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- PDB-1b3k: Plasminogen activator inhibitor-1 -

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Basic information

Entry
Database: PDB / ID: 1b3k
TitlePlasminogen activator inhibitor-1
ComponentsPLASMINOGEN ACTIVATOR INHIBITOR-1
KeywordsBLOOD CLOTTING / SERPIN / PAI-1 / INHIBITOR
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 blood coagulation ...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 blood coagulation / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / regulation of signaling receptor activity / Dissolution of Fibrin Clot / positive regulation of monocyte chemotaxis / 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 / negative regulation of cell migration / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Platelet degranulation / collagen-containing extracellular matrix / angiogenesis / cellular response to lipopolysaccharide / protease binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsSharp, A.M. / Stein, P.E. / Pannu, N.S. / Read, R.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The active conformation of plasminogen activator inhibitor 1, a target for drugs to control fibrinolysis and cell adhesion.
Authors: Sharp, A.M. / Stein, P.E. / Pannu, N.S. / Carrell, R.W. / Berkenpas, M.B. / Ginsburg, D. / Lawrence, D.A. / Read, R.J.
History
DepositionDec 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 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: PLASMINOGEN ACTIVATOR INHIBITOR-1
B: PLASMINOGEN ACTIVATOR INHIBITOR-1
C: PLASMINOGEN ACTIVATOR INHIBITOR-1
D: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)171,1284
Polymers171,1284
Non-polymers00
Water0
1
A: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)42,7821
Polymers42,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)42,7821
Polymers42,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)42,7821
Polymers42,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)42,7821
Polymers42,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.472, 74.930, 103.691
Angle α, β, γ (deg.)90.97, 93.33, 115.94
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.902329, -0.412926, -0.123668), (0.104192, 0.487333, -0.866978), (0.418266, 0.769414, 0.482759)34.1904, -3.3229, -18.8686
2given(0.999999, 0.001296, 0.000126), (0.001296, -0.999999, 0.000609), (0.000127, -0.000609, -1)32.8111, -0.2263, -37.4223
3given(0.902629, 0.411423, 0.126463), (0.10062, -0.487366, 0.867381), (0.418494, -0.770198, -0.481308)68.6277, 32.1938, -23.3988
4given(0.904155, -0.408402, -0.125348), (0.101468, 0.490316, -0.865618), (0.41498, 0.769934, 0.484761)34.1206, -3.5258, -19.0349
5given(0.999998, 0.002146, 0.000361), (0.002146, -0.999997, 0.001106), (0.000363, -0.001105, -0.999999)32.8376, -0.1782, -37.4341
6given(0.907207, 0.401126, 0.126783), (0.096275, -0.491338, 0.865631), (0.40952, -0.773101, -0.484364)68.5868, 31.7011, -24.2302
7given(0.999999, 0.001185, -0.0003), (0.001185, -0.999999, 2.5E-5), (-0.0003, -2.5E-5, -1)32.8023, -0.248, -37.4544
8given(-0.085602, 0.980397, 0.102407), (0.128464, -0.135542, 0.988829), (0.988013, 0.143007, -0.108303)-20.7863, 80.9359, 67.553

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Components

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


Mass: 42782.023 Da / Num. of mol.: 4 / Mutation: N150H, K154T, Q319L, M354I
Source method: isolated from a genetically manipulated source
Details: ACTIVE FORM / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / 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: 2.7 Å3/Da / Density % sol: 53.83 % / Description: LATENT PAI-1 STRUCTURE BY E.GOLDSMITH
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, ...Details: CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, 0.25 M NA CL AND 10 MM CACODYLATE PH 6.8 AT ROOM TEMPERATURE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2NACLSodium chloride11
3EDTAEthylenediaminetetraacetic acid11
4AMMONIUM SULPHATE12
5NACLSodium chloride12
6SODIUM CACODYLATE12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127-32 %satammonium sulfate1reservoir
20.25 M1reservoirNaCl
310 mMcacodylate1reservoir
41
51
61

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 15, 1996
RadiationMonochromator: QUARTZ / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.99→24.35 Å / Num. obs: 25373 / % possible obs: 70.7 % / Redundancy: 1.6 % / Biso Wilson estimate: 2.8 Å2 / Rmerge(I) obs: 0.1016 / Net I/σ(I): 5.11
Reflection shellResolution: 2.99→3.16 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.3361 / Mean I/σ(I) obs: 1.03 / % possible all: 20.3
Reflection shell
*PLUS
% possible obs: 20.3 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
BIOMOLdata reduction
AMoREphasing
CNS0.3refinement
X-GENdata reduction
BIOMOLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LATENT PAI-1

Resolution: 2.99→24.35 Å / Rfactor Rfree error: 0.002 / Data cutoff high rms absF: 1112462.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2576 10.2 %THIN SHELLS
Rwork0.247 ---
all-25369 --
obs-25369 70.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å22.37 Å22.2 Å2
2---4.56 Å2-0.57 Å2
3---3.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å1.01 Å
Refinement stepCycle: LAST / Resolution: 2.99→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11658 0 0 0 11658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
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
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION2300
22X-RAY DIFFRACTION2300
33X-RAY DIFFRACTION2300
44X-RAY DIFFRACTION2300
LS refinement shellResolution: 2.99→3.16 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.428 126 10.1 %
Rwork0.43 1127 -
obs--20.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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