21-[(benzenesulfonyl)amino]-3,11,20-trioxo-2,5,8,12,19-pentaazatetracyclo[21.2.2.2~5,8~.2~13,16~]hentriaconta-1(25),13,15,23,26,28-hexaene-18-carboxamide


Mass: 780.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H48N8O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 14% PEG 4000, 90-140 mM Ammonium sulfate, 100 mM MES
PH range: 4.5 - 5.0

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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: Apr 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→92.32 Å / Num. obs: 76283 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.81 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Rsym value: 0.044 / Net I/av σ(I): 9.1 / Net I/σ(I): 20.6 / Num. measured all: 484926
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
1.47-1.556.40.2023.770130109840.0860.220.2026.899.1
1.55-1.646.30.1474.966506104920.0630.160.1479100
1.64-1.766.10.1126.36058698910.0490.1220.11211.4100
1.76-1.96.40.0818.45905291970.0350.0880.08116100
1.9-2.086.50.062115520284550.0260.0680.06222.1100
2.08-2.326.30.0513.44844577160.0210.0540.0527.1100
2.32-2.686.30.044154245267820.0190.0480.04430.9100
2.68-3.286.70.037173850757610.0160.040.03738.7100
3.28-4.656.30.03218.72809544800.0140.0350.03244.8100
4.65-48.6386.30.03214.91595125250.0140.0350.0324499.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.19.2-4258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→48.64 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 3817 5.01 %
Rwork0.1728 72443 -
obs0.1737 76260 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.49 Å2 / Biso mean: 22.1898 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.47→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 244 468 4433
Biso mean--22.31 29.15 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.490.23131400.20452568270897
1.49-1.510.22151420.189926372779100
1.51-1.530.20851510.178827122863100
1.53-1.550.20051440.177826432787100
1.55-1.570.19141510.175827062857100
1.57-1.60.20741400.174626222762100
1.6-1.620.18451330.165727192852100
1.62-1.650.20641390.16926022741100
1.65-1.680.18651410.163827172858100
1.68-1.710.20731280.175326542782100
1.71-1.750.21191190.192927352854100
1.75-1.790.20331440.182326512795100
1.79-1.830.22121350.177726522787100
1.83-1.870.19741570.172127012858100
1.87-1.920.20831250.168926992824100
1.92-1.980.19081200.166226872807100
1.98-2.050.19051220.172126892811100
2.05-2.120.17941350.174827262861100
2.12-2.20.17911320.16426752807100
2.2-2.30.1711500.168726762826100
2.3-2.430.20611520.17327022854100
2.43-2.580.19221490.1826812830100
2.58-2.780.21621500.181926782828100
2.78-3.060.17311830.179526832866100
3.06-3.50.17851530.172427012854100
3.5-4.410.17221080.155627572865100
4.41-48.640.18161740.177127702944100
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)
12.2460.410.29652.89290.84461.6361-0.0095-0.00970.0615-0.06820.0149-0.7105-0.00170.4847-0.00760.1094-0.018-0.01520.25490.00970.283442.1934-26.780934.4584
21.70160.00830.03822.28930.26332.216-0.04310.2263-0.0565-0.28380.0422-0.4429-0.0630.39320.06410.1531-0.00560.04330.1831-0.01250.203937.5287-31.341828.2173
32.4861-0.4091-2.17191.58870.2712.04840.0667-0.22490.21310.16950.0229-0.1434-0.24850.2396-0.10680.2154-0.0411-0.02830.21870.00090.165132.3333-20.608140.5527
44.4295-1.2799-1.01442.67630.6231.5736-0.0644-0.11990.18490.13090.00190.0534-0.1270.07630.05980.17460.0009-0.02610.1104-0.00210.085420.6153-19.082939.4533
51.1753-0.0742-0.1931.78720.53691.64810.0268-0.0603-0.08850.0588-0.0381-0.09330.01540.11870.01620.1015-0.0069-0.01660.11090.02040.095629.8241-29.952736.1605
60.7830.0003-0.05631.3130.30170.7676-0.01490.0070.01810.05040.0261-0.0266-0.00910.012-0.00590.06720.0134-0.0080.0834-0.00240.084620.835-5.164510.7285
72.60450.1983-0.68092.18830.90893.00670.0448-0.2376-0.07050.28670.0123-0.09160.20420.12790.03840.15380.0187-0.02570.11760.00520.093219.9697-2.895822.8699
81.57390.2070.30850.766-0.00610.77050.00340.03120.1254-0.0197-0.01770.0568-0.0687-0.0373-0.00390.07870.01870.00380.0788-0.01020.090912.96570.30259.2909
90.7321-0.9080.8534.8208-3.14982.15530.2942-0.424-0.34790.57270.03380.31550.7238-0.6078-0.22240.3961-0.0701-0.05590.27380.04510.207820.049-18.423618.8856
100.80330.32170.58281.29520.32640.80290.0342-0.03520.03450.024-0.06750.11590.0206-0.1070.03860.06310.00910.00510.0843-0.01140.08995.2539-6.64547.695
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 678 )A601 - 678
3X-RAY DIFFRACTION3chain 'A' and (resid 679 through 710 )A679 - 710
4X-RAY DIFFRACTION4chain 'A' and (resid 711 through 737 )A711 - 737
5X-RAY DIFFRACTION5chain 'A' and (resid 738 through 791 )A738 - 791
6X-RAY DIFFRACTION6chain 'B' and (resid 542 through 600 )B542 - 600
7X-RAY DIFFRACTION7chain 'B' and (resid 601 through 640 )B601 - 640
8X-RAY DIFFRACTION8chain 'B' and (resid 641 through 684 )B641 - 684
9X-RAY DIFFRACTION9chain 'B' and (resid 685 through 697 )B685 - 697
10X-RAY DIFFRACTION10chain 'B' and (resid 698 through 791 )B698 - 791

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