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- PDB-1pk4: CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN PLASMINOGEN KRINGLE 4 RE... -

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Basic information

Entry
Database: PDB / ID: 1pk4
TitleCRYSTAL AND MOLECULAR STRUCTURE OF HUMAN PLASMINOGEN KRINGLE 4 REFINED AT 1.9-ANGSTROMS RESOLUTION
ComponentsPLASMINOGEN KRINGLE 4
KeywordsHYDROLASE(SERINE PROTEASE)
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site ...Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsTulinsky, A. / Mulichak, A.M.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal and molecular structure of human plasminogen kringle 4 refined at 1.9-A resolution.
Authors: Mulichak, A.M. / Tulinsky, A. / Ravichandran, K.G.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution
Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H.
#2: Journal: Blood Coagulation Fibrinolysis / Year: 1990
Title: Structure of the Lysine-Fibrin Binding Subsite of Human Plasminogen Kringle 4
Authors: Mulichak, A.M. / Tulinsky, A.
#3: Journal: Proteins / Year: 1988
Title: Lysine(Slash)Fibrin Binding Sites of Kringles Modeled After the Structure of Kringle 1 of Prothrombin
Authors: Tulinsky, A. / Park, C.H. / Mao, B. / Llinas, M.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution
Authors: Tulinsky, A. / Park, C.H. / Skrzypczak-Jankun, E.
History
DepositionJul 18, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN KRINGLE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1372
Polymers9,0411
Non-polymers961
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.110, 49.090, 49.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 30

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Components

#1: Protein PLASMINOGEN KRINGLE 4


Mass: 9040.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00747
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(w/v)PEG80001reservoir
20.12 Mammonium sulfate1reservoir
31.2 %dimethylformamide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 6665 / Num. obs: 4869 / % possible obs: 73 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.41

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.142 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 5 96 711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Num. reflection obs: 4919 / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.044
X-RAY DIFFRACTIONp_planar_d0.047
X-RAY DIFFRACTIONp_plane_restr0.015
X-RAY DIFFRACTIONp_chiral_restr0.23
X-RAY DIFFRACTIONp_mcbond_it2.8
X-RAY DIFFRACTIONp_scbond_it3.6
X-RAY DIFFRACTIONp_mcangle_it3.5
X-RAY DIFFRACTIONp_scangle_it4.4

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