1YR5: 1.7-A structure of calmodulin

1.7-A structure of calmodulin bound to a peptide from DAP kinase. Determined by X-ray diffraction at 1.7 Å resolution. Released 4 Jul 2006.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,595
Mol. weight: 19.27 kDa
Ligands: CA
Released: 4 Jul 2006

Explore 1YR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YR5 contains 9 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: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	27	1	1
α-helix	29-38	10
α-helix	45-53	9
β-strand	63	1	1
α-helix	65-75	11
α-helix	83-92	10
β-strand	99-100	2	2
α-helix	102-112	11
α-helix	118-128	11
β-strand	136-137	2	2
α-helix	138-144	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	304-318	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
calmodulin	A	protein	148	Homo sapiens	P0DP23 (AlphaFold model)
19-mer from Death-associated protein kinase 1	B	protein	19		P53355 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1YR5_1 calmodulin (chains A)
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN
GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE
VDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 2 (B), FASTA

>1YR5_2 19-mer from Death-associated protein kinase 1 (chains B)
RKKWKQSVRLISLCQRLSR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

Recognition of human death-associated protein kinases by calmodulin. Kursula, P., Vahokoski, J., Wilmanns, M. To be published.

Other PDB entries of the same protein (UniProt P0DP23 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MXD 1.17 Å, Human E104A calmodulin:MLCK RM20 complex
7BF1 1.24 Å, Ca2+-Calmodulin in complex with peptide from brain-type creatine kinase in extended 1:2…
6XXX 1.25 Å, 1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex
4DJC 1.35 Å, 1.35 A crystal structure of the NaV1.5 DIII-IV-Ca/CaM complex
7BF2 1.43 Å, Ca2+-Calmodulin in complex with human muscle form creatine kinase peptide in extended…
2F3Y 1.45 Å, Calmodulin/IQ domain complex
2W73 1.45 Å, High-resolution structure of the complex between calmodulin and a peptide from…
4LZX 1.5 Å, Complex of IQCG and Ca2+-free CaM
5V03 1.58 Å, A positive allosteric modulator binding pocket in SK2 ion channels is shared by Riluzole…
9MVW 1.58 Å, Crystal structure of S101F calmodulin - CaM:RM20 analog complex
2F3Z 1.6 Å, Calmodulin/IQ-AA domain complex
6M7H 1.6 Å, Structure of calmodulin with KN93

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