2KDU: Calmodulin

Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin binding motif with a bipartite binding mode. Determined by solution NMR. Released 15 Dec 2009.

Method: Solution NMR
Organism: Xenopus laevis
Chains: 2
Atoms: 1,463
Mol. weight: 21.06 kDa
Ligands: CA
Released: 15 Dec 2009

Explore 2KDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KDU contains 12 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-19	14
β-strand	26-28	3	1
α-helix	29-38	10
α-helix	45-55	11
α-helix	57-59	3
β-strand	62-64	3	1
α-helix	65-74	10
α-helix	84-92	9
β-strand	100	1	2
α-helix	102-111	10
α-helix	118-128	11
β-strand	136	1	2
α-helix	138-145	8

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	459-478	20
α-helix	487-490	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin	A	protein	148	Xenopus laevis	P0DP33 (AlphaFold model)
Protein unc-13 homolog A	B	protein	36		Q62768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KDU_1 Calmodulin (chains A)
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN
GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE
VDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 2 (B), FASTA

>2KDU_2 Protein unc-13 homolog A (chains B)
GSRAKANWLRAFNKVRMQLQEARGEGEMSKSLWFKG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

Modular architecture of Munc13/calmodulin complexes: dual regulation by Ca2+ and possible function in short-term synaptic plasticity. Rodriguez-Castaneda, F., Maestre-Martinez, M., Coudevylle, N. et al. EMBO J (2010) 29:680-691. DOI 10.1038/emboj.2009.373 · PubMed

Other PDB entries of the same protein (UniProt P0DP33 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IQ5 1.8 Å, Calmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment
2COL 2.2 Å, Crystal structure analysis of CyaA/C-Cam with Pyrophosphate
4R8G 3.5 Å, Crystal Structure of Myosin-1c tail in complex with Calmodulin
1Y0V 3.6 Å, Crystal structure of anthrax edema factor (EF) in complex with calmodulin and…
1CFC Calcium-free calmodulin
1CFD Calcium-free calmodulin
1CFF NMR solution structure of a complex of calmodulin with a binding peptide of the CA2+-pump
1CKK Calmodulin/rat CA2+/CALMODULIN dependent protein kinase fragment
1DMO Calmodulin, NMR, 30 structures
1F70 Refined solution structure of calmodulin N-terminal domain
1F71 Refined solution structure of calmodulin C-terminal domain
1MUX Solution NMR structure of calmodulin/w-7 complex: the basis of diversity in molecular…

Browse structure collections

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