SMTL ID : 9o53.1

Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small molecule inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-4-4-mer

Ligands

4 x 01: N-(2,1,3-benzoxadiazol-4-yl)-3-(4-methoxybenzene-1-sulfonamido)benzamide

01.1: 17 residues within 4Å: Chain A: L.205, L.206, S.209, I.210, L.212, W.213, A.216, I.243, S.244, F.247, L.248, T.269, M.272, T.277, V.280 Chain B: I.271, A.274 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.216, A:I.243, A:F.247, A:F.247, A:L.248, A:T.269, A:V.280, B:I.271 Hydrogen bonds: A:S.209, A:S.209, A:S.209 pi-Stacking: A:W.213, A:F.247 01.6: 17 residues within 4Å: Chain B: L.205, L.206, S.209, I.210, L.212, W.213, A.216, I.243, S.244, F.247, L.248, T.269, M.272, T.277, V.280 Chain C: I.271, A.274 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:I.271, B:A.216, B:I.243, B:F.247, B:F.247, B:L.248, B:T.269, B:V.280 Hydrogen bonds: B:S.209, B:S.209, B:S.209 pi-Stacking: B:W.213, B:F.247 01.7: 17 residues within 4Å: Chain C: L.205, L.206, S.209, I.210, L.212, W.213, A.216, I.243, S.244, F.247, L.248, T.269, M.272, T.277, V.280 Chain D: I.271, A.274 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.216, C:I.243, C:F.247, C:F.247, C:L.248, C:T.269, C:V.280, D:I.271 Hydrogen bonds: C:S.209, C:S.209, C:S.209 pi-Stacking: C:W.213, C:F.247 01.8: 17 residues within 4Å: Chain A: I.271, A.274 Chain D: L.205, L.206, S.209, I.210, L.212, W.213, A.216, I.243, S.244, F.247, L.248, T.269, M.272, T.277, V.280 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.216, D:I.243, D:F.247, D:F.247, D:L.248, D:T.269, D:V.280, A:I.271 Hydrogen bonds: D:S.209, D:S.209, D:S.209 pi-Stacking: D:W.213, D:F.247

4 x K: POTASSIUM ION(Non-covalent)

K.2: 9 residues within 4Å: Chain A: G.251, Y.252 Chain B: G.251, Y.252 Chain C: G.251, Y.252 Chain D: G.251, Y.252 Ligands: K.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C Metal complexes: A:G.251, D:G.251, B:G.251, B:Y.252, C:G.251 K.3: 10 residues within 4Å: Chain A: I.250, G.251 Chain B: I.250, G.251 Chain C: I.250, G.251 Chain D: I.250, G.251 Ligands: K.2, K.4 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:I.250, A:G.251, D:G.251, B:G.251, C:G.251 K.4: 10 residues within 4Å: Chain A: S.249, I.250 Chain B: S.249, I.250 Chain C: S.249, I.250 Chain D: S.249, I.250 Ligands: K.3, K.5 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:S.249, B:S.249, A:S.249, C:S.249 K.5: 5 residues within 4Å: Chain A: S.249 Chain B: S.249 Chain C: S.249 Chain D: S.249 Ligands: K.4 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:S.249, B:S.249, A:S.249, C:S.249

16 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain E: D.21, D.23, D.25, T.27, T.29, E.32 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.23, E:D.25, E:T.27, E:E.32, E:E.32 CA.10: 5 residues within 4Å: Chain E: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.59, E:D.59, E:T.63, E:E.68, E:E.68 CA.11: 6 residues within 4Å: Chain E: D.94, D.96, N.98, Y.100, I.101, E.105 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.94, E:D.96, E:D.96, E:Y.100 CA.12: 6 residues within 4Å: Chain E: D.130, D.132, D.134, Q.136, E.140, E.141 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.132, E:D.132, E:D.134, E:E.141 CA.13: 5 residues within 4Å: Chain F: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.21, F:D.23, F:D.25, F:T.27, F:E.32 CA.14: 6 residues within 4Å: Chain F: D.57, D.59, N.61, T.63, D.65, E.68 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.57, F:D.59, F:T.63, F:E.68 CA.15: 6 residues within 4Å: Chain F: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.94, F:D.96, F:D.96, F:Y.100, F:E.105 CA.16: 5 residues within 4Å: Chain F: D.132, D.134, Q.136, N.138, E.141 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.132, F:D.132, F:D.134, F:Q.136, F:E.141 CA.17: 5 residues within 4Å: Chain G: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.23, G:D.25, G:T.27, G:E.32, G:E.32 CA.18: 6 residues within 4Å: Chain G: D.57, D.59, N.61, T.63, D.65, E.68 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.57, G:D.59, G:T.63, G:E.68 CA.19: 6 residues within 4Å: Chain G: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.94, G:D.96, G:D.96, G:Y.100, G:E.105 CA.20: 5 residues within 4Å: Chain G: D.132, D.134, Q.136, N.138, E.141 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.132, G:D.132, G:D.134, G:Q.136, G:E.141 CA.21: 5 residues within 4Å: Chain H: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.21, H:D.23, H:T.27, H:E.32, H:E.32 CA.22: 6 residues within 4Å: Chain H: D.57, D.59, N.61, T.63, D.65, E.68 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.57, H:D.59, H:T.63, H:E.68 CA.23: 6 residues within 4Å: Chain H: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.94, H:D.96, H:D.96, H:Y.100, H:E.105 CA.24: 5 residues within 4Å: Chain H: D.132, D.134, Q.136, N.138, E.141 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.132, H:D.132, H:D.134, H:Q.136, H:E.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cassell, S.J. et al., Mechanism of SK2 channel gating and its modulation by the bee toxin apamin and small molecules. To Be Published

Release Date

2025-07-09

Peptides

Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera: ABCD
Calmodulin-1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera

Calmodulin-1

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