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- PDB-3ut3: A novel PAI-I inhibitor and its structural mechanism -

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Basic information

Entry
Database: PDB / ID: 3ut3
TitleA novel PAI-I inhibitor and its structural mechanism
ComponentsPlasminogen activator inhibitor 1
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 / 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 / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / 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 / 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 receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / protease binding / 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
Chem-EMJ / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsLin, Z.H. / Hong, Z.B. / Shi, X.L. / Hu, L.H. / Andreasen, P.A. / Huang, M.D.
CitationJournal: To be Published
Title: A novel PAI-I inhibitor and its structural mechanism
Authors: Lin, Z.H. / Hong, Z.B. / Shi, X.L. / Hu, L.H. / Andreasen, P.A. / Huang, M.D.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,5325
Polymers169,2384
Non-polymers2941
Water00
1
A: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,3091
Polymers42,3091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6042
Polymers42,3091
Non-polymers2941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,3091
Polymers42,3091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,3091
Polymers42,3091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.252, 74.953, 103.775
Angle α, β, γ (deg.)90.89, 93.33, 115.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Plasminogen activator inhibitor 1 / PAI / PAI-1 / Endothelial plasminogen activator inhibitor / Serpin E1


Mass: 42309.492 Da / Num. of mol.: 4 / Mutation: N150H, K154T, Q319L, M354I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Plasmid: pT7-PL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05121
#2: Chemical ChemComp-EMJ / 2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione


Mass: 294.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26O4

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.1
Details: ammonium sulfate, pH 6.1, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.42→103.49 Å / Num. obs: 64869 / % possible obs: 96.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.3
Reflection shellResolution: 2.42→2.49 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.1 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DVM and 1B3K

1dvm

1b3k


Resolution: 2.42→58.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.353 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24485 3288 5.1 %RANDOM
Rwork0.20247 ---
obs0.20461 61573 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.63 Å20.18 Å2
2---1.63 Å2-0.17 Å2
3---2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.42→58.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11617 0 21 0 11638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911920
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211449
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.95516160
X-RAY DIFFRACTIONr_angle_other_deg0.87326304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90151447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94323.846546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.367152039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7881570
X-RAY DIFFRACTIONr_chiral_restr0.0930.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022820
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.422→2.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 230 -
Rwork0.318 4545 -
obs--96.54 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6EMB.paramEMB.top

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