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- PDB-1pmk: KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1pmk
TitleKRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES
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 / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / negative regulation of cell population proliferation / protein domain specific binding / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsPadmanabhan, K. / Tulinsky, A.
Citation
Journal: Protein Sci. / Year: 1994
Title: Kringle-kringle interactions in multimer kringle structures.
Authors: Padmanabhan, K. / Wu, T.P. / Ravichandran, K.G. / Tulinsky, A.
#1: Journal: 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. / Kelly, R.F. / Padmanabhan, K. / Tulinsky, A. / Westbrook, M.L. / Kossiakoff, A.A.
#2: Journal: Biochemistry / Year: 1991
Title: Crystal and Molecular Structure of Human Plasminogen Kringle 4 Refined to 1.9A Resolution
Authors: Mulichak, A.M. / Tulinsky, A. / Ravichandran, K.G.
#3: Journal: Biochemistry / Year: 1991
Title: The Refined Structure of the Epsilon-Aminocaproic Acid Complex of Human Plasminogen Kringle 4
Authors: Wu, T.-P. / Padmanabhan, K. / Tulinsky, A. / Mulichak, A.M.
History
DepositionApr 25, 1994Processing site: BNL
Revision 1.0Jun 22, 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 / Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMINOGEN KRINGLE 4
B: PLASMINOGEN KRINGLE 4


Theoretical massNumber of molelcules
Total (without water)19,8002
Polymers19,8002
Non-polymers00
Water2,162120
1
A: PLASMINOGEN KRINGLE 4


Theoretical massNumber of molelcules
Total (without water)9,9001
Polymers9,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PLASMINOGEN KRINGLE 4


Theoretical massNumber of molelcules
Total (without water)9,9001
Polymers9,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.730, 49.090, 46.150
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95258, 0.03032, 0.3028), (0.01994, -0.9991, 0.0373), (0.30363, -0.0295, -0.952)
Vector: -4.82118, 72.48057, 23.52269)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B.

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Components

#1: Protein PLASMINOGEN KRINGLE 4


Mass: 9899.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00747, plasmin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.84 Å3/Da / Density % sol: 33.13 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Mammonium sulfate1reservoir
335 %PEG80001reservoir
40.8 %n-butanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. all: 6943 / Num. obs: 4328 / % possible obs: 62 % / Observed criterion σ(I): 2
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.5 Å / % possible obs: 39 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.25→7 Å / σ(I): 2
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE INTERKRINGLE RESIDUES -2 - 0 AND 81 - 87 IN BOTH MOLECULES.
RfactorNum. reflection
obs0.165 3985
Refinement stepCycle: LAST / Resolution: 2.25→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 120 1364
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
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
Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.046
X-RAY DIFFRACTIONp_planar_d0.060.055
X-RAY DIFFRACTIONp_chiral_restr0.150.16
X-RAY DIFFRACTIONp_mcbond_it1.50.9
X-RAY DIFFRACTIONp_scbond_it21.4
X-RAY DIFFRACTIONp_mcangle_it21.5
X-RAY DIFFRACTIONp_scangle_it2.52

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