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- PDB-1pkr: THE STRUCTURE OF RECOMBINANT PLASMINOGEN KRINGLE 1 AND THE FIBRIN... -

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Basic information

Entry
Database: PDB / ID: 1pkr
TitleTHE STRUCTURE OF RECOMBINANT PLASMINOGEN KRINGLE 1 AND THE FIBRIN BINDING SITE
ComponentsPLASMINOGEN
KeywordsPLASMINOGEN
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / 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 / : / protease binding / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / 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 ...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 / 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 / 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: 2.48 Å
AuthorsWu, T.-P. / Tulinsky, A.
Citation
Journal: Blood Coagulation Fibrinolysis / Year: 1994
Title: The structure of recombinant plasminogen kringle 1 and the fibrin binding site.
Authors: Wu, T.P. / Padmanabhan, K.P. / Tulinsky, A.
#1: Journal: To be Published
Title: The Amino Acids of the Recombinant Kringle 1 Domain of Human Plasminogen that Stabilize its Interaction with W-Amino Acids
Authors: Hoover, G.J. / Menhart, N. / Martin, A. / Warder, S. / Castellino, F.J.
History
DepositionAug 3, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 / 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: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4793
Polymers9,4081
Non-polymers712
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.930, 58.930, 54.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 30

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Components

#1: Protein PLASMINOGEN


Mass: 9408.268 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mmagnesium chloride1reservoir
20.1 MN-[2-acetamido[-2-imino diacetic acid1reservoir
330 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.48 Å / Lowest resolution: 2.63 Å / Num. obs: 2987 / % possible obs: 87 % / Observed criterion σ(I): 4.8 / Rmerge(I) obs: 0.059

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.159 / Highest resolution: 2.48 Å
Refinement stepCycle: LAST / Highest resolution: 2.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 2 71 715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.2
X-RAY DIFFRACTIONp_angle_d6
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
Refinement
*PLUS
Lowest resolution: 7 Å / Num. reflection obs: 2695
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0430.035
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15

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