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- PDB-6nmb: Tranexamic Acid is an Active Site Inhibitor of Urokinase Plasmino... -

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Basic information

Entry
Database: PDB / ID: 6nmb
TitleTranexamic Acid is an Active Site Inhibitor of Urokinase Plasminogen Activator
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / serine protease / fibrinolysis / inhibitor
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / 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
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / NITRATE ION / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLaw, R.H.P. / Wu, G.
CitationJournal: Blood Adv / Year: 2019
Title: Tranexamic acid is an active site inhibitor of urokinase plasminogen activator.
Authors: Wu, G. / Mazzitelli, B.A. / Quek, A.J. / Veldman, M.J. / Conroy, P.J. / Caradoc-Davies, T.T. / Ooms, L.M. / Tuck, K.L. / Schoenecker, J.G. / Whisstock, J.C. / Law, R.H.P.
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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: Urokinase-type plasminogen activator
B: Urokinase-type plasminogen activator
C: Urokinase-type plasminogen activator
D: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,91112
Polymers128,0344
Non-polymers8778
Water5,423301
1
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2283
Polymers32,0081
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2283
Polymers32,0081
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2283
Polymers32,0081
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2283
Polymers32,0081
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.043, 65.446, 111.136
Angle α, β, γ (deg.)90.000, 97.415, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Urokinase-type plasminogen activator / uPA


Mass: 32008.475 Da / Num. of mol.: 4 / Fragment: UNP residues 164-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pSecTag / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / Tissue (production host): Embryonic kidney / References: UniProt: P00749, u-plasminogen activator
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H15NO2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.06 Å3/Da / Density % sol: 40.22 % / Description: small rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 0.1 M Tris bicine, 25% v/v PEG500, 10% v/v PEG20000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.56 Å / Num. obs: 42244 / % possible obs: 89.99 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.087 / Rrim(I) all: 0.226 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.42 Å / CC1/2: 0.817 / Rpim(I) all: 0.439 / Rrim(I) all: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VNT

