3i4w

Crystal Structure of the third PDZ domain of PSD-95

Method: X-RAY DIFFRACTION D_max: 88.7 Å Quality: REASONABLE

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

Disks large homolog 4

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 302–403	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 302–403	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 302–403	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 302–403	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

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 3I4W	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 ligand/ion 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
3K82 Crystal Structure of the third PDZ domain of PSD-95 Deposited 2009-10-13	Different construct 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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
5JXB PSD-95 extended PDZ3 in complex with SynGAP PBM Deposited 2016-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 309–413（105 aa） Chain C 309–413（105 aa）	Not recorded	No recorded non-water small molecule	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
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 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 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 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 ligand/ion 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 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：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 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：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 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：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 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：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 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：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 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：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 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：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 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：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 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 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 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 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 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 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 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 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 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 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 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	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 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	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 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 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：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 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）	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 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 36 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 3–104； UniProt 302–403 Author chain B； PDBConstruct 3–104； UniProt 302–403 Author chain C； PDBConstruct 3–104； UniProt 302–403 Author chain D； PDBConstruct 3–104； UniProt 302–403

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	3i4w
Deposition date deposition_date	2009-07-03
Structure title title	Crystal Structure of the third PDZ domain of PSD-95
Keywords keywords	;alpha and beta protein, Cell junction, Cell membrane, Lipoprotein, Membrane, Palmitate, Phosphoprotein, Postsynaptic cell membrane, SH3 domain, Synapse, 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	24.78 Å
Radius of gyration Rg (electron density) rg_electron	23.93 Å
Forward intensity I(0) i0	31925100.00
Molecular weight molecular_weight	42289.0 kDa
Excluded volume excluded_volume	52642 Å³
Envelope volume envelope_volume	66814 Å³
Hydration-shell volume shell_volume	24110 Å³
Envelope diameter envelope_diameter	87.7 Å
Shell Rg shell_rg	29.99 Å
Envelope Rg envelope_rg	23.97 Å
Shape Rg shape_rg	23.93 Å
Total Rg total_rg	24.70 Å
Total atoms total_atoms	2988
Residues n_residues	388
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	88.7 Å
Rg (real space) rg_real	24.81 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	3.1930e+07
I(0) uncertainty (real space) i0_real_error	4.8100e+05
Rg (reciprocal space) rg_reciprocal	24.81 Å
I(0) (reciprocal space) i0_reciprocal	31920000.0000
Solution quality estimate total_estimate	0.5718
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.205
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11360000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.684; Stabil: 0.989; Sysdev: 0.184; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Disks large homolog 4
Molecular weight formula_weight	11129.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3241

MGLGEEDIPREPRRIVIHRGSTGLGFNIVGGENGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3i4wa_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3i4wb_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3i4wc_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3i4wd_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

CATH v4.4 (4 domains)

Domain ID domain_id	3i4wA00
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	3i4wB00
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	3i4wC00
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	3i4wD00
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	43.322 Å
Unit-cell length b length_b	42.152 Å
Unit-cell length c length_c	47.602 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	92.08 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	47.619 Å
R factor r_factor	0.1890
R_work r_work	0.1870
R_free r_free	0.2160

fit	/app/data/saxs_computation/i4/3i4w/3i4w.fit
pddf	/app/data/pr_computation/i4/3i4w/3i4w.pr.out
profile	/app/data/saxs_computation/i4/3i4w/3i4w.dat