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- PDB-1tpk: CRYSTAL STRUCTURE OF THE KRINGLE-2 DOMAIN OF TISSUE PLASMINOGEN A... -

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Basic information

Entry
Database: PDB / ID: 1tpk
TitleCRYSTAL STRUCTURE OF THE KRINGLE-2 DOMAIN OF TISSUE PLASMINOGEN ACTIVATOR AT 2.4-ANGSTROMS RESOLUTION
ComponentsTISSUE PLASMINOGEN ACTIVATOR
KeywordsPLASMINOGEN ACTIVATOR
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 / protein modification process / Schaffer collateral - CA1 synapse / blood coagulation / apical part of cell / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain ...Tissue plasminogen activator / Fibronectin type I domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tissue-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsDe vos, A.M. / Ultsch, M.H. / Kelley, R.F. / Padmanabhan, K. / Tulinsky, A. / Westbrook, M.L. / Kossiakoff, A.A.
CitationJournal: Biochemistry / Year: 1992
Title: Crystal structure of the kringle 2 domain of tissue plasminogen activator at 2.4-A resolution.
Authors: de Vos, A.M. / Ultsch, M.H. / Kelley, R.F. / Padmanabhan, K. / Tulinsky, A. / Westbrook, M.L. / Kossiakoff, A.A.
History
DepositionSep 24, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
A: TISSUE PLASMINOGEN ACTIVATOR
B: TISSUE PLASMINOGEN ACTIVATOR
C: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0686
Polymers28,9613
Non-polymers1063
Water1,63991
1
A: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6892
Polymers9,6541
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6892
Polymers9,6541
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6892
Polymers9,6541
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 63.580, 46.580
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TISSUE PLASMINOGEN ACTIVATOR


Mass: 9653.769 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00750, EC: 3.4.21.31
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
27 %sat1dropNH4Cl
350 mM1dropNH4HCO3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.43 Å / Lowest resolution: 10 Å / Num. obs: 7103 / % possible obs: 92 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.4→10 Å /
RfactorNum. reflection
Rwork0.184 -
obs-9687
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 3 91 2119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.43 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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