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- PDB-1c5g: PLASMINOGEN ACTIVATOR INHIBITOR-1 -

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Basic information

Entry
Database: PDB / ID: 1c5g
TitlePLASMINOGEN ACTIVATOR INHIBITOR-1
ComponentsPLASMINOGEN ACTIVATOR INHIBITOR-1
KeywordsBLOOD CLOTTING / SERPIN / SERINE PROTEASE INHIBITOR / PLASMA / PLASMINOGEN ACTIVATION / GLYCOPROTEIN / POLYMORPHISM
Function / homology
Function and homology information


positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of endopeptidase activity ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / negative regulation of blood coagulation / positive regulation of monocyte chemotaxis / regulation of signaling receptor activity / Dissolution of Fibrin Clot / replicative senescence / ECM proteoglycans / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / negative regulation of cell migration / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / protease binding / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsGoldsmith, E.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Engineering of plasminogen activator inhibitor-1 to reduce the rate of latency transition.
Authors: Tucker, H.M. / Mottonen, J. / Goldsmith, E.J. / Gerard, R.D.
#1: Journal: Nature / Year: 1992
Title: Structural Basis of Latency in Plasminogen Activator Inhibitor-1
Authors: Mottenen, J. / Strand, A. / Symersky, J. / Sweet, R.M. / Danley, D.E. / Geoghegan, K.F. / Gerard, R.D. / Goldsmith, E.J.
#2: Journal: Proteins / Year: 1991
Title: Preliminary X-Ray Analysis of Crystals of Plasminogen Activator Inhibitor-1
Authors: Goldsmith, E.J. / Sheng-Cheng, C. / Danley, D.E. / Gerard, R.D. / Geoghegan, K.F. / Mottenen, J. / Strand, A.
History
DepositionDec 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)45,1101
Polymers45,1101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.590, 47.840, 62.880
Angle α, β, γ (deg.)90.00, 107.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PLASMINOGEN ACTIVATOR INHIBITOR-1 / PAI-1


Mass: 45109.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LATENT FORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPAIST-7HS / Production host: Escherichia coli (E. coli) / References: UniProt: P05121

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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: 2.5 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.54
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
FASTdata scaling
X-PLORphasing
RefinementResolution: 2.6→6 Å / Data cutoff high absF: 2
Details: PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974); PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976); NONBONDED TERMS JORGENSEN JACS 103:3976; W/ RC1-4 = 1.80 EC1-4 = 0.1
Num. reflection% reflection
obs12239 87.4 %
Displacement parametersBiso mean: 28.38 Å2
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 0 3013
Xplor fileSerial no: 1 / Param file: PAR19X.PRO / Topol file: TOPH19X.PRO

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