5hdy

The third PDZ domain from the synaptic protein PSD-95

Method: X-RAY DIFFRACTION D_max: 56.4 Å Quality: GOOD

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

Disks large homolog 4

Rattus norvegicus

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 302–402	Fragment：PDZ-3 domain (UNP residues 302-402)	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

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 5HDY	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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–151（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–151（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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
1RGR Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability Deposited 2003-11-12	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 A 62–154（93 aa） Fragment：PDZ1 domain of PSD-95	Not recorded	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
1TP3 PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand Deposited 2004-06-15	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 ligand/ion 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 method Different experimental conditions Different structure-quality metrics	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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–402（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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 302–402（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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 6–106； UniProt 302–402

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	5hdy
Deposition date deposition_date	2016-01-05
Structure title title	The third PDZ domain from the synaptic protein PSD-95
Keywords keywords	PDZ, GLGF, DHR, adhesion, synapse, synaptic density, peptide-binding domain, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	15.61 Å
Radius of gyration Rg (electron density) rg_electron	14.26 Å
Forward intensity I(0) i0	3498280.00
Molecular weight molecular_weight	12666.0 kDa
Excluded volume excluded_volume	15685 Å³
Envelope volume envelope_volume	18323 Å³
Hydration-shell volume shell_volume	11291 Å³
Envelope diameter envelope_diameter	53.5 Å
Shell Rg shell_rg	19.65 Å
Envelope Rg envelope_rg	14.76 Å
Shape Rg shape_rg	14.26 Å
Total Rg total_rg	15.41 Å
Total atoms total_atoms	1770
Residues n_residues	117
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	56.4 Å
Rg (real space) rg_real	15.56 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	3.4980e+06
I(0) uncertainty (real space) i0_real_error	4.0730e+04
Rg (reciprocal space) rg_reciprocal	15.57 Å
I(0) (reciprocal space) i0_reciprocal	3498000.0000
Solution quality estimate total_estimate	0.8466
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.262
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	528400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.993

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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	12738.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2337

GSPEFLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEANSRVDSSGRIVTD

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5hdya1
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	d5hdya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hdya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	5hdyA00
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	89.657 Å
Unit-cell length b length_b	89.657 Å
Unit-cell length c length_c	89.657 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	1.801 Å
Low-resolution limit resolution_low	40.096 Å
R factor r_factor	0.1899
R_work r_work	0.1865
R_free r_free	0.2198

fit	/app/data/saxs_computation/hd/5hdy/5hdy.fit
pddf	/app/data/pr_computation/hd/5hdy/5hdy.pr.out
profile	/app/data/saxs_computation/hd/5hdy/5hdy.dat