5NIN: AKAP79 calmodulin binding domain peptide

Crystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin. Determined by X-ray diffraction at 1.7 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,945
Mol. weight: 38.13 kDa
Ligands: CA
Released: 6 Dec 2017

Explore 5NIN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NIN contains 18 α-helices and 8 β-strands across 4 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	6-17	12
β-strand	26-28	3	3
α-helix	29-38	10
α-helix	45-54	10
β-strand	62-64	3	3
α-helix	65-78	14
α-helix	81-92	12
β-strand	99-100	2	4
α-helix	102-111	10
α-helix	118-128	11
β-strand	136-137	2	4
α-helix	138-145	8

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	26-28	3	1
α-helix	29-38	10
α-helix	45-53	9
β-strand	62-64	3	1
α-helix	65-78	14
α-helix	81-92	12
β-strand	99-100	2	2
α-helix	102-112	11
α-helix	118-128	11
β-strand	136-137	2	2
α-helix	138-146	9

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	79-83	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	80-83	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin	A, B	protein	149	Homo sapiens	P0DP23 (AlphaFold model)
A-kinase anchor protein 5	C, D	protein	16	Homo sapiens	P24588 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5NIN_1 Calmodulin (chains A, B)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 2 (C, D), FASTA

>5NIN_2 A-kinase anchor protein 5 (chains C, D)
GAWASLKRLVTRRKRS

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular basis of AKAP79 regulation by calmodulin. Patel, N., Stengel, F., Aebersold, R. et al. Nat Commun (2017) 8:1681-1681. DOI 10.1038/s41467-017-01715-w · PubMed

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

Browse structure collections

About this viewer

MolViewer shows 5NIN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.