5jxb

PSD-95 extended PDZ3 in complex with SynGAP PBM

Method: X-RAY DIFFRACTION D_max: 82.1 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Disks large homolog 4,SynGAP

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 309–413 Chain C； UniProt 309–413	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000	Resolution 2.90 Å R-free 0.287

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5JXB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KEF PDZ1 of SAP90 Deposited 2001-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 105–197（93 aa） Fragment：PDZ1 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR sample composition 1.0 mM protein, 10 mM phosphate buffer, 150 mM NaCl, pH 6.8 \| 10 mM phosphate buffer, 150 mM NaCl	Resolution not provided
2MES Backbone 1H, 13C, 15N resonance assignments of calcium-bound calmodulin in complex with PSD95 N-terminal peptide Deposited 2013-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–71（71 aa） Fragment：UNP residues 1-71	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；310 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 400 uM [U-99% 13C; U-99% 15N] Calmodulin, PSD95NT, DTT, Tris, CaCl2, 600 uM PSD95_N-terminal_peptide, 20 mM Tris-d11, 50 mM NaCl, 5 mM CaCl2, 5 mM DTT-d, 93 % H2O, 7 % D2O, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
3I4W Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa） Fragment：Third PDZ domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions capillary contradiffusion；pH 4.6；298 K；0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K	Resolution 1.35 Å R-free 0.216
3I4W Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa） Fragment：Third PDZ domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions capillary contradiffusion；pH 4.6；298 K；0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K	Resolution 1.35 Å R-free 0.216
3I4W Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 302–403（102 aa） Fragment：Third PDZ domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions capillary contradiffusion；pH 4.6；298 K；0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K	Resolution 1.35 Å R-free 0.216
3I4W Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 302–403（102 aa） Fragment：Third PDZ domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions capillary contradiffusion；pH 4.6；298 K；0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K	Resolution 1.35 Å R-free 0.216
3K82 Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 305–402（98 aa） Fragment：Third PDZ domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES sodium pH 7.5, 0.8M sodium phosphate monobasic monohydrate, 0.8M potassium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.40 Å R-free 0.210
3ZRT Crystal structure of human PSD-95 PDZ1-2 Deposited 2011-06-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–249（189 aa） Fragment：PDZ1-2, REISDUES 61-249 Chain C 61–249（189 aa） Fragment：PDZ1-2, REISDUES 61-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M SODIUM ACETATE TRIHYDRATE PH 6.0, 2.0 M SODIUM FORMATE AND 5 % PEG 4000 (DROP SIZE: 1 UL SAMPLE AND 1UL RESERVOIR SOLUTION)	Resolution 3.40 Å R-free 0.264
3ZRT Crystal structure of human PSD-95 PDZ1-2 Deposited 2011-06-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 61–249（189 aa） Fragment：PDZ1-2, REISDUES 61-249 Chain D 61–249（189 aa） Fragment：PDZ1-2, REISDUES 61-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M SODIUM ACETATE TRIHYDRATE PH 6.0, 2.0 M SODIUM FORMATE AND 5 % PEG 4000 (DROP SIZE: 1 UL SAMPLE AND 1UL RESERVOIR SOLUTION)	Resolution 3.40 Å R-free 0.264
5J7J NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95 Deposited 2016-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–19（19 aa） Fragment：UNP residues 1-19	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6QJD Crystal Structure of the truncated form of the third PDZ domain of PSD-95: residues 302-392 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–393（92 aa） Fragment：PDZ domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.2 M ammonium sulphate, 30% PEG 4000	Resolution 1.55 Å R-free 0.259
6QJD Crystal Structure of the truncated form of the third PDZ domain of PSD-95: residues 302-392 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–393（92 aa） Fragment：PDZ domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.2 M ammonium sulphate, 30% PEG 4000	Resolution 1.55 Å R-free 0.259
6QJD Crystal Structure of the truncated form of the third PDZ domain of PSD-95: residues 302-392 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 302–393（92 aa） Fragment：PDZ domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.2 M ammonium sulphate, 30% PEG 4000	Resolution 1.55 Å R-free 0.259
6QJD Crystal Structure of the truncated form of the third PDZ domain of PSD-95: residues 302-392 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 302–393（92 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.2 M ammonium sulphate, 30% PEG 4000	Resolution 1.55 Å R-free 0.259
6QJF Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 1 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.16 M ammonium dihydrogenphosphate, 50 mM Tris, 20 % glycerol	Resolution 1.50 Å R-free 0.199
6QJF Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 1 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.16 M ammonium dihydrogenphosphate, 50 mM Tris, 20 % glycerol	Resolution 1.50 Å R-free 0.199
6QJF Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 1 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.16 M ammonium dihydrogenphosphate, 50 mM Tris, 20 % glycerol	Resolution 1.50 Å R-free 0.199
6QJF Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 1 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.16 M ammonium dihydrogenphosphate, 50 mM Tris, 20 % glycerol	Resolution 1.50 Å R-free 0.199
6QJG Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 2 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 30 % PEG 8000	Resolution 2.00 Å R-free 0.246
6QJG Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 2 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 30 % PEG 8000	Resolution 2.00 Å R-free 0.246
6QJG Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 2 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 30 % PEG 8000	Resolution 2.00 Å R-free 0.246
6QJG Crystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 2 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 302–403（102 aa） Fragment：PDZ domain	Mutation：D332P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 30 % PEG 8000	Resolution 2.00 Å R-free 0.246
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJI Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 305–403（99 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M AMMONIUM SULPHATE, 30% PEG 4000	Resolution 1.50 Å R-free 0.261
6QJJ Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3221 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 305–403（99 aa） Fragment：PDZ domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium sulphate, 30% PEG 4000	Resolution 1.70 Å R-free 0.223
6QJK Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P43 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 348–446（99 aa） Fragment：PDZ domain	Mutation：D332G	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.17 M ammonium sulphate , 25.5% PEG 8000 , 15% Glycerol	Resolution 1.05 Å R-free 0.145
6QJL Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P21 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa） Fragment：PDZ domain	Mutation：D332G	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.17 M ammonium sulphate , 25.5% PEG 8000 , 15% Glycerol	Resolution 1.04 Å R-free 0.174
6QJL Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P21 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa） Fragment：PDZ domain	Mutation：D332G	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.17 M ammonium sulphate , 25.5% PEG 8000 , 15% Glycerol	Resolution 1.04 Å R-free 0.174
6QJN Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group I4122 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa） Fragment：PDZ domain	Mutation：D332G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1 M sodium citrate, 20% 2-Propanol, 20% PEG 4000, 5% Glycerol	Resolution 1.80 Å R-free 0.227
6QJN Crystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group I4122 Deposited 2019-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa） Fragment：PDZ domain	Mutation：D332G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1 M sodium citrate, 20% 2-Propanol, 20% PEG 4000, 5% Glycerol	Resolution 1.80 Å R-free 0.227
6SPV Crystal structure of PDZ1-2 from PSD-95 Deposited 2019-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 55–249（195 aa）	Not recorded	GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2 M calcium acetate; 0.1 M sodium cacodylate; 40% v/v PEG 400	Resolution 2.04 Å R-free 0.260
6SPZ Crystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains Deposited 2019-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 55–249（195 aa）	Not recorded	GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200. Matrix microseeding with Apo crystal form (PDB ID: 6spv).	Resolution 2.08 Å R-free 0.240
9TNF Crystal Structure of the third PDZ domain of PSD-95 protein Y397E mutant Deposited 2025-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa）	Mutation：Y397E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.2 M ammonium sulphate, 30% w/v PEG 4000, 0.1 M sodium acetate	Resolution 1.45 Å R-free 0.201
9TNF Crystal Structure of the third PDZ domain of PSD-95 protein Y397E mutant Deposited 2025-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 302–403（102 aa）	Mutation：Y397E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.2 M ammonium sulphate, 30% w/v PEG 4000, 0.1 M sodium acetate	Resolution 1.45 Å R-free 0.201
9TNG Crystal Structure of the third PDZ domain of PSD-95 protein E401R mutant Deposited 2025-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–403（102 aa）	Mutation：E401R	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.2 M ammonium sulphate, 25% w/v PEG 4000, 0.1 M sodium acetate	Resolution 0.95 Å R-free 0.168

