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1rgr

Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability

Method: SOLUTION NMR Dmax: 44.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Presynaptic density protein 95

Rattus norvegicus

UniProt P31016

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 62–154 Fragment：PDZ1 domain of PSD-95 postsynaptic protein CRIPT peptide × 1 BAL BETA-ALANINE × 1 SOLUTION NMR NMR sample composition：1mM PZ1 U-15N,13C, 3mM peptide, 10 mM phospate buffer 150 mM NaCl, pH 6.8 | 90% H2O/10% D2O 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 1RGR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BE9 THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 IN COMPLEX WITH A C-TERMINAL PEPTIDE DERIVED FROM CRIPT. Deposited 1998-05-20 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 295–420（126 aa） Fragment：THE THIRD PDZ DOMAIN OF PSD-95
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.8 M SODIUM CITRATE, 0.1 M HEPES, PH 7.5
Resolution 1.82 Å R-free 0.278
1BFE THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 Deposited 1998-05-20 Different construct Different oligomeric state 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 302–402（101 aa） Fragment：THE THIRD PDZ DOMAIN OF PSD-95
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.8 M SODIUM CITRATE, 0.1 M HEPES, PH 7.5
Resolution 2.30 Å R-free 0.315
1IU0 The first PDZ domain of PSD-95 Deposited 2002-02-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 61–151（91 aa） Fragment：PDZ1 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1
NMR sample composition 20mM KPi | 10% D2O, 90% H2O
NMR sample composition 20mM KPi | 100% D2O
Resolution not provided
1IU2 The first PDZ domain of PSD-95 Deposited 2002-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 61–151（91 aa） Fragment：PDZ1 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1
NMR sample composition 20mM KPi, 100mM KCl | 10% D2O, 90% H2O
NMR sample composition 20mM KPi, 100mM KCl | 100% D2O
Resolution not provided
1JXM CRYSTAL STRUCTURE OF THE GMP BOUND SH3-HOOK-GK FRAGMENT OF PSD-95 Deposited 2001-09-07 Different construct Different oligomeric state 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 430–724（295 aa） Fragment：SH3-HOOK-GK
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 GAI GUANIDINE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；277 K；2-methyl-2,4-pentanediol, HEPES buffer, guanidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.00 Å R-free 0.260
1JXO Crystal Structure of the SH3-HOOK-GK Fragment of PSD-95 Deposited 2001-09-07 Different construct Different oligomeric state 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 430–724（295 aa） Fragment：SH3-HOOK-GK
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；2-methyl-2,4-pentanediol, MES buffer, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.264
1JXO Crystal Structure of the SH3-HOOK-GK Fragment of PSD-95 Deposited 2001-09-07 Different construct Different oligomeric state 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 430–724（295 aa） Fragment：SH3-HOOK-GK
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；2-methyl-2,4-pentanediol, MES buffer, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.264
1KJW SH3-Guanylate Kinase Module from PSD-95 Deposited 2001-12-05 Different construct Different oligomeric state 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 430–724（295 aa） Fragment：SH3 Domain/Guanylate Kinase Domain
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Ammonium sulfate, PEG 4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 15K
Resolution 1.80 Å R-free 0.250
1QLC Solution structure of the second PDZ domain of Postsynaptic Density-95 Deposited 1999-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–249（95 aa） Fragment：THE SECOND PDZ DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 100；Pressure 1
Resolution not provided
1TP3 PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand Deposited 2004-06-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ 3; residues 302-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；1.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.99 Å R-free 0.296
1TP5 Crystal structure of PDZ3 domain of PSD-95 protein complexed with a peptide ligand KKETWV Deposited 2004-06-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：third PDZ domain (residues 302-402)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；288 K；1.0 M sodium citrate, 0.1 M HEPES, 10 mM sodium chloride, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.54 Å R-free 0.229
1TP5 Crystal structure of PDZ3 domain of PSD-95 protein complexed with a peptide ligand KKETWV Deposited 2004-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 302–402（101 aa） Fragment：third PDZ domain (residues 302-402)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；288 K；1.0 M sodium citrate, 0.1 M HEPES, 10 mM sodium chloride, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 1.54 Å R-free 0.229
1TQ3 Higher resolution crystal structure of the third PDZ domain of post synaptic PSD-95 protein Deposited 2004-06-16 Different construct Different oligomeric state 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 302–402（101 aa） Fragment：third PDZ domain (residues 302-402)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；1.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.89 Å R-free 0.296
2KA9 Solution structure of PSD-95 PDZ12 complexed with cypin peptide Deposited 2008-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 61–249（189 aa） Fragment：N-terminal PDZ12 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 1mM [U-15N] PSD95 PDZ12, 1mM cypin peptide, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2MHO Solution State Structure PSD-95 PDZ1 with 5HT2C Receptor peptide Deposited 2013-11-29 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 60–155（96 aa） Fragment：PDZ 1, UNP residues 60-155
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] protein_1, 2.5 mM protein_2, 1 mM DTT, 0.01 w/v sodium azide, 20 mM sodium phosphate, 90% H2O/10% D2O
Resolution not provided
