6nid

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

Method: X-RAY DIFFRACTION D_max: 68.7 Å Quality: EXCELLENT

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

Peripheral plasma membrane protein CASK

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 102–187	Not recorded	Neurexin-1 × 1 （Q9ULB1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 102–187	Not recorded	Neurexin-1 × 1 （Q9ULB1） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 102–187	Not recorded	Neurexin-1 × 1 （Q9ULB1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240

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 6NID	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KGD Crystal Structure of the Guanylate Kinase-like Domain of Human CASK Deposited 2001-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 734–909（176 aa） Fragment：guanylate kinase like domain	Not recorded	FMT FORMIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；sodium formate, potassium chloride, magnesium chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.31 Å R-free 0.212
1KWA HUMAN CASK/LIN-2 PDZ DOMAIN Deposited 1998-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 487–572（86 aa） Fragment：PDZ DOMAIN	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；294 K；PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K	Resolution 1.93 Å R-free 0.298
1KWA HUMAN CASK/LIN-2 PDZ DOMAIN Deposited 1998-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 487–572（86 aa） Fragment：PDZ DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；294 K；PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K	Resolution 1.93 Å R-free 0.298
1KWA HUMAN CASK/LIN-2 PDZ DOMAIN Deposited 1998-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 487–572（86 aa） Fragment：PDZ DOMAIN Chain B 487–572（86 aa） Fragment：PDZ DOMAIN	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；294 K；PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K	Resolution 1.93 Å R-free 0.298
1KWA HUMAN CASK/LIN-2 PDZ DOMAIN Deposited 1998-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 487–572（86 aa） Fragment：PDZ DOMAIN Chain B 487–572（86 aa） Fragment：PDZ DOMAIN	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；294 K；PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K	Resolution 1.93 Å R-free 0.298
1KWA HUMAN CASK/LIN-2 PDZ DOMAIN Deposited 1998-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 487–572（86 aa） Fragment：PDZ DOMAIN Chain B 487–572（86 aa） Fragment：PDZ DOMAIN	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；294 K；PROTEIN WAS CRYSTALLIZED IN 1.8M AMMONIUM SULFATE AND 100MM MES PH 6.5 AT 21 DEGREES C., temperature 294K	Resolution 1.93 Å R-free 0.298
1ZL8 NMR structure of L27 heterodimer from C. elegans Lin-7 and H. sapiens Lin-2 scaffold proteins Deposited 2005-05-05	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 403–456（54 aa） Fragment：L27 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2mM Lin-7/Lin-2C; 20mM HEPES, 5mM TCEP, 0.05% DSS, 0.05% sodium azide, 90% H2O, 10% D2O \| 90% D2O, 10% D2O	Resolution not provided
3C0G CASK CaM-Kinase Domain- 3'-AMP complex, P1 form Deposited 2008-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CaM-Kinase Domain	Not recorded	3AM [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.270
3C0G CASK CaM-Kinase Domain- 3'-AMP complex, P1 form Deposited 2008-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa） Fragment：CaM-Kinase Domain	Not recorded	3AM [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.270
3C0H CASK CaM-Kinase Domain- AMPPNP complex, P1 form Deposited 2008-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CaM-Kinase Domain	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.239
3C0H CASK CaM-Kinase Domain- AMPPNP complex, P1 form Deposited 2008-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa） Fragment：CaM-Kinase Domain	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.239
3C0I CASK CaM-Kinase Domain- 3'-AMP complex, P212121 form Deposited 2008-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CaM-Kinase Domain	Not recorded	3AM [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.85 Å R-free 0.234
3MFR CASK-4M CaM Kinase Domain, native Deposited 2010-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CASK-4M CaM kinase domain, residues 1-337	Mutation：Pro22Ala, His145Glu, Gly162Asp, Cys146Asn	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5 % (v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.241
3MFS CASK-4M CaM Kinase Domain, AMPPNP Deposited 2010-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CASK-4M CaM kinase domain, rersidues 1-337	Mutation：Pro22Ala, His145Glu, Gly162Asp, Cys146Asn	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5 % (v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.268
3MFT CASK-4M CaM Kinase Domain, Mn2+ Deposited 2010-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CASK-4M CaM kinase domain, residues 1-337	Mutation：Pro22Ala, His145Glu, Gly162Asp, Cys146Asn	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5 % (v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.270
3MFU CASK-4M CaM Kinase Domain, AMPPNP-Mn2+ Deposited 2010-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa） Fragment：CASK-4M CaM kinase domain, residues 1-337	Mutation：Pro22Ala, His145Glu, Gly162Asp, Cys146Asn	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；12.5 % (v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.234
3TAC Crystal Structure of the Liprin-alpha/CASK complex Deposited 2011-08-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–345（345 aa） Fragment：UNP residues 1-345	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.4M ammonium sulfate, 0.2M NaCl, MES buffer, pH 6.5, vapor diffusion, hanging drop, temperature 289K	Resolution 2.20 Å R-free 0.236
6KMH The crystal structure of CASK/Mint1 complex Deposited 2019-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–319（319 aa）	Not recorded	IOD IODIDE ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KI, 20% PEG 3350, pH 7.0	Resolution 2.40 Å R-free 0.224
6KMH The crystal structure of CASK/Mint1 complex Deposited 2019-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–319（319 aa）	Not recorded	IOD IODIDE ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KI, 20% PEG 3350, pH 7.0	Resolution 2.40 Å R-free 0.224