18 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DLG4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–107； UniProt 309–413 Author chain C； PDBConstruct 3–107； UniProt 309–413

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jxb
Deposition date deposition_date	2016-05-13
Structure title title	PSD-95 extended PDZ3 in complex with SynGAP PBM
Keywords keywords	PSD-95, PDZ, SynGAP, Extension, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.33 Å
Radius of gyration Rg (electron density) rg_electron	21.76 Å
Forward intensity I(0) i0	11577100.00
Molecular weight molecular_weight	25113.0 kDa
Excluded volume excluded_volume	31334 Å³
Envelope volume envelope_volume	38593 Å³
Hydration-shell volume shell_volume	16314 Å³
Envelope diameter envelope_diameter	85.7 Å
Shell Rg shell_rg	26.13 Å
Envelope Rg envelope_rg	21.92 Å
Shape Rg shape_rg	21.75 Å
Total Rg total_rg	22.43 Å
Total atoms total_atoms	1777
Residues n_residues	236
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.1 Å
Rg (real space) rg_real	22.54 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.1580e+07
I(0) uncertainty (real space) i0_real_error	1.8970e+05
Rg (reciprocal space) rg_reciprocal	22.49 Å
I(0) (reciprocal space) i0_reciprocal	11580000.0000
Solution quality estimate total_estimate	0.7167
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.630
Kurtosis Kurtosis kurtosis	0.096
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3024000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.546; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.676; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5jxbA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	5jxbC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	70.286 Å
Unit-cell length b length_b	71.094 Å
Unit-cell length c length_c	115.791 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	45.890 Å
R factor r_factor	0.2411
R_work r_work	0.2407
R_free r_free	0.2874

Description description	Disks large homolog 4,SynGAP
Molecular weight formula_weight	13408.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1781

PSD-95 extended PDZ3 in complex with SynGAP PBM

1. Protein Identity and Related Structures Protein Identity & Related Structures

Disks large homolog 4,SynGAP

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

fit	/app/data/saxs_computation/jx/5jxb/5jxb.fit
pddf	/app/data/pr_computation/jx/5jxb/5jxb.pr.out
profile	/app/data/saxs_computation/jx/5jxb/5jxb.dat