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- PDB-2o8w: Crystal Structure and Binding Epitopes of Urokinase-type Plasmino... -

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Basic information

Entry
Database: PDB / ID: 2o8w
TitleCrystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors
ComponentsUrokinase plasminogen activator
KeywordsHYDROLASE / urokinase-type plasminogen activator / benzamidine / phenylguanidine / contact area
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 / kinase activity / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / phosphorylation / 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. / EGF-like domain signature 1. ...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
1-phenylguanidine / Urokinase-type plasminogen activator / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsZhao, G. / Yuan, C. / Jiang, L. / Huang, Z. / Huang, M.
CitationJournal: To be Published
Title: Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors
Authors: Zhao, G. / Yuan, C. / Jiang, L. / Huang, Z. / Huang, M.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8524
Polymers28,4261
Non-polymers4253
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.875, 120.875, 42.591
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 plasminogen activator / UPA


Mass: 28426.373 Da / Num. of mol.: 1 / Fragment: residues 16-250 (159-411) / Mutation: C122A/N145Q/S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33
References: UniProt: Q5PY49, UniProt: P00749*PLUS, u-plasminogen activator
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PL0 / 1-phenylguanidine


Mass: 135.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.05M sodium citrate (pH4.5) buffer, 1.95M (NH4)2SO4, 0.05% NaN3, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→60.24 Å / Num. all: 35982 / Num. obs: 15503 / % possible obs: 79.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.88 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.1136 / Rsym value: 0.1136 / Net I/σ(I): 7.34
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.1136 / Mean I/σ(I) obs: 7.34 / Num. unique all: 13005 / Rsym value: 0.1136 / % possible all: 79.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→60.24 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2081182.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 797 5.1 %RANDOM
Rwork0.213 ---
obs0.213 15503 79.5 %-
all-35982 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.8931 Å2 / ksol: 0.377311 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å2-1.03 Å20 Å2
2---3.52 Å20 Å2
3---7.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.86→60.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 28 292 2252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.86→1.98 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.356 567 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2PG4_par.txt
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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