2XKX Single particle analysis of PSD-95 in negative stain Deposited 2010-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Mutation：YES Mutation：YES No recorded non-water small molecule Experimental method not declared
cryo-EM buffer 20MM TRIS/HCL, 5MM DTT, 1MM EDTA,；pH 7.5；20MM TRIS/HCL, 5MM DTT, 1MM EDTA,
Resolution 22.90 Å
3GSL Crystal structure of PSD-95 tandem PDZ domains 1 and 2 Deposited 2009-03-27 Different construct Different oligomeric state 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 61–249（189 aa） Fragment：PDZ domains 1 and 2: UNP residues 61-249
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；35% v/v 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0. 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.05 Å R-free 0.281
3GSL Crystal structure of PSD-95 tandem PDZ domains 1 and 2 Deposited 2009-03-27 Different construct Different oligomeric state 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 61–249（189 aa） Fragment：PDZ domains 1 and 2: UNP residues 61-249
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；35% v/v 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0. 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.05 Å R-free 0.281
3WP0 Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide Deposited 2014-01-08 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa） Fragment：UNP residues 533-713
Not recorded GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.2M lithium chloride, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.04 Å R-free 0.202
3WP1 Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl Deposited 2014-01-08 Different construct 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 531–713（183 aa） Fragment：UNP residues 531-713
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.268
5D13 Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide Deposited 2015-08-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：unp residues 302-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；20 mM HEPES 100 mM NaCl 1.8 M tri-sodium citrate
Resolution 2.15 Å R-free 0.257
5D13 Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide Deposited 2015-08-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–402（101 aa） Fragment：unp residues 302-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；20 mM HEPES 100 mM NaCl 1.8 M tri-sodium citrate
Resolution 2.15 Å R-free 0.257
5D13 Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 302–402（101 aa） Fragment：unp residues 302-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；20 mM HEPES 100 mM NaCl 1.8 M tri-sodium citrate
Resolution 2.15 Å R-free 0.257
5D13 Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide Deposited 2015-08-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 302–402（101 aa） Fragment：unp residues 302-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；20 mM HEPES 100 mM NaCl 1.8 M tri-sodium citrate
Resolution 2.15 Å R-free 0.257
5GNV Structure of PSD-95/MAP1A complex reveals unique target recognition mode of MAGUK GK domain Deposited 2016-07-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa） Fragment：UNP residues 531-713
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；289 K；0.2M lithium sulfate, 0.1M Bis-Tris pH 6.5 and 25%(w/v) polyethylene glycol 3350
Resolution 2.60 Å R-free 0.257
5HDY The third PDZ domain from the synaptic protein PSD-95 Deposited 2016-01-05 Different construct Different oligomeric state 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 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against microliters of crystallization buffer (1.0 M sodium citrate) at 289 K. Diamond-shaped crystals appeared either spontaneously or with microseeding after 1-5 days and grew to 100-200 microns in length over several weeks.
Resolution 1.80 Å R-free 0.220
5HEB The third PDZ domain from the synaptic protein PSD-95 in complex with a C-terminal peptide derived from CRIPT Deposited 2016-01-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.65 Å R-free 0.195
5HED The third PDZ domain from the synaptic protein PSD-95 in complex with a mutant C-terminal peptide derived from CRIPT (T-2F) Deposited 2016-01-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：T-2F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.125 M sodium citrate, pH 7.1. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.70 Å R-free 0.197
5HET The third PDZ domain from the synaptic protein PSD-95 (G330T mutant) Deposited 2016-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Reservoir solution contained 1.05 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (7 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 2.00 Å R-free 0.213
5HEY The third PDZ domain from the synaptic protein PSD-95 (G330T mutant) in complex with a C-terminal peptide derived from CRIPT Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (8 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.50 Å R-free 0.203
5HF1 The third PDZ domain from the synaptic protein PSD-95 (G330T mutant) in complex with a mutant C-terminal peptide derived from CRIPT (T-2F) Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 6.8. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.75 Å R-free 0.218
5HF4 The third PDZ domain from the synaptic protein PSD-95 (H372A mutant) Deposited 2016-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：H372A GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Reservoir solution contained 0.95 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.75 Å R-free 0.221
5HFB The third PDZ domain from the synaptic protein PSD-95 (H372A mutant) in complex with a C-terminal peptide derived from CRIPT Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：H372A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (8 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.62 Å R-free 0.203
5HFC The third PDZ domain from the synaptic protein PSD-95 (H372A mutant) in complex with a mutant C-terminal peptide derived from CRIPT (T-2F) Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：H372A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.05 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (7 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.85 Å R-free 0.207
