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- PDB-6ar4: Crystal structure of PICK1 in complex with the small molecule inh... -

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Basic information

Entry
Database: PDB / ID: 6ar4
TitleCrystal structure of PICK1 in complex with the small molecule inhibitor 1o
ComponentsPRKCA-binding protein
KeywordsActin Binding protein / PDZ domain PDZ inhibitor
Function / homology
Function and homology information


membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / genomic imprinting / protein kinase C-activating G protein-coupled receptor signaling pathway / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / dendritic spine organization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / regulation of insulin secretion / positive regulation of receptor internalization / cellular response to glucose starvation / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / Cell surface interactions at the vascular wall / phospholipid binding / intracellular protein transport / endocytic vesicle membrane / actin filament binding / synaptic vesicle / presynaptic membrane / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / signaling receptor binding / protein phosphorylation / synapse / perinuclear region of cytoplasm / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain ...PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-BQA / PRKCA-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsMarcotte, D.
CitationJournal: Sci Rep / Year: 2018
Title: Potent PDZ-Domain PICK1 Inhibitors that Modulate Amyloid Beta-Mediated Synaptic Dysfunction.
Authors: Lin, E.Y.S. / Silvian, L.F. / Marcotte, D.J. / Banos, C.C. / Jow, F. / Chan, T.R. / Arduini, R.M. / Qian, F. / Baker, D.P. / Bergeron, C. / Hession, C.A. / Huganir, R.L. / Borenstein, C.F. / ...Authors: Lin, E.Y.S. / Silvian, L.F. / Marcotte, D.J. / Banos, C.C. / Jow, F. / Chan, T.R. / Arduini, R.M. / Qian, F. / Baker, D.P. / Bergeron, C. / Hession, C.A. / Huganir, R.L. / Borenstein, C.F. / Enyedy, I. / Zou, J. / Rohde, E. / Wittmann, M. / Kumaravel, G. / Rhodes, K.J. / Scannevin, R.H. / Dunah, A.W. / Guckian, K.M.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PRKCA-binding protein
B: PRKCA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1884
Polymers27,0812
Non-polymers1,1072
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer has been formed artificially using peptide linker and oxidation of cysteines.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.311, 54.311, 77.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein PRKCA-binding protein / Protein interacting with C kinase 1 / Protein kinase C-alpha-binding protein


Mass: 13540.405 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PICK1, PRKCABP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRD5
#2: Chemical ChemComp-BQA / N-[4-(4-bromophenyl)-1-{[2-(trifluoromethyl)phenyl]methyl}piperidine-4-carbonyl]-3-cyclopropyl-L-alanine


Mass: 553.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28BrF3N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1M BisTRIS pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→47.03 Å / Num. obs: 28410 / % possible obs: 99.1 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.69-1.724.41.24314030.4940.6351.40297.8
9.1-47.035.10.021460.9990.010.02378

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOLREPv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HPK

3hpk


Resolution: 1.69→25.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.362 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.017
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 1424 5 %RANDOM
Rwork0.157 ---
obs0.1588 27103 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 28.638 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.69→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 70 247 1583
Biso mean--41.06 37.41 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0191371
X-RAY DIFFRACTIONr_bond_other_d0.0030.021320
X-RAY DIFFRACTIONr_angle_refined_deg2.8562.0391868
X-RAY DIFFRACTIONr_angle_other_deg1.52233077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3726.81844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.542152
X-RAY DIFFRACTIONr_chiral_restr0.1960.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021490
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02234
LS refinement shellResolution: 1.69→1.734 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.111 112 -
Rwork0.07 1945 -
all-2057 -
obs--99.28 %

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