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- PDB-5zc5: uPA-NU-09F -

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Basic information

Entry
Database: PDB / ID: 5zc5
TitleuPA-NU-09F
ComponentsUrokinase-type plasminogen activator chain B
KeywordsHYDROLASE / uPA / 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 / 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
Chem-09I / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, L.G. / Buckley, B.J. / Huang, M.D. / Kelso, M.J. / Ranson, M.
CitationJournal: J. Med. Chem. / Year: 2018
Title: 6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer.
Authors: Buckley, B.J. / Aboelela, A. / Minaei, E. / Jiang, L.X. / Xu, Z. / Ali, U. / Fildes, K. / Cheung, C.Y. / Cook, S.M. / Johnson, D.C. / Bachovchin, D.A. / Cook, G.M. / Apte, M. / Huang, M. / ...Authors: Buckley, B.J. / Aboelela, A. / Minaei, E. / Jiang, L.X. / Xu, Z. / Ali, U. / Fildes, K. / Cheung, C.Y. / Cook, S.M. / Johnson, D.C. / Bachovchin, D.A. / Cook, G.M. / Apte, M. / Huang, M. / Ranson, M. / Kelso, M.J.
History
DepositionFeb 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8542
Polymers28,4421
Non-polymers4111
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.698, 120.698, 42.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Urokinase-type plasminogen activator chain B / uPA


Mass: 28442.373 Da / Num. of mol.: 1 / Mutation: C122A, N145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator
#2: Chemical ChemComp-09I / 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(4-fluoranyl-1-benzofuran-2-yl)pyrazine-2-carboxamide


Mass: 411.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22FN7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 18272 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.796

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVE

4dve


Resolution: 1.9→60 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.172 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 875 4.8 %RANDOM
Rwork0.203 ---
obs0.205 17397 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0.4 Å20 Å2
2---0.81 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 30 60 2023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192019
X-RAY DIFFRACTIONr_bond_other_d0.0020.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9622740
X-RAY DIFFRACTIONr_angle_other_deg0.92234293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45123.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3511513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02475
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6643.578978
X-RAY DIFFRACTIONr_mcbond_other1.6593.577977
X-RAY DIFFRACTIONr_mcangle_it2.735.3611219
X-RAY DIFFRACTIONr_mcangle_other2.7295.3621220
X-RAY DIFFRACTIONr_scbond_it1.8693.9251041
X-RAY DIFFRACTIONr_scbond_other1.8683.9241042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1445.7641521
X-RAY DIFFRACTIONr_long_range_B_refined4.81929.1222265
X-RAY DIFFRACTIONr_long_range_B_other4.71529.0672257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 63 -
Rwork0.234 1301 -
obs--99.78 %

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