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- PDB-1a5h: CATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR ... -

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Basic information

Entry
Database: PDB / ID: 1a5h
TitleCATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR COMPLEX OF A BIS-BENZAMIDINE
Components(TISSUE PLASMINOGEN ACTIVATOR) x 2
KeywordsHYDROLASE / TRYPSIN LIKE SERINE PROTEASE / FIBRINOLYTIC ENZYME
Function / homology
Function and homology information


t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis ...t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis / serine protease inhibitor complex / fibrinolysis / secretory granule / negative regulation of proteolysis / phosphoprotein binding / Schaffer collateral - CA1 synapse / protein modification process / blood coagulation / apical part of cell / response to hypoxia / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site ...Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE / Tissue-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRenatus, M. / Bode, W. / Stubbs, M.T.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Structural mapping of the active site specificity determinants of human tissue-type plasminogen activator. Implications for the design of low molecular weight substrates and inhibitors.
Authors: Renatus, M. / Bode, W. / Huber, R. / Sturzebecher, J. / Prasa, D. / Fischer, S. / Kohnert, U. / Stubbs, M.T.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1997
Title: Tissue-Type Plasminogen Activator: Variants and Crystal/Solution Structures Demarcate Structural Determinants of Function
Authors: Bode, W. / Renatus, M.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: The 2.3 A Crystal Structure of the Catalytic Domain of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator
Authors: Lamba, D. / Bauer, M. / Huber, R. / Fischer, S. / Rudolph, R. / Kohnert, U. / Bode, W.
History
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 5, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: TISSUE PLASMINOGEN ACTIVATOR
A: TISSUE PLASMINOGEN ACTIVATOR
D: TISSUE PLASMINOGEN ACTIVATOR
B: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7516
Polymers57,9984
Non-polymers7532
Water1,63991
1
C: TISSUE PLASMINOGEN ACTIVATOR
A: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3753
Polymers28,9992
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: TISSUE PLASMINOGEN ACTIVATOR
B: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3753
Polymers28,9992
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.830, 60.500, 62.610
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.803136, 0.001692, 0.595794), (0.036418, -0.998266, -0.046257), (0.594682, 0.058848, -0.801804)-22.5717, 91.9319, 62.3393
2given(0.757677, 0.005193, 0.65261), (0.006892, -0.999976, -4.5E-5), (0.652594, 0.004532, -0.757694)-23.8418, 91.3804, 62.9584

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Components

#1: Protein/peptide TISSUE PLASMINOGEN ACTIVATOR /


Mass: 840.968 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN FRAGMENT, CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00750, t-plasminogen activator
#2: Protein TISSUE PLASMINOGEN ACTIVATOR / / TC-TPA(BISB)


Mass: 28157.883 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN, CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00750, t-plasminogen activator
#3: Chemical ChemComp-BBA / 2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE / BIS-BENZAMIDINE


Mass: 376.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28N4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.8 mg/mlprotein1drop
210 mMacetate1drop
30.8 mMinhibitor1drop
40.1 Macetate1reservoir
50.1 Mammonium acetate1reservoir
625 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 28, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 12586 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.8→3.1 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.25 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 25355
Reflection shell
*PLUS
% possible obs: 86.2 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTF

1rtf


Resolution: 2.9→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.25 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.178 --
obs0.178 9017 81 %
Displacement parametersBiso mean: 14.2 Å2
Refinement stepCycle: LAST / Resolution: 2.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 51 91 4208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.428
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
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: 2.9→3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.2367 657 -
obs--60.38 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.158
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
LS refinement shell
*PLUS
Lowest resolution: 3 Å

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