2w2c

STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA

Method: X-RAY DIFFRACTION

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

CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 14	ACETATE ION × 14 CADMIUM ION × 6 water × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KCC2D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–144； UniProt 334–475 Author chain B； PDBConstruct 3–144； UniProt 334–475 Author chain C； PDBConstruct 3–144； UniProt 334–475 Author chain D； PDBConstruct 3–144； UniProt 334–475 Author chain E； PDBConstruct 3–144； UniProt 334–475 Author chain F； PDBConstruct 3–144； UniProt 334–475 Author chain G； PDBConstruct 3–144； UniProt 334–475 Author chain H； PDBConstruct 3–144； UniProt 334–475 Author chain I； PDBConstruct 3–144； UniProt 334–475 Author chain J； PDBConstruct 3–144； UniProt 334–475 Author chain K； PDBConstruct 3–144； UniProt 334–475 Author chain L； PDBConstruct 3–144； UniProt 334–475 Author chain M； PDBConstruct 3–144； UniProt 334–475 Author chain N； PDBConstruct 3–144； UniProt 334–475

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	2w2c
Deposition date deposition_date	2008-10-28
Structure title title	STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA
Keywords keywords	SERINE/THREONINE-PROTEIN KINASE, KINASE, TRANSFERASE, ATP-BINDING, PHOSPHOPROTEIN, CALMODULIN-BINDING, NUCLEOTIDE-BINDING; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2w2c__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2w2c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w2c__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.61 Å
Rg (electron density)	42.70 Å
Total Rg	43.18 Å
Atom count	13974
Residues	1787
Excluded volume	244760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w2c__assembly_1__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
Molecular weight formula_weight	16414.4 kDa
EC 编号 ec_number	2.7.11.17
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	14067

SMSNTTIEDEDVKARKQEIIKVTEQLIEAINNGDFEAYTKICDPGLTAFEPEALGNLVEGMDFHRFYFENALSKSNKPIHTIILNPHVHLVGDDAACIAYIRLTQYMDGSGMPKTMQSEETRVWHRRDGKWQNVHFHRSGSPTV

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d2w2ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2ce_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2ch_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2ci_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2ck_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

Domain ID domain_id	d2w2cn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

CATH v4.4 (14 domains)

Domain ID domain_id	2w2cA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cH00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cJ00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cL00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cM00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2w2cN00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	149.546 Å
Unit-cell length b length_b	117.803 Å
Unit-cell length c length_c	160.761 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	56

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	44.800 Å
R factor r_factor	0.2120
R_work r_work	0.2110
R_free r_free	0.2450

STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA

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

CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2w2c__assembly_1__model_1

2w2c__assembly_1__model_1 | I(q)

2w2c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (1)

STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA

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

CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2w2c__assembly_1__model_1

2w2c__assembly_1__model_1 | I(q)

2w2c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (1)