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- PDB-4fu9: Crystal Structure of the Urokinase -

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Basic information

Entry
Database: PDB / ID: 4fu9
TitleCrystal Structure of the Urokinase
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex ...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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex / regulation of smooth muscle cell migration / 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 / 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
6-[(Z)-AMINO(IMINO)METHYL]-N-PHENYL-2-NAPHTHAMIDE / ACETATE ION / SUCCINIC ACID / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V.
CitationJournal: To be Published
Title: Crystal Structure of the Urokinase
Authors: Kang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,08214
Polymers27,7161
Non-polymers1,36613
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.100, 52.400, 80.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Urokinase-type plasminogen activator / U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type ...U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type plasminogen activator short chain A / Urokinase-type plasminogen activator chain B


Mass: 27715.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Escherichia coli (E. coli) / References: UniProt: P00749, u-plasminogen activator

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Non-polymers , 6 types, 347 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-675 / 6-[(Z)-AMINO(IMINO)METHYL]-N-PHENYL-2-NAPHTHAMIDE / 6-(N-PHENYLCARBAMYL)-2-NAPHTHALENECARBOXAMIDINE


Mass: 289.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N3O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15 M Li2SO4, 20% polyethylene glycol MW 4000 in succinate buffer, pH 4.8-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291 - 298.0K
PH range: 4.8-6.0

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 30737 / % possible obs: 97.9 % / Rmerge(I) obs: 0.08 / Χ2: 0.855 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.640.3417730.55186.7
1.64-1.680.30220330.536197.5
1.68-1.720.2720070.536197.9
1.72-1.770.21920380.574199.1
1.77-1.830.19320220.594198.6
1.83-1.90.1620580.643199.7
1.9-1.970.12920840.651199.8
1.97-2.060.11120600.739199.8
2.06-2.170.09620870.803199.8
2.17-2.310.09220760.889199.6
2.31-2.490.07920660.982198.9
2.49-2.740.0820761.103199
2.74-3.130.06820921.145198.7
3.13-3.940.05521171.292198.1
3.94-400.0521481.265194.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→18.99 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9511 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1535 5 %RANDOM
Rwork0.1504 ---
obs0.152 30696 97.97 %-
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 15.1059 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.1362 Å20 Å20 Å2
2--1.033 Å20 Å2
3----0.8967 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→18.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 89 334 2345
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d866SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes642HARMONIC5
X-RAY DIFFRACTIONt_it4001HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4753SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4001HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7174HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.49
X-RAY DIFFRACTIONt_other_torsion13.32
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2652 131 4.8 %
Rwork0.207 2601 -
all0.2096 2732 -
obs--97.97 %

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