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- PDB-9pai: CLEAVED SUBSTRATE VARIANT OF PLASMINOGEN ACTIVATOR INHIBITOR-1 -

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Basic information

Entry
Database: PDB / ID: 9pai
TitleCLEAVED SUBSTRATE VARIANT OF PLASMINOGEN ACTIVATOR INHIBITOR-1
Components
  • PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 19-364
  • PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 365-397
KeywordsHYDROLASE INHIBITOR / SERPIN
Function / homology
Function and homology information


positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of smooth muscle cell migration / negative regulation of endopeptidase activity / negative regulation of wound healing ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of smooth muscle cell migration / negative regulation of endopeptidase activity / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of plasminogen activation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / replicative senescence / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / ECM proteoglycans / 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 expression / negative regulation of cell migration / platelet alpha granule lumen / positive regulation of interleukin-8 production / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / protease binding / : / defense response to Gram-negative bacterium / angiogenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAertgeerts, K. / De Bondt, H.L. / De Ranter, C.J. / Declerck, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Mechanisms contributing to the conformational and functional flexibility of plasminogen activator inhibitor-1.
Authors: Aertgeerts, K. / De Bondt, H.L. / De Ranter, C.J. / Declerck, P.J.
History
DepositionMar 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 19-364
B: PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 365-397


Theoretical massNumber of molelcules
Total (without water)42,8632
Polymers42,8632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-37 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.860, 47.520, 62.730
Angle α, β, γ (deg.)90.00, 113.95, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 19-364


Mass: 39056.625 Da / Num. of mol.: 1 / Mutation: A335P
Source method: isolated from a genetically manipulated source
Details: CLEAVED SUBSTRATE VARIANT / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05121
#2: Protein/peptide PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-1) residues 365-397


Mass: 3806.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLEAVED SUBSTRATE VARIANT / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05121
Sequence detailsTHE CLEAVAGE SITE IS BETWEEN RESIDUES 364 365 (THIS NUMBERING SCHEME) 346 347 (ALTERNATIVE SCHEME) ...THE CLEAVAGE SITE IS BETWEEN RESIDUES 364 365 (THIS NUMBERING SCHEME) 346 347 (ALTERNATIVE SCHEME) SER ALA ARG MET ALA PRO

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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: 2.1 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.5 / Details: 19% (W/V) PEG 4000, 100 MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 15, 1994
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 9914 / % possible obs: 71 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.124 / Net I/σ(I): 9.92
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 61

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
FRAMBOdata collection
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LATENT PAI-1

Resolution: 2.7→10 Å / Isotropic thermal model: GROUPED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 869 10.6 %RANDOM
Rwork0.181 ---
all-8174 --
obs-8174 73 %-
Displacement parametersBiso mean: 23.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.25 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 0 0 3015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.555 75 11.7 %
Rwork0.401 566 -
obs--39.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT

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