SAXSdb — 3gp2

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

Calmodulin

Gallus gallus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–148	Not recorded	Calcium/calmodulin-dependent protein kinase type II delta chain × 2 （Q13557） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–148	Not recorded	Calcium/calmodulin-dependent protein kinase type II delta chain × 1 （Q13557） 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

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 3GP2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AHR CALMODULIN MUTANT WITH A TWO RESIDUE DELETION IN THE CENTRAL HELIX Deposited 1997-04-10	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 1–148（148 aa）	Mutation：DEL(T79), DEL(D80)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.25；28-33% MPD, 15% ETHANOL, 5MM CACL, 20MM NA ACETATE, PH 4.25	Resolution 1.80 Å
1UP5 Chicken Calmodulin Deposited 2003-09-27	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 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；HANGING DROPS 12UL CAM 12MG/ML + 8UL PRECIPITANT, SEEDED 10MM NAOAC, PH 4.0, 30% MPD, 15% ISOPROPANOL	Resolution 1.90 Å R-free 0.259
1UP5 Chicken Calmodulin Deposited 2003-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；HANGING DROPS 12UL CAM 12MG/ML + 8UL PRECIPITANT, SEEDED 10MM NAOAC, PH 4.0, 30% MPD, 15% ISOPROPANOL	Resolution 1.90 Å R-free 0.259
2BCX Crystal structure of calmodulin in complex with a ryanodine receptor peptide Deposited 2005-10-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；23% PEG 4000, 0.1 M sodium acetate, 5 mM DTT, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.249
2BKI Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure Deposited 2005-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–148（148 aa） Chain D 1–148（148 aa）	Not recorded	SO4 SULFATE ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL	Resolution 2.90 Å R-free 0.304
2KZ2 Calmodulin, C-terminal domain, F92E mutant Deposited 2010-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–149（73 aa） Fragment：UNP residues 77-149	Mutation：F92E	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.9；293 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] cCaMF92E-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] cCaMF92E-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M3S Calmodulin, i85l, f92e, h107i, l112r, a128t, m144r mutant Deposited 2013-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa） Fragment：UNP residues 1-149	Mutation：I85L, F92E, H107I, L107I, A128T, M144R	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.91；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.68 mM [U-100% 13C; U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2O5G Calmodulin-smooth muscle light chain kinase peptide complex Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；30% PEG 400, 0.2 M sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.08 Å R-free 0.165
2O60 Calmodulin bound to peptide from neuronal nitric oxide synthase Deposited 2006-12-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；20% PEG 4000, 0.2 M sodium acetate, 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.55 Å R-free 0.244
2VB6 Myosin VI (MD-insert2-CaM, Delta Insert1) Post-rigor state (crystal form 2) Deposited 2007-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 10% PEG 8000, 50MM GLYCINE PH 9.5, 6% MPD	Resolution 2.30 Å R-free 0.253
3GOF Calmodulin bound to peptide from macrophage nitric oxide synthase Deposited 2009-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.45 Å R-free 0.208
3GOF Calmodulin bound to peptide from macrophage nitric oxide synthase Deposited 2009-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.45 Å R-free 0.208
5HIT Crystal Structure Analysis of Ca2+-calmodulin and a C-terminal EAG1 channel fragment Deposited 2016-01-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–148（147 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；di-ammonium citrate, PEG 3350	Resolution 2.85 Å R-free 0.268
6BNV CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state, backbone-averaged with side chains truncated to alanine Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain O 4–148（145 aa） Chain P 4–148（145 aa） Chain Q 4–148（145 aa） Chain R 4–148（145 aa） Chain S 4–148（145 aa） Chain T 4–148（145 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer was filtered through 0.44 um filter and degassed. cryo-EM vitrification conditions Cryogen ETHANE；Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An additional 3 uL of myosin VI was applied. After 60 seconds, 3 uL solution was removed, and the grid was blotted for 3 seconds from the backside with filter paper.	Resolution 4.60 Å

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–147； UniProt 2–148

Calcium/calmodulin-dependent protein kinase type II delta chain

OrganismNot specified

UniProt Q13557

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 294–311	Fragment：residues 294-311 Non-standard monomer：Yes (specific site not provided by mmCIF)	Calmodulin × 2 （P62149） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 294–311	Fragment：residues 294-311 Non-standard monomer：Yes (specific site not provided by mmCIF)	Calmodulin × 1 （P62149） 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

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 3GP2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VN9 Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD Deposited 2008-01-31	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 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	Different construct Different mutation/modification 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 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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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
5VLO The structure of human CamKII with bound inhibitor Deposited 2017-04-25	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 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	Different construct Different mutation/modification 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 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	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 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	Different construct Different mutation/modification 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 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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	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 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	Different construct Different mutation/modification 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 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

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KCC2D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–20； UniProt 294–311

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gp2
Deposition date deposition_date	2009-03-20
Structure title title	Calmodulin bound to peptide from calmodulin kinase II (CaMKII)
Keywords keywords	;metal binding protein, kinase, ATP-binding, Calmodulin-binding, Nucleotide-binding, Serine/threonine-protein kinase, Transferase, metal binding protein-Transferase complex ;; metal binding protein/Transferase
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	17.04 Å
Radius of gyration Rg (electron density) rg_electron	15.54 Å
Forward intensity I(0) i0	7404400.00
Molecular weight molecular_weight	18835.0 kDa
Excluded volume excluded_volume	23130 Å³
Envelope volume envelope_volume	26773 Å³
Hydration-shell volume shell_volume	14577 Å³
Envelope diameter envelope_diameter	51.6 Å
Shell Rg shell_rg	21.34 Å
Envelope Rg envelope_rg	15.74 Å
Shape Rg shape_rg	15.56 Å
Total Rg total_rg	16.50 Å
Total atoms total_atoms	1309
Residues n_residues	166
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	52.8 Å
Rg (real space) rg_real	16.93 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	7.4040e+06
I(0) uncertainty (real space) i0_real_error	7.9770e+04
Rg (reciprocal space) rg_reciprocal	16.94 Å
I(0) (reciprocal space) i0_reciprocal	7404000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	984000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.975

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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	Calmodulin
Molecular weight formula_weight	16592.2 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	1538

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calcium/calmodulin-dependent protein kinase type II delta chain
Molecular weight formula_weight	2191.7 kDa
EC 编号 ec_number	2.7.11.17
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XSFNARRKLKGAILTTMLATAX

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	200

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3gp2a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

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8. Citations (1)

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Unit-cell length a length_a	69.599 Å
Unit-cell length b length_b	38.409 Å
Unit-cell length c length_c	75.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.460 Å
Low-resolution limit resolution_low	25.080 Å
R factor r_factor	0.1614
R_work r_work	0.1596
R_free r_free	0.1922

fit	/app/data/saxs_computation/gp/3gp2/3gp2.fit
pddf	/app/data/pr_computation/gp/3gp2/3gp2.pr.out
profile	/app/data/saxs_computation/gp/3gp2/3gp2.dat

Calmodulin bound to peptide from calmodulin kinase II (CaMKII)

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

Calmodulin

State in the Current Structure

Other States of the Same Protein in the Database

Calcium/calmodulin-dependent protein kinase type II delta chain

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

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) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)