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1kef

PDZ1 of SAP90

Method: SOLUTION NMR Dmax: 44.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

synapse associated protein-90

Homo sapiens

UniProt P78352

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 105–197 Fragment：PDZ1 domain No other associated polymer 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

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 1KEF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 oligomeric state Different ligand/ion Different experimental conditions 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 experimental method 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 experimental method 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 conditions 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 experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 ligand/ion Different experimental method 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 1–93； UniProt 105–197

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

SAXS profile for 1kef

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kef
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kef
Deposition date deposition_date2001-11-15
Structure title titlePDZ1 of SAP90
Keywords keywordsbeta-sheet, anti-parallel beta-sandwich, GLGF loop, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.28 Å
Radius of gyration Rg (electron density) rg_electron12.54 Å
Forward intensity I(0) i02286940.00
Molecular weight molecular_weight10015.0 kDa
Excluded volume excluded_volume12472 ų
Envelope volume envelope_volume15212 ų
Hydration-shell volume shell_volume10415 ų
Envelope diameter envelope_diameter44.5 Å
Shell Rg shell_rg18.14 Å
Envelope Rg envelope_rg12.83 Å
Shape Rg shape_rg12.53 Å
Total Rg total_rg13.98 Å
Total atoms total_atoms1412
Residues n_residues93
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax44.3 Å
Rg (real space) rg_real14.16 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real2.2870e+06
I(0) uncertainty (real space) i0_real_error2.6910e+04
Rg (reciprocal space) rg_reciprocal14.17 Å
I(0) (reciprocal space) i0_reciprocal2287000.0000
Solution quality estimate total_estimate0.8180
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.1 Å
Skewness Skewness skewness0.061
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha430300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kefa_
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.1 — PDZ domain

CATH v4.4 (1 domains)

Domain ID domain_id1kefA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
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8. Citations (1)

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9. Files and Curves (10)