SMTL ID : 9jo4.1

Cryo-EM structure of human BKca channel-compound 51b complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 01: 5-(5-morpholin-4-ylpentylamino)-2-[2,3,5,6-tetrakis(fluoranyl)-4-(trifluoromethyl)phenoxy]phenol

01.1: 7 residues within 4Å: Chain A: R.20, W.22, W.203, S.259, P.262, N.269 Ligands: Y01.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.22, A:W.203 Hydrogen bonds: A:W.203, A:S.259 pi-Stacking: A:W.22 01.11: 11 residues within 4Å: Chain B: W.22, I.138, E.139, W.203, F.252, S.259, P.262, F.266, N.269, L.299 Ligands: Y01.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.22, B:F.266 Hydrogen bonds: B:W.203, B:S.259 pi-Stacking: B:W.22 01.20: 10 residues within 4Å: Chain C: W.22, I.138, E.139, W.203, S.259, P.262, F.266, N.269, L.299 Ligands: Y01.25 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.138, C:W.203, C:F.266, C:F.266 Hydrogen bonds: C:W.203, C:S.259 pi-Stacking: C:W.22, C:W.22 01.28: 11 residues within 4Å: Chain D: R.20, W.22, I.138, W.203, F.252, S.259, P.262, F.266, N.269, L.299 Ligands: Y01.33 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.138, D:F.266 Hydrogen bonds: D:S.259 pi-Stacking: D:W.22, D:W.22

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.374, T.396, E.399 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.399 MG.12: 2 residues within 4Å: Chain B: E.374, E.399 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.374, B:E.399 MG.21: 3 residues within 4Å: Chain C: E.374, T.396, E.399 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain D: E.374, E.399 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.399

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.367, R.514, S.533, E.535, S.600 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.367, A:R.514, A:S.533, A:E.535, A:S.600 CA.4: 5 residues within 4Å: Chain A: Q.947, D.950, D.953, D.955 Chain D: N.449 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Q.947, A:D.950, A:D.953, A:D.955, A:D.955 CA.13: 5 residues within 4Å: Chain B: D.367, R.514, S.533, E.535, S.600 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.367, B:R.514, B:S.533, B:E.535, B:S.600 CA.14: 5 residues within 4Å: Chain A: N.449 Chain B: Q.947, D.950, D.953, D.955 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Q.947, B:D.950, B:D.953, B:D.955, B:D.955 CA.22: 5 residues within 4Å: Chain C: D.367, R.514, S.533, E.535, S.600 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.367, C:R.514, C:S.533, C:E.535, C:S.600 CA.23: 5 residues within 4Å: Chain B: N.449 Chain C: Q.947, D.950, D.953, D.955 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Q.947, C:D.950, C:D.953, C:D.955, C:D.955 CA.30: 5 residues within 4Å: Chain C: N.449 Chain D: Q.947, D.950, D.953, D.955 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:Q.947, D:D.950, D:D.953, D:D.953, D:D.955 CA.31: 5 residues within 4Å: Chain D: D.367, R.514, S.533, E.535, S.600 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.367, D:R.514, D:S.533, D:E.535, D:S.600

3 x K: POTASSIUM ION(Non-covalent)

K.5: 9 residues within 4Å: Chain A: T.287, V.288 Chain B: T.287, V.288 Chain C: T.287, V.288 Chain D: T.287, V.288 Ligands: K.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:V.288, A:T.287 K.6: 5 residues within 4Å: Chain A: T.287 Chain B: T.287 Chain C: T.287 Chain D: T.287 Ligands: K.5 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Metal complexes: B:T.287, D:T.287, C:T.287 K.15: 6 residues within 4Å: Chain A: G.289, Y.290 Chain B: G.289, Y.290 Chain C: G.289 Chain D: G.289 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:G.289, D:G.289, A:G.289, B:G.289

