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- PDB-6yx1: Crystal structure of SHANK1 PDZ in complex with a peptide-small m... -

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Basic information

Entry
Database: PDB / ID: 6yx1
TitleCrystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
ComponentsSH3 and multiple ankyrin repeat domains protein 1
KeywordsPEPTIDE BINDING PROTEIN / protein protein interactions / PDZ domain / hybrid structures / fragment-based drug discovery / beta-sheets acylhydrazone
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / Neurexins and neuroligins / adult behavior / positive regulation of dendritic spine development / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / SH3 domain binding / scaffold protein binding / protein-containing complex assembly / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
ARGININE / LEUCINE / Chem-PWT / THREONINE / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.J. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N035267/1 United Kingdom
European CommissionMSCA-IF-2016-749012 United Kingdom
Royal SocietySRF/R1/191087 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.
Authors: Hegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.Y. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 1
B: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,06210
Polymers24,6832
Non-polymers1,3808
Water2,036113
1
A: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0315
Polymers12,3411
Non-polymers6904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0315
Polymers12,3411
Non-polymers6904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.668, 65.912, 85.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / Somatostatin receptor-interacting protein / SSTRIP


Mass: 12341.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y566

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-PWT / 2-[[2-(5-oxidanylidenepentanoyl)hydrazinyl]methyl]benzoic acid


Mass: 264.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O4
#3: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7.75 PEG 400 40% 30% w/v Trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.708→52.232 Å / Num. obs: 23326 / % possible obs: 81.88 % / Redundancy: 12.3 % / Biso Wilson estimate: 33.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Net I/σ(I): 19.1
Reflection shellResolution: 1.708→1.808 Å / Rmerge(I) obs: 1.838 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 11510 / CC1/2: 0.706 / Rpim(I) all: 0.612

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Processing

Software
NameVersionClassification
REFMAC5.5.0026refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
autoPROCdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o


Resolution: 1.8→52.23 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 1914 8.61 %
Rwork0.2222 20312 -
obs0.225 22226 92.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 92 113 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821733
X-RAY DIFFRACTIONf_angle_d0.88342332
X-RAY DIFFRACTIONf_chiral_restr0.0587258
X-RAY DIFFRACTIONf_plane_restr0.0063302
X-RAY DIFFRACTIONf_dihedral_angle_d20.8415674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.2816990.281045X-RAY DIFFRACTION68.05
1.85-1.890.30571210.28351289X-RAY DIFFRACTION82.46
1.9-1.950.27011130.27521197X-RAY DIFFRACTION77.42
1.95-2.010.30871450.25871535X-RAY DIFFRACTION99.94
2.01-2.090.26011250.24431320X-RAY DIFFRACTION85.1
2.09-2.170.27061450.22921548X-RAY DIFFRACTION99.82
2.17-2.270.30161150.25051212X-RAY DIFFRACTION77.15
2.27-2.390.27111460.2321551X-RAY DIFFRACTION99.82
2.39-2.540.27691480.23651570X-RAY DIFFRACTION100
2.54-2.730.28571470.24561557X-RAY DIFFRACTION99.88
2.73-3.010.31031500.24841592X-RAY DIFFRACTION100
3.01-3.440.24831500.22631596X-RAY DIFFRACTION99.83
3.44-4.340.22491490.18271600X-RAY DIFFRACTION99.94
4.34-52.230.22831610.2121700X-RAY DIFFRACTION99.63

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