5V03: PDB entry 5V03

A positive allosteric modulator binding pocket in SK2 ion channels is shared by Riluzole and CyPPA. Determined by X-ray diffraction at 1.58 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 1.58 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,080
Mol. weight: 29.57 kDa
Ligands: CA, 658
Released: 7 Mar 2018

Explore 5V03 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V03 contains 11 α-helices and 6 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 B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	400-401	2	1
α-helix	414-439	26
α-helix	446-485	40
α-helix	486-488	3

Chain R: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	27	1	2
α-helix	29-38	10
α-helix	45-55	11
β-strand	63	1	2
α-helix	65-74	10
β-strand	78-79	2	1
α-helix	82-90	9
β-strand	99-101	3	3
α-helix	102-109	8
α-helix	118-128	11
β-strand	135-137	3	3
α-helix	138-146	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Small conductance calcium-activated potassium channel protein 2	B	protein	102	Homo sapiens	Q9H2S1 (AlphaFold model)
Calmodulin	R	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5V03_1 Small conductance calcium-activated potassium channel protein 2 (chains B)
MGRKLELTKAEKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQ
RKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQLEHHHHHH

Sequence of entity 2 (R), FASTA

>5V03_2 Calmodulin (chains R)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
658	N-(4-chlorophenyl)-2-(3,5-dimethyl-1H-pyrazol-1-yl)pyrimidin-4-amine	C15 H14 Cl N5	1

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

Primary citation

An Intracellular Allosteric Modulator Binding Pocket in SK2 Ion Channels Is Shared by Multiple Chemotypes. Cho, L.T., Alexandrou, A.J., Torella, R. et al. Structure (2018) 26:533-544.e3. DOI 10.1016/j.str.2018.02.017 · PubMed

Other PDB entries of the same protein (UniProt Q9H2S1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V02 1.78 Å, A positive allosteric modulator binding pocket in SK2 ion channels is shared by Riluzole…
5WBX 1.9 Å, Structural insights into the potency of SK/IK channel positive modulators
5WC5 2.3 Å, Structural insights into the potency of SK/IK channel positive modulators
6ALE 2.5 Å, A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves…
9ZRQ 2.77 Å, Cryo-EM structure of KCa2.2/calmodulin channel in complex with SKA31.
9VUC 2.96 Å, channel B complex with 2
9O48 3.1 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex in the Ca2+…
9O5O 3.1 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small…
9O52 3.18 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to the bee…
9VUA 3.23 Å, channel A complex with 1
9O53 3.3 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small…
9ZRR 3.31 Å, Cryo-EM structure of KCa2.2/calmodulin channel in complex with SKA111.

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