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- PDB-1bda: CATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVAT... -

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Basic information

Entry
Database: PDB / ID: 1bda
TitleCATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVATOR IN COMPLEX WITH DANSYL-EGR-CMK (DANSYL-GLU-GLY-ARG CHLOROMETHYL KETONE)
ComponentsSINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN LIKE SERINE PROTEASE / FIBRINOLYTIC ENZYMES / PLASMINOGEN ACTIVATORS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


t-plasminogen activator / trans-synaptic signaling by BDNF, modulating synaptic transmission / prevention of polyspermy / 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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / prevention of polyspermy / 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 / negative regulation of proteolysis / secretory granule / phosphoprotein binding / protein modification process / Schaffer collateral - CA1 synapse / 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 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
dansylglutamyl-glycyl-arginine chloromethyl ketone / Chem-2Z0 / Tissue-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsBode, W. / Renatus, M. / Engh, R.A.
Citation
Journal: EMBO J. / Year: 1997
Title: Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA.
Authors: Renatus, M. / Engh, R.A. / Stubbs, M.T. / Huber, R. / Fischer, S. / Kohnert, U. / Bode, W.
#1: Journal: Biochemistry / Year: 1997
Title: Catalytic Domain Structure of Vampire Bat Plasminogen Activator: A Molecular Paradigm for Proteolysis without Activation Cleavage
Authors: Renatus, M. / Stubbs, M.T. / Huber, R. / Bringmann, P. / Donner, P. / Schleuning, W.D. / Bode, W.
#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
DepositionMay 7, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR
B: SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7064
Polymers59,4512
Non-polymers1,2542
Water34219
1
A: SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3532
Polymers29,7261
Non-polymers6271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3532
Polymers29,7261
Non-polymers6271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.990, 80.780, 159.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999957, -0.001563, -0.009178), (0.001411, -0.999863, 0.016518), (-0.009203, 0.016504, 0.999821)22.413, 64.0911, -0.2599
2given(-0.998807, -0.037285, -0.031526), (0.036553, -0.999055, 0.0235), (-0.032372, 0.02232, 0.999227)25.053, 63.2516, -0.2925

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Components

#1: Protein SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR / SC-TPA


Mass: 29725.654 Da / Num. of mol.: 2 / Fragment: UNP residues 298-562 / Mutation: DELETION MUTANT
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: Chemical ChemComp-2Z0 / N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide / DANSYL-EGRCMK / dansyl-Glu-Gly-Arg-chloromethyl-ketone


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 627.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H37ClN7O7S
References: dansylglutamyl-glycyl-arginine chloromethyl ketone
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS DANSYL-GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH ...THE UNBOUND FORM OF THE INHIBITOR IS DANSYL-GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.2 / Details: pH 8.2
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.8 mg/mlprotein1drop
210 mMacetate1drop
30.1 Macetate1reservoir
40.2 M1reservoirMgCl2
58 %mPEG60001reservoir
64 %methane pentanediol1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 13, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 9414 / % possible obs: 86.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 3.6
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.2 / % possible all: 55.2
Reflection
*PLUS
Num. measured all: 27265
Reflection shell
*PLUS
% possible obs: 55.2 % / Rmerge(I) obs: 0.63

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAGRdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
ROTAGRdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTF

1rtf


Resolution: 3.35→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.25 / Isotropic thermal model: RESTRAINED / Cross valid method: NO FREE R-FACTOR / σ(F): 2 /
Num. reflection% reflection
obs6845 81 %
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 3.35→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 82 19 4271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.671
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.74
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.386
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.09
X-RAY DIFFRACTIONx_mcangle_it3.581
X-RAY DIFFRACTIONx_scbond_it2.661
X-RAY DIFFRACTIONx_scangle_it4.228
LS refinement shellResolution: 3.25→3.35 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.311 240 -
obs--29 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2037
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.745
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.386

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