5HFD The third PDZ domain from the synaptic protein PSD-95 (G330T, H372A double mutant) Deposited 2016-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T H372A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (13 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.60 Å R-free 0.197
5HFE The third PDZ domain from the synaptic protein PSD-95 (G330T, H372A double mutant) in complex with a C-terminal peptide derived from CRIPT Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T H372A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.25 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.80 Å R-free 0.211
5HFF The third PDZ domain from the synaptic protein PSD-95 (G330T, H372A double mutant) in complex with a mutant C-terminal peptide derived from CRIPT (T-2F) Deposited 2016-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–402（101 aa） Fragment：PDZ-3 domain (UNP residues 302-402)
Mutation：G330T, H372A GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；289 K；Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 6.75. Equal amounts (1.5 microliters) of protein (7 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.
Resolution 1.75 Å R-free 0.221
5MZ7 Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine Deposited 2017-01-31 Different construct Different mutation/modification Different oligomeric state 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 303–402（100 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1.1 M sodium citrate, 0.1 M HEPES
Resolution 1.53 Å R-free 0.221
5MZ7 Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine Deposited 2017-01-31 Different construct Different mutation/modification Different oligomeric state 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 303–402（100 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1.1 M sodium citrate, 0.1 M HEPES
Resolution 1.53 Å R-free 0.221
5MZ7 Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine Deposited 2017-01-31 Different construct Different mutation/modification Different oligomeric state 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 303–402（100 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1.1 M sodium citrate, 0.1 M HEPES
Resolution 1.53 Å R-free 0.221
5MZ7 Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine Deposited 2017-01-31 Different construct Different mutation/modification Different oligomeric state 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 303–402（100 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1.1 M sodium citrate, 0.1 M HEPES
Resolution 1.53 Å R-free 0.221
5W72 Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography Deposited 2017-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 301–402（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5YPO Crystal structure of PSD-95 GK domain in complex with phospho-SAPAP peptide Deposited 2017-11-02 Different construct 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 531–713（183 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；289 K；Condition: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000
Resolution 2.29 Å R-free 0.226
5YPO Crystal structure of PSD-95 GK domain in complex with phospho-SAPAP peptide Deposited 2017-11-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；289 K；Condition: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000
Resolution 2.29 Å R-free 0.226
5YPR Crystal Structure of PSD-95 SH3-GK domain in complex with a synthesized inhibitor Deposited 2017-11-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 426–721（296 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.1M tris pH 8.0, 35% tert-Butanol
Resolution 2.35 Å R-free 0.264
7CQF Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 309–422（114 aa）
Not recorded CL CHLORIDE ION × 1 CHT CHOLINE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M choline chloride, 0.1 M Tris-HCl (pH 7.5), 14 % (w/v) PEG 2000 MME
Resolution 1.80 Å R-free 0.205
7F7G a linear Peptide Inhibitors in complex with GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；(0.02 M Citric acid, 0.08 M BIS-TRIS propane / pH 8.8), 16% w/v Polyethylene glycol 3,350
Resolution 2.45 Å R-free 0.256
7F7G a linear Peptide Inhibitors in complex with GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；(0.02 M Citric acid, 0.08 M BIS-TRIS propane / pH 8.8), 16% w/v Polyethylene glycol 3,350
Resolution 2.45 Å R-free 0.256
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
7F7I Stapled Peptide Inhibitor in complex with PSD95 GK domain Deposited 2021-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 531–713（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；35 % w/v PEP 629, 100 mM HEPES (pH7.5)
Resolution 2.60 Å R-free 0.262
9IUI Crystal structure of PSD-95 GK domain in complex with GK_FingR Deposited 2024-07-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 531–713（183 aa） Fragment：GK domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；289 K；0.1M Sodium Citrate pH 5.0, 20% PEG 20000
Resolution 1.93 Å R-free 0.278
9IUI Crystal structure of PSD-95 GK domain in complex with GK_FingR Deposited 2024-07-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 531–713（183 aa） Fragment：GK domain
Not recorded GOL GLYCEROL × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；289 K；0.1M Sodium Citrate pH 5.0, 20% PEG 20000
Resolution 1.93 Å R-free 0.278
9UDJ Crystal structure of PSD95 in complex with 4-dimethylaminophenol Deposited 2025-04-07 Different construct Different oligomeric state 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 533–713（181 aa） Fragment：Guanylate kinase-like
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 18% w/v Polyethylene glycol 3,350.
Resolution 2.44 Å R-free 0.274
9UDJ Crystal structure of PSD95 in complex with 4-dimethylaminophenol Deposited 2025-04-07 Different construct Different oligomeric state 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 533–713（181 aa） Fragment：Guanylate kinase-like
Not recorded A1EOW 4-(dimethylamino)phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 18% w/v Polyethylene glycol 3,350.
Resolution 2.44 Å R-free 0.274