16 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 6 residues within 4Å: Chain A: W.22, L.26, P.262, W.263 Ligands: 01.1, Y01.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.26, A:P.262, A:W.263 Y01.8: 3 residues within 4Å: Chain A: W.263 Ligands: Y01.7, Y01.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.263, A:W.263, A:W.263, A:W.263, A:W.263 Y01.9: 8 residues within 4Å: Chain A: F.131, S.134, S.135, W.246, Y.274, W.275 Chain D: F.306 Ligands: Y01.10 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.131, A:F.131, A:F.131, A:W.246, A:Y.274, A:Y.274, A:W.275, D:F.306 Hydrogen bonds: A:S.135 Y01.10: 7 residues within 4Å: Chain A: W.275 Chain D: E.264, K.296, T.298, R.301 Ligands: Y01.9, Y01.34 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Salt bridges: D:R.301 Hydrophobic interactions: A:W.275, A:W.275 Y01.16: 8 residues within 4Å: Chain B: F.131, S.134, S.135, W.246, L.247, Y.274, W.275 Ligands: Y01.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.131, B:F.131, B:W.246, B:L.247, B:Y.274, B:W.275 Hydrogen bonds: B:S.135 Y01.17: 6 residues within 4Å: Chain B: W.22, P.262, W.263, N.265 Ligands: 01.11, Y01.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.22, B:P.262 Hydrogen bonds: B:N.265, B:N.265 Y01.18: 5 residues within 4Å: Chain B: W.263, E.264, L.302 Ligands: Y01.17, Y01.27 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.263, B:W.263, B:W.263, B:W.263, B:W.263, B:W.263, B:L.302 Y01.19: 6 residues within 4Å: Chain A: E.264, N.268, F.306 Chain B: W.275 Ligands: Y01.8, Y01.16 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.306, B:W.275, B:W.275, B:W.275 Hydrogen bonds: A:N.268 Y01.24: 9 residues within 4Å: Chain C: F.131, S.134, S.135, I.243, W.246, Y.274, W.275, V.278 Ligands: Y01.27 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.131, C:F.131, C:F.131, C:F.131, C:I.243, C:W.246, C:Y.274, C:W.275, C:V.278 Hydrogen bonds: C:S.135 Y01.25: 7 residues within 4Å: Chain C: W.22, L.26, M.30, P.262, W.263 Ligands: 01.20, Y01.26 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.22, C:L.26, C:P.262, C:W.263 Y01.26: 5 residues within 4Å: Chain C: W.263, L.302, F.306 Ligands: Y01.25, Y01.35 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.263, C:W.263, C:W.263, C:W.263, C:W.263, C:L.302, C:F.306 Y01.27: 8 residues within 4Å: Chain B: K.296, T.298, R.301, L.302 Chain C: W.275, E.276 Ligands: Y01.18, Y01.24 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.275, C:W.275, B:T.298, B:L.302 Hydrogen bonds: C:E.276 Salt bridges: B:R.301 Y01.32: 4 residues within 4Å: Chain D: F.131, I.132, S.135 Ligands: Y01.35 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.131, D:F.131, D:F.131, D:I.132 Hydrogen bonds: D:S.135 Y01.33: 6 residues within 4Å: Chain D: W.22, P.262, W.263, N.265 Ligands: 01.28, Y01.34 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.22, D:W.22, D:P.262, D:W.263, D:W.263 Hydrogen bonds: D:N.265 Y01.34: 4 residues within 4Å: Chain D: W.263, L.302 Ligands: Y01.10, Y01.33 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.263, D:W.263, D:W.263, D:W.263, D:W.263, D:W.263, D:L.302 Y01.35: 5 residues within 4Å: Chain C: F.306 Chain D: W.275, E.276 Ligands: Y01.26, Y01.32 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.275, D:W.275, D:W.275, C:F.306 Hydrogen bonds: D:E.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, S.B. et al., Discovery of Diphenyl Ether Derivatives as Novel BK Ca Channel Activators: Structure-Activity Relationship, Cryo-EM Complex Structures, and In Vivo Animal Studies. J.Med.Chem. (2025)

Release Date

2025-02-26

Peptides

Calcium-activated potassium channel subunit alpha-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Calcium-activated potassium channel subunit alpha-1

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