2vnt


Resolution: 2.3→48.56 Å / SU ML: 0.3162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4776
RfactorNum. reflection% reflection
Rfree0.2712 1987 4.73 %
Rwork0.221 --
obs0.2233 42014 89.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7666 0 60 301 8027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01687942
X-RAY DIFFRACTIONf_angle_d1.845110810
X-RAY DIFFRACTIONf_chiral_restr0.11681190
X-RAY DIFFRACTIONf_plane_restr0.00891374
X-RAY DIFFRACTIONf_dihedral_angle_d22.64282852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.36891330.31172661X-RAY DIFFRACTION83.55
2.36-2.420.36241490.28843028X-RAY DIFFRACTION96.42
2.42-2.490.31651540.28073092X-RAY DIFFRACTION98.75
2.49-2.570.34071560.28213130X-RAY DIFFRACTION99.52
2.57-2.660.32761200.25872412X-RAY DIFFRACTION98.25
2.66-2.770.3396990.25431999X-RAY DIFFRACTION97.49
2.77-2.890.30141570.24933151X-RAY DIFFRACTION99.7
2.89-3.050.3111570.24373166X-RAY DIFFRACTION99.7
3.05-3.240.28691560.2253139X-RAY DIFFRACTION99.76
3.24-3.490.26211220.20482468X-RAY DIFFRACTION77.01
3.49-3.840.25131290.19612631X-RAY DIFFRACTION82.88
3.84-4.390.20821370.16922749X-RAY DIFFRACTION86.05
4.39-5.540.20081560.16753174X-RAY DIFFRACTION98.96
5.54-48.570.23151620.20213227X-RAY DIFFRACTION98.2
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)
14.3950763069-1.580395196241.505187566092.76796529517-0.5306899916032.26244423538-0.2051172602490.157542642959-0.808055707970.3565641826880.3677238163770.4897197092930.0677305450322-0.130260766522-0.2107775316230.175421691171-0.04828005276860.01232528133570.2610930315890.04381099759760.52132082750449.7355239244-20.8037041064119.310150794
21.256714811040.04955876602960.6721203963821.67124439088-0.3785273141372.446524359360.00756767106468-0.1716119686250.2178660116750.3382138316960.0831111527743-0.0928096256713-0.263176433308-0.225005483581-0.0829533279840.1468898678230.02788140302420.03167774723530.208155615346-0.03226462749540.34246394741659.5878781491-11.0290629503123.388491507
32.199300292440.237072947838-0.6475232999712.08535662325-0.089761264182.491816860330.105476991687-0.0786428799074-0.172310979335-0.231822959088-0.01411403398160.165020612336-0.0725841947611-0.0386930300961-0.04277381273630.1244252835820.00410806983976-0.05207426271480.143436230018-0.01128320856080.19443978677853.4953433627-10.862732167105.751809275
43.49241724425-0.569406497351-0.8107726107932.440022530180.2106610756913.751469738860.173039012260.1714709708340.31209649067-0.263164632093-0.09329921464590.338579829770.028915789776-0.173380817059-0.09681503933580.15553238575-0.008750018861270.01182695607760.1264927844310.01313718333050.23918800067858.4590750347-12.0177837475104.619503077
51.661594868890.157818131328-1.050454727781.18297341145-0.3355042387060.981707976811-0.12205724591-0.0769832121156-0.209857518418-0.2021640672890.0577617851-0.1585866932080.0201742125362-0.2082965948650.09194527170770.0209382268513-0.0190235241014-0.02907546709740.163333335578-0.06197467139090.44312845544863.3375785394-16.3456408751111.89226659
66.175723309692.196821192173.307428415232.084723726990.2473247134822.40403014633-0.00389983421680.262427416398-1.300334553620.2424488447460.41420545999-0.5936592701140.4589278019960.312921772392-0.4403958268070.2800803674330.07451090122150.02535812736760.283687609548-0.09775605960890.45093853607660.2312015228-51.9696111965155.687395984
73.39988490582-1.001877704060.1820431296513.228636349350.7333201246792.737192346550.0300537641710.4013491538420.647010894574-0.625600241833-0.0860086013792-0.389350223015-0.3420478127090.1970257174620.08205751776230.321493420452-0.04802607987370.02240046497460.2522048065390.06724530534140.16893417187453.4984713498-37.4304956054148.806662036
82.11827271709-0.29737625145-0.1664063619582.2457995385-0.384621236981.206536032620.01223544049840.0588441218314-0.0626765540538-0.1067958934420.07732190786880.180308604850.0703415107321-0.0499369627324-0.08529855581890.210967685468-0.0210246383675-0.05007341049130.160579842178-0.01628992101990.14539442636947.371532113-45.7621838022156.184929959
93.100242449141.326170456451.480847474139.651858563755.607019418465.837695086590.0445602251968-0.07569836021630.484923658939-0.2106663193960.393348735497-0.640151252977-0.1870161309820.244664997209-0.3124164344860.154860711988-0.01465985873050.04500010698120.2343456623750.01080390780910.24518955658665.3445373834-35.0521737336161.91967394
101.15578888932-0.13037816219-0.1170035154521.189891318271.110545414641.110036441910.259958662674-0.20260961614-0.3989955142810.632629558328-0.4765481880580.03971318388080.0729511779738-0.06775365026420.09306610611510.409382681025-0.01720106004030.007068614775290.3407946705610.02224109503740.063888008767550.3023339228-45.2963350855175.522043658
113.148170834980.421504048427-1.101809925512.70969581322-0.1697745221043.25542959467-0.112507048662-0.3505366657630.223352992320.2545309826950.0338978196239-0.2001857655620.1895991508970.07641765137890.1231705525030.202514324256-0.00447768689676-0.01618690882330.161546038574-0.06702355284280.15519042272951.7592061116-41.9005734952170.931268156
121.72137593316-0.707779641664-0.7168213872352.71531883948-0.3056125266020.706211325731-0.0565990543571-0.173370103468-0.561227576857-0.00535953992911-0.163254857015-0.02318225510190.334667448172-0.1486713080370.06172612376170.252066223891-0.0462793475013-0.02699888811160.2359965564290.0353231037722-0.082720988315849.7542876231-51.2113982448162.138648524
133.658355900830.992491290020.8616502543452.534329656040.770556511481.33831417722-0.07006036438890.128660444455-0.1779951414620.1803280934760.1449643138170.411457967575-0.06124306081920.0934860258273-0.1048067421010.1638778426390.01177550086970.02922414739750.1979414089180.06213251808650.052626836506945.0807161618-43.1603837153164.654827551
