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- PDB-2l0s: Solution Structure of Human Plasminogen Kringle 3 -

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Basic information

Entry
Database: PDB / ID: 2l0s
TitleSolution Structure of Human Plasminogen Kringle 3
ComponentsPlasminogenPlasmin
KeywordsBLOOD CLOTTING / Plasminogen / Kringle Domain / SERINE PROTEASE / FIBRINOLYSIS
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site ...Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsChristen, M.T. / Frank, P. / Schaller, J. / Llinas, M.
CitationJournal: Biochemistry / Year: 2010
Title: Human plasminogen kringle 3: solution structure, functional insights, phylogenetic landscape.
Authors: Christen, M.T. / Frank, P. / Schaller, J. / Llinas, M.
History
DepositionJul 15, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen


Theoretical massNumber of molelcules
Total (without water)9,5251
Polymers9,5251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Plasminogen / Plasmin


Mass: 9525.428 Da / Num. of mol.: 1 / Fragment: UNP residues 272-354, Kringle 3 Domain / Mutation: C43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Expressed in 15N-labeled M9 minimal medium / Gene: PLG / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P00747, plasmin

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1413D HNHA
1513D HNHB
1612D 1H-1H COSY
1712D 1H-1H TOCSY
1812D 1H-1H NOESY
2912D 1H-15N HSQC
NMR detailsText: The structure was determined using data collected at pH* 5.7

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Sample preparation

DetailsContents: 1.0 mM [U-97% 15N] hPgn rK3-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: hPgn rK3-1 / Isotopic labeling: [U-97% 15N]
Sample conditions
Conditions-IDIonic strengthPressure (kPa)Temperature (K)
10 ambient 298 K
20 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
xwinnmr2.6Bruker Biospincollection
Felix98Accelrys Software Inc.processing
CcpNMR1CCPNpeak picking
CcpNMR1CCPNchemical shift assignment
CcpNMR1CCPNdata analysis
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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