6NH9 Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain Deposited 2018-12-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–187（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；291 K；30% v/v PEG 400 0.1M CAPS	Resolution 1.85 Å R-free 0.263
6NH9 Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain Deposited 2018-12-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 102–187（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；291 K；30% v/v PEG 400 0.1M CAPS	Resolution 1.85 Å R-free 0.263
6NH9 Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain Deposited 2018-12-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 102–187（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；291 K；30% v/v PEG 400 0.1M CAPS	Resolution 1.85 Å R-free 0.263
7OAI Crystal structure of pseudokinase CASK in complex with PFE-PKIS12 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	V5W 4-(Cyclopentylamino)-2-[(2,5-dichlorophenyl)methylamino]-N-[3-(2-oxo-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M MES pH 6.0, 0.1 M magnesium acetate, 0.1 M KCl	Resolution 2.30 Å R-free 0.213
7OAI Crystal structure of pseudokinase CASK in complex with PFE-PKIS12 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	V5W 4-(Cyclopentylamino)-2-[(2,5-dichlorophenyl)methylamino]-N-[3-(2-oxo-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M MES pH 6.0, 0.1 M magnesium acetate, 0.1 M KCl	Resolution 2.30 Å R-free 0.213
7OAI Crystal structure of pseudokinase CASK in complex with PFE-PKIS12 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–337（337 aa）	Not recorded	V5W 4-(Cyclopentylamino)-2-[(2,5-dichlorophenyl)methylamino]-N-[3-(2-oxo-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M MES pH 6.0, 0.1 M magnesium acetate, 0.1 M KCl	Resolution 2.30 Å R-free 0.213
7OAI Crystal structure of pseudokinase CASK in complex with PFE-PKIS12 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–337（337 aa）	Not recorded	V5W 4-(Cyclopentylamino)-2-[(2,5-dichlorophenyl)methylamino]-N-[3-(2-oxo-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M MES pH 6.0, 0.1 M magnesium acetate, 0.1 M KCl	Resolution 2.30 Å R-free 0.213
7OAJ Crystal structure of pseudokinase CASK in complex with compound 7 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	V6E 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5	Resolution 1.93 Å R-free 0.224
7OAJ Crystal structure of pseudokinase CASK in complex with compound 7 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	V6E 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5	Resolution 1.93 Å R-free 0.224
7OAJ Crystal structure of pseudokinase CASK in complex with compound 7 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–337（337 aa）	Not recorded	V6E 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5	Resolution 1.93 Å R-free 0.224
7OAJ Crystal structure of pseudokinase CASK in complex with compound 7 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–337（337 aa）	Not recorded	V6E 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5	Resolution 1.93 Å R-free 0.224
7OAK Crystal structure of pseudokinase CASK in complex with compound 26 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	V6B 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M MES, pH 6.0	Resolution 2.23 Å R-free 0.264
7OAK Crystal structure of pseudokinase CASK in complex with compound 26 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	V6B 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M MES, pH 6.0	Resolution 2.23 Å R-free 0.264
7OAK Crystal structure of pseudokinase CASK in complex with compound 26 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–337（337 aa）	Not recorded	V6B 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M MES, pH 6.0	Resolution 2.23 Å R-free 0.264
7OAK Crystal structure of pseudokinase CASK in complex with compound 26 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–337（337 aa）	Not recorded	V6B 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；12% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M MES, pH 6.0	Resolution 2.23 Å R-free 0.264
7OAL Crystal structure of pseudokinase CASK in complex with compound 25 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	V62 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0	Resolution 2.17 Å R-free 0.274
7OAL Crystal structure of pseudokinase CASK in complex with compound 25 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	V62 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0	Resolution 2.17 Å R-free 0.274
7OAL Crystal structure of pseudokinase CASK in complex with compound 25 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–337（337 aa）	Not recorded	V62 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0	Resolution 2.17 Å R-free 0.274
7OAL Crystal structure of pseudokinase CASK in complex with compound 25 Deposited 2021-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–337（337 aa）	Not recorded	V62 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0	Resolution 2.17 Å R-free 0.274
8Y68 the crystal structure of apo CASK-CaMK Deposited 2024-02-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–332（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG6000.	Resolution 2.20 Å R-free 0.264
8Y68 the crystal structure of apo CASK-CaMK Deposited 2024-02-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–332（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG6000.	Resolution 2.20 Å R-free 0.264
9KYS the Ca2+/CaM-CASK-ARD complex Deposited 2024-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 287–332（46 aa） Chain D 287–332（46 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；magnesium chloride, PEG 3350	Resolution 1.76 Å R-free 0.231
9M5Y the crystal structure of the Ca2+/CaM-CASK-CaMK complex Deposited 2025-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–332（332 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG 6000.	Resolution 1.80 Å R-free 0.197
9M6G the crystal structure of the Ca2+/CaM-CASK-CaMK-Mint1-CID complex Deposited 2025-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–319（319 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MLI MALONATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；0.1 M Sodium malonate, pH 5.0, 12% (v/v) PEG 3350	Resolution 1.70 Å R-free 0.187

