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- PDB-8hck: NMR fragment-based screening against the two PDZ do-mains of MDA-9 -

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Basic information

Entry
Database: PDB / ID: 8hck
TitleNMR fragment-based screening against the two PDZ do-mains of MDA-9
ComponentsSyntenin-1
KeywordsCELL INVASION / e.g.MDA-9 / PDZdomain / inhibitor / therapeutic target
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / protein sequestering activity / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / ionotropic glutamate receptor binding / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / cytoskeleton / blood microparticle / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: NMR fragment-based screening against the two PDZ do-mains of MDA-9
Authors: Tang, H.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6356
Polymers8,9501
Non-polymers6855
Water27015
1
A: Syntenin-1
hetero molecules

A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,27012
Polymers17,9012
Non-polymers1,36910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2390 Å2
ΔGint-62 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.353, 49.353, 75.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

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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: 8950.381 Da / Num. of mol.: 1
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-P1Z / 4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE


Mass: 308.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: e.g.Cobalt chlonde hexahydrate, MES monohydrate, Ammouium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25.59 Å / Num. obs: 7824 / % possible obs: 99.9 % / Redundancy: 19 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 37.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.535 / Num. unique obs: 504

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N99

1n99


Resolution: 2→25.587 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 935 13.89 %
Rwork0.2321 5796 -
obs0.2368 6731 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.32 Å2 / Biso mean: 34.8806 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 2→25.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms615 0 45 15 675
Biso mean--59.7 33.92 -
Num. residues----81
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008665
X-RAY DIFFRACTIONf_angle_d0.879891
X-RAY DIFFRACTIONf_chiral_restr0.05797
X-RAY DIFFRACTIONf_plane_restr0.004111
X-RAY DIFFRACTIONf_dihedral_angle_d13.968390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0001-2.10550.31121230.2401796
2.1055-2.23730.35581210.2485825
2.2373-2.410.27911370.2513801
2.41-2.65230.33371210.2623818
2.6523-3.03550.24991470.2512812
3.0355-3.82240.23821440.2405833
3.8224-250.24681420.2039911

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