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- PDB-2exg: Making Protein-Protein Interactions Drugable: Discovery of Low-Mo... -

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Basic information

Entry
Database: PDB / ID: 2exg
TitleMaking Protein-Protein Interactions Drugable: Discovery of Low-Molecular-Weight Ligands for the AF6 PDZ Domain
ComponentsAfadin
KeywordsCELL ADHESION / Inhibitors of protein-protein interactions / low-molecular-weight ligands / protein structure / NMR screening / PDZ domains
Function / homology
Function and homology information


positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / establishment of endothelial intestinal barrier / pore complex assembly / positive regulation of cell-cell adhesion / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction ...positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / establishment of endothelial intestinal barrier / pore complex assembly / positive regulation of cell-cell adhesion / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction / pore complex / cell adhesion molecule binding / negative regulation of cell migration / adherens junction / small GTPase binding / actin filament binding / cell-cell junction / cell junction / cell-cell signaling / regulation of protein localization / cell adhesion / nuclear speck / cadherin binding / positive regulation of gene expression / signal transduction / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA 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 / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsional angle dynamics
AuthorsJoshi, M. / Vargas, C. / Boisguerin, P. / Krause, G. / Schade, M. / Oschkinat, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Discovery of low-molecular-weight ligands for the AF6 PDZ domain.
Authors: Joshi, M. / Vargas, C. / Boisguerin, P. / Diehl, A. / Krause, G. / Schmieder, P. / Moelling, K. / Hagen, V. / Schade, M. / Oschkinat, H.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Afadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6842
Polymers10,3931
Non-polymers2911
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Afadin / AF-6 protein


Mass: 10392.987 Da / Num. of mol.: 1 / Fragment: PDZ domain (residues 985-1079)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55196
#2: Chemical ChemComp-STF / (5R)-2-SULFANYL-5-[4-(TRIFLUOROMETHYL)BENZYL]-1,3-THIAZOL-4-ONE


Mass: 291.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8F3NOS2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM PDZ domain U-15N, 20mM phosphate buffer, 50mM Sodium chloride, 90%H2O, 10% D2O90% H2O/10% D2O
21.5 mM PDZ domain U-15N, 13C, 1.5 mM 5f, 20mM phosphate buffer, 50mM Sodium chloride, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM Phosphate, 50 mM NaCl 6.5Ambient 295 K
220 mM Phosphate, 50 mM NaCl 6.5Ambient 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
DIANA1.0.6Guentert, P.structure solution
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
Sparky3.1Goddard and Knellerdata analysis
DIANA1.0.6Guentert, P.refinement
RefinementMethod: Torsional angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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