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- PDB-4fu8: Crystal Structure of the Urokinase -

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Basic information

Entry
Database: PDB / ID: 4fu8
TitleCrystal Structure of the Urokinase
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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
naphthalene-2-carboximidamide / ACETATE ION / SUCCINIC ACID / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.1Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5069
Polymers27,7161
Non-polymers7918
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.299, 52.782, 79.787
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 , 5 types, 249 molecules

#2: Chemical ChemComp-2UP / naphthalene-2-carboximidamide


Mass: 170.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
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 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: 2.197→19.95 Å / Num. obs: 11520 / % possible obs: 92.8 % / Biso Wilson estimate: 26.43 Å2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.95 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9041 / Occupancy max: 1 / Occupancy min: 0.01 / SU R Cruickshank DPI: 0.405 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 554 4.81 %RANDOM
Rwork0.1927 ---
obs0.1948 11520 93.38 %-
Displacement parametersBiso max: 94.36 Å2 / Biso mean: 21.5575 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.3186 Å20 Å20 Å2
2--1.6094 Å20 Å2
3----1.2908 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 49 241 2222
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d926SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes300HARMONIC5
X-RAY DIFFRACTIONt_it2049HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
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_contact2482SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2049HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg2782HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion2.56
LS refinement shellResolution: 2.2→2.41 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2698 151 5.44 %
Rwork0.2125 2624 -
all0.2157 2775 -
obs--93.38 %
Refinement TLS params.Method: refined / Origin x: -13.973 Å / Origin y: -9.9287 Å / Origin z: -10.8999 Å
111213212223313233
T-0.0368 Å2-0.002 Å20.0046 Å2--0.0221 Å2-0.0085 Å2---0.0263 Å2
L0.4052 °20.119 °20.0581 °2-0.9735 °2-0.2264 °2--0.388 °2
S0.0117 Å °0.0183 Å °-0.0116 Å °-0.0007 Å °-0.0083 Å °-0.024 Å °0.0135 Å °0.0068 Å °-0.0034 Å °
Refinement TLS groupSelection details: { A|* }

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