40 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DLG4_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–93； UniProt 62–154

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 1rgr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1rgr
Deposition date deposition_date2003-11-12
Structure title titleCyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability
Keywords keywordsPDZ1 domain, STRUCTURAL PROTEIN-DE NOVO PROTEIN COMPLEX; STRUCTURAL PROTEIN/DE NOVO PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.98 Å
Radius of gyration Rg (electron density) rg_electron12.53 Å
Forward intensity I(0) i0796664000.00
Molecular weight molecular_weight238090.0 kDa
Excluded volume excluded_volume297860 ų
Envelope volume envelope_volume25008 ų
Hydration-shell volume shell_volume14181 ų
Envelope diameter envelope_diameter48.4 Å
Shell Rg shell_rg20.83 Å
Envelope Rg envelope_rg15.04 Å
Shape Rg shape_rg12.51 Å
Total Rg total_rg12.72 Å
Total atoms total_atoms33682
Residues n_residues2178
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 dmax44.4 Å
Rg (real space) rg_real12.88 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real7.9670e+08
I(0) uncertainty (real space) i0_real_error8.8080e+06
Rg (reciprocal space) rg_reciprocal12.89 Å
I(0) (reciprocal space) i0_reciprocal796700000.0000
Solution quality estimate total_estimate0.8630
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.9 Å
Skewness Skewness skewness0.058
Kurtosis Kurtosis kurtosis-0.396
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha255700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1rgra_
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_id1rgrA00
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)