143.29715460739-1.05393684527-1.084543263360.671841108668-0.536979620293.0217863747-0.0817848097463-0.06278229052290.6945263905290.2022490531960.292172844404-0.70831283086-0.3323106428560.0841750261788-0.2392720898520.168102399182-0.0497281149931-0.003935101947640.226882328961-0.09024818578490.5109689626929.8353279157-32.9581745664120.854930219
153.870269301021.025959875070.4600623979943.870028592240.6326586494693.47835745666-0.0227778247122-0.72536247729-0.6684368338420.5760192007850.0569585224883-0.2258859783890.4313539001280.254322921823-0.02868505832410.2431620139620.05094399426760.02681619062880.3399257814490.08000378903580.36677679929723.6351278605-44.0421095173126.969897504
162.21556360359-0.627449606570.4401995882991.64544050058-0.4886091074831.531147475420.0538244385328-0.02134327180540.0460404512466-0.01677264668120.04066255102960.15030675254-0.0177982360443-0.0053507891031-0.07461218745470.128218009955-0.01005174122550.03479642653140.139386290286-0.001953072065940.35254601796621.8423174282-37.7903009637111.456396884
172.014846651540.06334073800360.252042710720.716704717526-0.02378515535240.08687509010930.04301083645150.001259972251850.034120114151-0.485233377988-0.07595293609010.476103140819-0.05632538553150.05710363428650.0632694459933-0.150889025331-0.008290304386890.07390951485960.198635030020.04617082186850.6106346776417.430313098-34.8486379125111.997404237
184.747733618443.91833785267-4.907906603483.34237160804-4.046516478915.078175762060.263955733090.4177983909221.032548557580.07015772094880.628474986650.792573183596-0.357135631982-0.55616070523-0.8608482811940.3072568411750.0568862821750.02290217389290.3216940217690.03575690930120.5005760236385.752576625735.00633760627157.866780031
196.84747498734-0.761920060693-0.3399238733017.881274679165.513492849438.38188757797-0.2857494428040.555201434114-0.3744817831860.536628665177-0.1905146857880.5513523377170.502879335407-0.451724638270.4122509207720.239298625142-0.08157887603370.002308360077420.3682638667250.02696459392360.1391491262628.37875660387-6.12471738841150.788375231
203.356071560140.3694021226560.1513528521972.637225683030.3455423987952.326576799770.0468645782170.525864902689-0.0338355350381-0.4235006399840.119182288194-0.0412471767030.0930098868482-0.124094420114-0.141329092750.249142985764-0.01271644538980.001833036943330.2490392693730.01680160312220.14857452783116.5416680534-7.03095012932150.314027211
212.220214060980.0472274910364-0.05937863614271.984124969441.114057690130.644982989575-0.09151663102020.1423521856580.474437255467-0.2515741815490.175676017758-0.20918756127-0.1234415856270.165706317676-0.1006012131340.250944874569-0.0274514939343-0.01536315070360.2156889142710.05715558743480.30735149775916.97868352337.5259550503161.04020538
221.306348051421.37720385645-0.9846916999127.75860291895-3.666124156013.01437756867-0.07543537969810.05997363296590.0430843826368-0.3866587646950.2883174711790.2109836984440.2528605725920.137668289633-0.2005462963510.2236784868590.0466627512902-0.003166522524520.256669317381-0.1051568432480.3082572777511.21643947404-10.6473212951161.888784201
231.92662038652-0.249833792998-0.2424466646530.872466364438-0.4323332694660.497544351179-0.0266856442845-0.2157397669620.08402524556240.385641341987-0.0888482421250.00762332394748-0.01186619350980.168248990810.119659555330.2826184005260.00841390098125-0.001454550484370.292682199198-0.04138439720680.090740295749818.5522147536-1.31285623966174.502711872
242.68865338062-1.1427969060.125692946166.724921938674.216437489246.95835079392-0.392700277597-0.2839870141430.2931138375840.6063018509810.3174371150090.5087262563580.663249059392-0.002167153970350.03816017888740.172762977123-0.03234989331660.02024744937170.281729118059-0.05317721769430.3509288663428.09980053923-4.01564223073170.05922056
253.0284599549-0.5621765136790.4304109529075.24526658714-0.9935744442612.0051702574-0.15919336232-0.1785150995660.636902840876-0.2458489426880.09104576495760.0281013291942-0.0056591355544-0.09484106703320.06196531194820.118964773804-0.03184595596740.005127816631080.198973719735-0.0724084679510.21366557939716.70427179335.5984955245162.221849049
265.044746368042.48020027109-1.89010761772.72169441395-2.171265443073.621786604310.01631840389770.0910940440913-0.09494009092970.0513122292074-0.032688397403-0.2667109989730.0726998771333-0.1051635844670.02687199926240.1539657256920.0359683275011-0.00328001595850.0898638156146-0.01072191926170.22660406155821.4558363422-2.62777149672164.871301798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 172 )
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 243 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 29 )
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 90 )
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 172 )
11X-RAY DIFFRACTION11chain 'B' and (resid 173 through 197 )
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 215 )
13X-RAY DIFFRACTION13chain 'B' and (resid 216 through 243 )
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 35 )
15X-RAY DIFFRACTION15chain 'C' and (resid 36 through 90 )
16X-RAY DIFFRACTION16chain 'C' and (resid 91 through 197 )
17X-RAY DIFFRACTION17chain 'C' and (resid 198 through 243 )
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 23 )
19X-RAY DIFFRACTION19chain 'D' and (resid 24 through 38 )
20X-RAY DIFFRACTION20chain 'D' and (resid 39 through 115 )
21X-RAY DIFFRACTION21chain 'D' and (resid 116 through 140 )
22X-RAY DIFFRACTION22chain 'D' and (resid 141 through 155 )
23X-RAY DIFFRACTION23chain 'D' and (resid 156 through 184 )
24X-RAY DIFFRACTION24chain 'D' and (resid 185 through 197 )
25X-RAY DIFFRACTION25chain 'D' and (resid 198 through 215 )
26X-RAY DIFFRACTION26chain 'D' and (resid 216 through 242 )

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