21 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSKP_HUMAN
Isoform	O14936-5
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–88； UniProt 102–187 Author chain B； PDBConstruct 3–88； UniProt 102–187 Author chain C； PDBConstruct 3–88； UniProt 102–187

Neurexin-1

OrganismNot specified

UniProt Q9ULB1

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 E； UniProt 1468–1477	Not recorded	Peripheral plasma membrane protein CASK × 1 （O14936）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1468–1477	Not recorded	Peripheral plasma membrane protein CASK × 1 （O14936） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1468–1477	Not recorded	Peripheral plasma membrane protein CASK × 1 （O14936）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.01M tri-sodium citrate 33% (w/v) PEG 6000	Resolution 1.86 Å R-free 0.240

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	NRX1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–10； UniProt 1468–1477 Author chain E； PDBConstruct 1–10； UniProt 1468–1477 Author chain F； PDBConstruct 1–10； UniProt 1468–1477

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	6nid
Deposition date deposition_date	2018-12-27
Structure title title	Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide
Keywords keywords	;PDZ domain, MAGUK protein family, peripheral plasma membrane protein, protein binding, c-terminal peptide binding, Neurexin, protein binding-peptide complex ;; protein binding/peptide
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	21.80 Å
Radius of gyration Rg (electron density) rg_electron	20.93 Å
Forward intensity I(0) i0	18459600.00
Molecular weight molecular_weight	31556.0 kDa
Excluded volume excluded_volume	39259 Å³
Envelope volume envelope_volume	49156 Å³
Hydration-shell volume shell_volume	20180 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	26.73 Å
Envelope Rg envelope_rg	20.91 Å
Shape Rg shape_rg	20.84 Å
Total Rg total_rg	21.97 Å
Total atoms total_atoms	2193
Residues n_residues	276
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	68.7 Å
Rg (real space) rg_real	21.73 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.8460e+07
I(0) uncertainty (real space) i0_real_error	2.3650e+05
Rg (reciprocal space) rg_reciprocal	21.75 Å
I(0) (reciprocal space) i0_reciprocal	18460000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5628000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Peripheral plasma membrane protein CASK
Molecular weight formula_weight	10118.9 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2472

MGRVRLVQFQKNTDEPMGITLKMNELNHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Neurexin-1
Molecular weight formula_weight	1318.5 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

KKNKDKEYYV

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6nidA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	6nidB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	6nidC00
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	36.328 Å
Unit-cell length b length_b	51.177 Å
Unit-cell length c length_c	72.412 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	41.666 Å
R factor r_factor	0.1942
R_work r_work	0.1918
R_free r_free	0.2396

fit	/app/data/saxs_computation/ni/6nid/6nid.fit
pddf	/app/data/pr_computation/ni/6nid/6nid.pr.out
profile	/app/data/saxs_computation/ni/6nid/6nid.dat

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

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

Peripheral plasma membrane protein CASK

State in the Current Structure

Other States of the Same Protein in the Database

Neurexin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)