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- PDB-6ag9: Crystal structure of uPA in complex with 3,5-bis(azanyl)-6-(1-ben... -

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Basic information

Entry
Database: PDB / ID: 6ag9
TitleCrystal structure of uPA in complex with 3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-N-carbamimidoyl-pyrazine-2- carboxamide
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / Urokinase / Amiloride
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 signaling receptor activity / regulation of smooth muscle cell migration ...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 signaling receptor activity / regulation of smooth muscle cell migration / 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 / 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-9XF / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBuckley, B. / Jiang, L.G. / Majed, H. / Huang, M.D. / Kelso, M. / Ranson, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)APP1100432 Australia
CitationJournal: To Be Published
Title: uPA-HMA
Authors: Buckley, B. / Jiang, L.G. / Huang, M.D. / Kelso, M. / Ranson, M.
History
DepositionAug 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8503
Polymers28,4421
Non-polymers4072
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.560, 120.560, 42.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Urokinase-type plasminogen activator / 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-9XF / 3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-N-carbamimidoyl-pyrazine-2-carboxamide


Mass: 311.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.63→34.8 Å / Num. obs: 28223 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 3.8
Reflection shellResolution: 1.63→1.67 Å / Rmerge(I) obs: 0.633 / Num. unique obs: 2106

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVA

4dva


Resolution: 1.63→28.871 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1380 4.89 %RANDOM
Rwork0.182 ---
obs0.1831 28220 98.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.68 Å2 / Biso mean: 30.1965 Å2 / Biso min: 12.97 Å2
Refinement stepCycle: final / Resolution: 1.63→28.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 28 149 2110
Biso mean--34.93 38.99 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.63-1.68830.32281672679100
1.6883-1.75590.30191482709100
1.7559-1.83580.29171412711100
1.8358-1.93250.251190.21322718100
1.9325-2.05360.23111340.19582718100
2.0536-2.21210.23511640.19062703100
2.2121-2.43460.17841350.1773269299
2.4346-2.78660.23171240.1844273699
2.7866-3.50990.1981210.1657269198
3.5099-28.870.15691270.1611248391

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