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- PDB-4cik: plasminogen kringle 1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4cik
Titleplasminogen kringle 1 in complex with inhibitor
ComponentsPLASMINOGEN
KeywordsHYDROLASE / FIBRINOLYSIS / PLASMINOGEN / PROTEIN-PROTEIN INTERACTION / KRINGLE LIGAND
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 / myoblast differentiation / negative regulation of cell-substrate adhesion / 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 / kinase binding / Schaffer collateral - CA1 synapse / 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 / protein domain specific binding / negative regulation of cell population proliferation / 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
Chem-XO3 / Plasminogen
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsXue, Y. / Johansson, C. / Cheng, L. / Pettersen, D. / Gustafsson, D.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Discovery of the Fibrinolysis Inhibitor Azd6564, Acting Via Interference of a Protein-Protein Interaction.
Authors: Cheng, L. / Pettersen, D. / Ohlsson, B. / Schell, P. / Karle, M. / Evertsson, E. / Pahlen, S. / Jonforsen, M. / Plowright, A.T. / Bostrom, J. / Fex, T. / Thelin, A. / Hilgendorf, C. / Xue, Y. ...Authors: Cheng, L. / Pettersen, D. / Ohlsson, B. / Schell, P. / Karle, M. / Evertsson, E. / Pahlen, S. / Jonforsen, M. / Plowright, A.T. / Bostrom, J. / Fex, T. / Thelin, A. / Hilgendorf, C. / Xue, Y. / Wahlund, G. / Lindberg, W. / Larsson, L. / Gustafsson, D.
History
DepositionDec 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8382
Polymers9,5801
Non-polymers2581
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.777, 57.594, 81.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein PLASMINOGEN


Mass: 9579.554 Da / Num. of mol.: 1 / Fragment: KRINGLE 1, RESIDUES 101-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P00747, plasmin
#2: Chemical ChemComp-XO3 / 5-[(2R,4S)-2-(phenylmethyl)piperidin-4-yl]-1,2-oxazol-3-one


Mass: 258.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→28.8 Å / Num. obs: 11799 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 14.818 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.6
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 10.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CEB

1ceb


Resolution: 1.78→47.04 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 559 4.74 %RANDOM
Rwork0.2509 ---
obs0.2529 11798 99.76 %-
Displacement parametersBiso mean: 14.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.5700885 Å20 Å20 Å2
2--0.32697971 Å20 Å2
3---0.24310879 Å2
Refinement stepCycle: LAST / Resolution: 1.78→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms647 0 19 183 849
LS refinement shellResolution: 1.78→1.89 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2819 91 4.88 %
Rwork0.2821 1774 -
all0.2821 1865 -
obs--99.76 %

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