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- PDB-6ak2: Crystal structure of the syntenin PDZ1 domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 6ak2
TitleCrystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor KSL-128018
Components
  • Syntenin-1
  • peptide inhibitor KSL-128018
KeywordsSIGNALING PROTEIN/INHIBITOR / Signaling protein / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Neurofascin interactions / RIPK1-mediated regulated necrosis / Regulation of necroptotic cell death / Ephrin signaling / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / presynapse assembly ...Neurofascin interactions / RIPK1-mediated regulated necrosis / Regulation of necroptotic cell death / Ephrin signaling / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / presynapse assembly / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / Neutrophil degranulation / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / ionotropic glutamate receptor binding / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / cell adhesion molecule binding / ephrin receptor binding / protein sequestering activity / adherens junction / melanosome / presynapse / positive regulation of cell growth / nuclear membrane / Ras protein signal transduction / cytoskeleton / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.868 Å
AuthorsJin, Z.Y. / Park, J.H. / Yun, J.H. / Haugaard-Kedstrom, L.M. / Lee, W.T.
CitationJournal: J.Med.Chem. / Year: 2021
Title: A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma.
Authors: Haugaard-Kedstrom, L.M. / Clemmensen, L.S. / Sereikaite, V. / Jin, Z. / Fernandes, E.F.A. / Wind, B. / Abalde-Gil, F. / Daberger, J. / Vistrup-Parry, M. / Aguilar-Morante, D. / Leblanc, R. / ...Authors: Haugaard-Kedstrom, L.M. / Clemmensen, L.S. / Sereikaite, V. / Jin, Z. / Fernandes, E.F.A. / Wind, B. / Abalde-Gil, F. / Daberger, J. / Vistrup-Parry, M. / Aguilar-Morante, D. / Leblanc, R. / Egea-Jimenez, A.L. / Albrigtsen, M. / Jensen, K.E. / Jensen, T.M.T. / Ivarsson, Y. / Vincentelli, R. / Hamerlik, P. / Andersen, J.H. / Zimmermann, P. / Lee, W. / Stromgaard, K.
History
DepositionAug 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Syntenin-1
B: Syntenin-1
D: peptide inhibitor KSL-128018
E: peptide inhibitor KSL-128018


Theoretical massNumber of molelcules
Total (without water)19,4824
Polymers19,4824
Non-polymers00
Water2,252125
1
A: Syntenin-1
D: peptide inhibitor KSL-128018


Theoretical massNumber of molelcules
Total (without water)9,7412
Polymers9,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-5 kcal/mol
Surface area5290 Å2
MethodPISA
2
B: Syntenin-1
E: peptide inhibitor KSL-128018


Theoretical massNumber of molelcules
Total (without water)9,7412
Polymers9,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-5 kcal/mol
Surface area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.580, 38.396, 56.777
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Syntenin-1 / / Syndecan-binding protein 1


Mass: 8837.221 Da / Num. of mol.: 2 / Fragment: UNP residues 113-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sdcbp / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JI92
#2: Protein/peptide peptide inhibitor KSL-128018


Mass: 904.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.67 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate Trihydrate (pH4.6), 30%Polythylene Glycol Monomethyl Ether 2,000.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.868→30.393 Å / Num. obs: 16918 / % possible obs: 97.63 % / Redundancy: 5.6 % / Biso Wilson estimate: 22.63 Å2 / Net I/σ(I): 42.88
Reflection shellResolution: 1.868→1.923 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9E

1w9e


Resolution: 1.868→30.393 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2407 1694 10.01 %
Rwork0.2086 --
obs0.2119 16918 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.868→30.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 0 125 1471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071362
X-RAY DIFFRACTIONf_angle_d0.9061831
X-RAY DIFFRACTIONf_dihedral_angle_d17.89800
X-RAY DIFFRACTIONf_chiral_restr0.062206
X-RAY DIFFRACTIONf_plane_restr0.005233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8685-1.92340.26171290.24071200X-RAY DIFFRACTION93
1.9234-1.98550.27331410.20961263X-RAY DIFFRACTION98
1.9855-2.05650.24671400.20681250X-RAY DIFFRACTION98
2.0565-2.13880.23741380.21311291X-RAY DIFFRACTION98
2.1388-2.23610.23741370.20251251X-RAY DIFFRACTION98
2.2361-2.35390.23321400.20871269X-RAY DIFFRACTION98
2.3539-2.50140.24421380.22041279X-RAY DIFFRACTION99
2.5014-2.69440.25081500.21871269X-RAY DIFFRACTION99
2.6944-2.96530.25981400.21881286X-RAY DIFFRACTION99
2.9653-3.39390.24391490.20691295X-RAY DIFFRACTION99
3.3939-4.27410.21611440.19031306X-RAY DIFFRACTION99
4.2741-30.39730.2411480.21111265X-RAY DIFFRACTION94

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