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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q13557 New Search
9PDB entries
15Biological assembly
28chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2VN9 Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD Deposited 2008-01-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 11–309（299 aa） Fragment：KINASE DOMAIN, RESIDUES 11-309
Not recorded PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.6 M NAKPO4 HEPES PH 7.5
Resolution 2.30 Å R-free 0.248
2VN9 Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD Deposited 2008-01-31 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 11–309（299 aa） Fragment：KINASE DOMAIN, RESIDUES 11-309
Not recorded PO4 PHOSPHATE ION × 2 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.6 M NAKPO4 HEPES PH 7.5
Resolution 2.30 Å R-free 0.248
2W2C STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA Deposited 2008-10-28 Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
Chain A 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain B 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain C 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain D 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain E 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain F 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain G 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain H 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain I 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain J 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain K 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain L 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain M 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Chain N 334–475（142 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 334-475
Not recorded ACT ACETATE ION × 14 CD CADMIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；30% PEG400, 0.1M CADMIUM CHLORIDE, 0.1M SODIUM ACETATE PH4.6
Resolution 2.70 Å R-free 0.245
2WEL Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin Deposited 2009-03-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 11–335（325 aa） Fragment：KINASE DOMAIN, RESIDUES 11-335
Not recorded K88 (3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE × 1 EDO 1,2-ETHANEDIOL × 6 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M SODIUM POTASSIUM PHOSPHATE, 20% PEG3350 10% ETHYLENE GLYCOL, pH 7.5
Resolution 1.90 Å R-free 0.199
3GP2 Calmodulin bound to peptide from calmodulin kinase II (CaMKII) Deposited 2009-03-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain B 294–311（18 aa） Fragment：residues 294-311
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.46 Å R-free 0.192
3GP2 Calmodulin bound to peptide from calmodulin kinase II (CaMKII) Deposited 2009-03-20 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 294–311（18 aa） Fragment：residues 294-311
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.46 Å R-free 0.192
5VLO The structure of human CamKII with bound inhibitor Deposited 2017-04-25 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 3–301（299 aa） Fragment：UNP residues 3-301
Not recorded 9EJ N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Resolution 2.05 Å R-free 0.226
5VLO The structure of human CamKII with bound inhibitor Deposited 2017-04-25 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 3–301（299 aa） Fragment：UNP residues 3-301
Not recorded 9EJ N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Resolution 2.05 Å R-free 0.226
6AYW The structure of human CamKII with bound inhibitor Deposited 2017-09-08 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 3–301（299 aa） Fragment：UNP residues 3-301
Not recorded C2V N-[2-(dimethylamino)ethyl]-3-[6-(thiophen-2-yl)imidazo[1,2-b]pyridazin-3-yl]benzamide × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 microL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Resolution 2.05 Å R-free 0.267
6AYW The structure of human CamKII with bound inhibitor Deposited 2017-09-08 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 3–301（299 aa） Fragment：UNP residues 3-301
Not recorded C2V N-[2-(dimethylamino)ethyl]-3-[6-(thiophen-2-yl)imidazo[1,2-b]pyridazin-3-yl]benzamide × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 microL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Resolution 2.05 Å R-free 0.267
7ZRP 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 294–315（22 aa）
Not recorded CA CALCIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 2 IMD IMIDAZOLE × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；200 mM Zinc acetate, 100 mM Imidazole pH8.0, 18% PEG3000
Resolution 2.65 Å R-free 0.272
7ZRP 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex Deposited 2022-05-04 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 294–315（22 aa）
Not recorded CA CALCIUM ION × 4 IMD IMIDAZOLE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；200 mM Zinc acetate, 100 mM Imidazole pH8.0, 18% PEG3000
Resolution 2.65 Å R-free 0.272
7ZRQ 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta peptide complex Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 294–315（22 aa）
Not recorded CA CALCIUM ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Na+-HEPES, 0.1 M MOPS (acid), pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
Resolution 1.68 Å R-free 0.244
9BLH Crystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib Deposited 2024-04-30 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 10–309（300 aa）
Not recorded 6ZZ 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M CaCl2, 0.15 M NaCl, 12% (w/v) PEG 3350, 0.7 mM ribociclib and 35% (w/v) ethylene glycol
Resolution 2.35 Å R-free 0.251
9BLH Crystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib Deposited 2024-04-30 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 10–309（300 aa）
Not recorded 6ZZ 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M CaCl2, 0.15 M NaCl, 12% (w/v) PEG 3350, 0.7 mM ribociclib and 35% (w/v) ethylene glycol
Resolution 2.35 Å R-free 0.251

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.