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- PDB-8aak: Crystal structure of the PDZ tandem of syntenin in complex with c... -

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Basic information

Entry
Database: PDB / ID: 8aak
TitleCrystal structure of the PDZ tandem of syntenin in complex with compound 29
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN / signaling protein cell adhesion PDZ domain syntenin syndecan drug design
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / Ephrin signaling / protein targeting to membrane / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / regulation of mitotic cell cycle / positive regulation of JNK cascade / adherens junction / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / chemical synaptic transmission / Ras protein signal transduction / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / synapse / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / 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
Chem-LL6 / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.554 Å
AuthorsFeracci, M. / Barral, K.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach.
Authors: Hoffer, L. / Garcia, M. / Leblanc, R. / Feracci, M. / Betzi, S. / Ben Yaala, K. / Daulat, A.M. / Zimmermann, P. / Roche, P. / Barral, K. / Morelli, X.
History
DepositionJul 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8345
Polymers36,0372
Non-polymers7973
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer, HTRF
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-7 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.660, 96.910, 103.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Syntenin-1 / Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain- ...Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain-interacting protein 18 / TACIP18 / Scaffold protein Pbp1 / Syndecan-binding protein 1


Mass: 18018.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Production host: Escherichia coli (E. coli) / References: UniProt: O00560
#2: Chemical ChemComp-LL6 / (2~{S})-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]propanoic acid


Mass: 352.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 100mM sodium acetate 200mM ammonium acetate 20% PEG3350
PH range: 4.4 - 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.554→48.45 Å / Num. obs: 11941 / % possible obs: 99.77 % / Redundancy: 7.7 % / Biso Wilson estimate: 76.11 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.05024 / Net I/σ(I): 9.71
Reflection shellResolution: 2.554→2.646 Å / Rmerge(I) obs: 1.34 / Num. unique obs: 1167 / Rpim(I) all: 0.5154

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.4 (11-DEC-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9E

1w9e


Resolution: 2.554→48.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.77 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.1 / SU Rfree Blow DPI: 0.343 / SU Rfree Cruickshank DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 597 5 %RANDOM
Rwork0.2144 ---
obs0.2178 11941 99.8 %-
Displacement parametersBiso max: 125.37 Å2 / Biso mean: 69.46 Å2 / Biso min: 30.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.3193 Å20 Å20 Å2
2--2.7486 Å20 Å2
3----0.4293 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.554→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 58 90 2644
Biso mean--59.46 58.61 -
Num. residues----328
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d943SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes474HARMONIC5
X-RAY DIFFRACTIONt_it2597HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1952SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2597HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3502HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.07
LS refinement shellResolution: 2.554→2.59 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4305 20 4.85 %
Rwork0.3265 392 -
obs--95.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26920.8968-0.06361.0069-1.3714.46170.09760.12890.0473-0.0882-0.006-0.04630.5791-0.298-0.09160.37220.00220.0212-0.2011-0.0275-0.1762-35.821688.39745.0575
20.84461.2565-0.98731.7286-1.56682.2597-0.0303-0.0679-0.06630.1165-0.059-0.0276-0.2906-0.04980.08930.26450.0221-0.0142-0.12150.0011-0.148-25.045107.36717.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A111 - 273
2X-RAY DIFFRACTION2{ B|* }B109 - 273

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