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- PDB-4g8o: Crystal Structure of a novel small molecule inactivator bound to ... -

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Basic information

Entry
Database: PDB / ID: 4g8o
TitleCrystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1
ComponentsPlasminogen activator inhibitor 1
KeywordsBLOOD CLOTTING/INHIBITOR / SERPIN / PAI-1 / INHIBITOR / BLOOD CLOTTING / BLOOD CLOTTING-INHIBITOR complex
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
Chem-96P / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsStuckey, J.A. / Lawrence, D.A. / Li, S.-H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1.
Authors: Li, S.H. / Reinke, A.A. / Sanders, K.L. / Emal, C.D. / Whisstock, J.C. / Stuckey, J.A. / Lawrence, D.A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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)170,74412
Polymers169,5224
Non-polymers1,2228
Water2,936163
1
A: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5393
Polymers42,3811
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4772
Polymers42,3811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5733
Polymers42,3811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1564
Polymers42,3811
Non-polymers7763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.335, 75.317, 105.002
Angle α, β, γ (deg.)91.32, 93.49, 115.65
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: 42380.570 Da / Num. of mol.: 4 / Fragment: UNP residues 28-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAI-1, PAI1, PLANH1, SERPINE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P05121
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-96P / (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate)


Mass: 583.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20F3NO12
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 298 K
Details: 0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
PH range: 6.5 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.71→20 Å / Num. obs: 42717 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 58.84 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.5
Reflection shellResolution: 2.71→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.351 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.8682 / Cor.coef. Fo:Fc free: 0.8362 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 2158 5.06 %RANDOM
Rwork0.2391 ---
obs0.2406 42667 87.61 %-
Displacement parametersBiso mean: 55.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.9951 Å2-2.7048 Å2-3.6934 Å2
2--19.9477 Å21.6526 Å2
3----23.9428 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11485 0 75 163 11723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811838HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9216078HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5396SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes270HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1737HARMONIC5
X-RAY DIFFRACTIONt_it11838HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion2.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12863SEMIHARMONIC4
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3471 52 5.24 %
Rwork0.2812 940 -
all0.2842 992 -
obs--87.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.00210.283-1.02081.13670.15880.2394-0.0040.00590.0145-0.02450.02090.02380.0210.0098-0.01690.0064-0.0395-0.0404-0.030.03520.0064-0.0046-0.04810.1166
21.6233-0.60030.89951.13770.10610.1661-0.0099-0.0021-0.00640.03080.02340.0261-0.00820.0126-0.0136-0.030.0530.0691-0.00910.04370.01586.50410.3749-46.2946
31.117-0.96940.80151.5564-0.52790.60260.00220.01990.0045-0.0261-0.0057-0.0284-0.00660.00570.0035-0.02710.04580.0198-0.01860.00250.024828.7433-30.1391-56.6013
42.26560.8601-1.10463.5442-0.68391.4604-0.0088-0.0425-0.00740.0658-0.0071-0.0917-0.01090.07670.0160.0033-0.0452-0.0129-0.0407-0.00710.047661.3613-31.5243-94.3775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 379
2X-RAY DIFFRACTION2{ B|* }B4 - 379
3X-RAY DIFFRACTION3{ C|* }C4 - 379
4X-RAY DIFFRACTION4{ D|* }D4 - 379

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