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- PDB-4ic0: Crystal Structure of PAI-1 in Complex with Gallate -

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Basic information

Entry
Database: PDB / ID: 4ic0
TitleCrystal Structure of PAI-1 in Complex with Gallate
ComponentsPlasminogen activator inhibitor 1
KeywordsHYDROLASE INHIBITOR / protease 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 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
3,4,5-trihydroxybenzoic acid / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsHong, Z.B. / Lin, Z.H. / Gong, L.H. / Huang, M.D.
CitationJournal: To be Published
Title: Crystal Structure of PAI-1 in Complex with Gallate
Authors: Hong, Z.B. / Lin, Z.H. / Gong, L.H. / Huang, M.D.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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_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)171,5216
Polymers171,1804
Non-polymers3402
Water00
1
A: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9652
Polymers42,7951
Non-polymers1701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,7951
Polymers42,7951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9652
Polymers42,7951
Non-polymers1701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,7951
Polymers42,7951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.280, 74.990, 103.873
Angle α, β, γ (deg.)90.91, 93.29, 115.82
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: 42795.066 Da / Num. of mol.: 4 / Mutation: N150H, K154T, D158Q, Q319L, M354I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05121
#2: Chemical ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate


Mass: 170.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O5

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 72504 / Num. obs: 68844 / % possible obs: 95.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→38.25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.785 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25751 3628 5 %RANDOM
Rwork0.20196 ---
obs0.20484 68844 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-1.24 Å20.21 Å2
2---2.6 Å20.04 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.32→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11589 0 24 0 11613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.95816190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66451441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68723.846546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.303152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6761570
X-RAY DIFFRACTIONr_chiral_restr0.1470.21817
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218970
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.317→2.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 192 -
Rwork0.227 4292 -
obs--78.86 %
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)
10.3540.2452-0.28370.3886-0.19030.3642-0.0359-0.0104-0.035-0.0277-0.0034-0.0622-0.0139-0.01870.03930.0366-0.0130.00840.0308-0.00990.0345-21.558415.34285.1115
20.56440.0315-0.22320.37080.11670.1971-0.03750.00280.0177-0.06450.03920.080.01990.0166-0.00170.0446-0.0204-0.00840.01980.00010.040821.8759-15.2535-5.1385
30.3919-0.26450.32260.3887-0.1940.328-0.03280.00310.0290.02470.0085-0.06130.0079-0.01990.02440.04290.01350.00330.0425-0.00460.0269-21.5471-50.824342.3292
40.5479-0.02910.23210.32760.07630.2197-0.0265-0.0096-0.00870.04070.03650.0783-0.01870.0245-0.010.03490.02460.01480.02950.00480.03221.8631-20.217252.5965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 379
2X-RAY DIFFRACTION2B5 - 379
3X-RAY DIFFRACTION3C5 - 379
4X-RAY DIFFRACTION4D4 - 379

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