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- PDB-1b2i: KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF ... -

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Basic information

Entry
Database: PDB / ID: 1b2i
TitleKRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID (AMCHA) COMPLEX
ComponentsPROTEIN (PLASMINOGEN)
KeywordsHYDROLASE / SERINE PROTEASE / FIBRINOLYSIS / LYSINE-BINDING DOMAIN / PLASMINOGEN / KRINGLE 2
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / kinase binding / Schaffer collateral - CA1 synapse / 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 / : / protease binding / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / 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 ...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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMIC SIMULATED ANNEALING
AuthorsMarti, D.N. / Schaller, J. / Llinas, M.
Citation
Journal: Biochemistry / Year: 1999
Title: Solution structure and dynamics of the plasminogen kringle 2-AMCHA complex: 3(1)-helix in homologous domains.
Authors: Marti, D.N. / Schaller, J. / Llinas, M.
#1: Journal: Biochemistry / Year: 1997
Title: Ligand Preferences of Kringle 2 and Homologous Domains of Human Plasminogen: Canvassing Weak, Intermediate and High-Affinity Binding Sites by 1H-NMR
Authors: Marti, D.N. / Hu, C.K. / An, S.S.A. / Von Haller, P. / Schaller, J. / Llinas, M.
#2: Journal: Biochemistry / Year: 1996
Title: Recombinant Gene Expression and 1H NMR Characteristics of the Kringle (2+3) Supermodule: Spectroscopic/Functional Individuality of Plasminogen Kringle Domains
Authors: Soehndel, S. / Hu, C.K. / Marti, D. / Affolter, M. / Schaller, J. / Llinas, M. / Rickli, E.E.
#3: Journal: Eur.J.Biochem. / Year: 1994
Title: Expression, Purification and Characterization of the Recombinant Kringle 2 and Kringle 3 Domains of Human Plasminogen and Analysis of Their Binding Affinity for Omega-Aminocarboxylic Acids
Authors: Marti, D. / Schaller, J. / Ochensberger, B. / Rickli, E.E.
History
DepositionSep 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Nov 3, 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 16, 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
A: PROTEIN (PLASMINOGEN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8092
Polymers9,6521
Non-polymers1571
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150TOTAL ENERGY, RAMACHANDRAN PLOT, LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (PLASMINOGEN)


Mass: 9651.812 Da / Num. of mol.: 1 / Fragment: KRINGLE 2 DOMAIN / Mutation: C181T, E182S, C188G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin
#2: Chemical ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121NOESY
131TOCSY
1413D-NOESY HSQC
1513D-TOCSY HSQC
161HNCA
171HN(CO)CA
181HCC(CO)NH

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: SEE PAPER / pH: 5.1 / Pressure: AMBIENT / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Bruker DRX600BrukerDRX6006002

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Processing

NMR software
NameVersionDeveloperClassification
CHARMM23.2BROOKS ET AL., J. COMPUT. CHEM. 4, 187-217 (1983)refinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMIC SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: TOTAL ENERGY, RAMACHANDRAN PLOT, LEAST RESTRAINT VIOLATION
Conformers calculated total number: 150 / Conformers submitted total number: 20

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