SMTL ID : 9dfx.1

Cryo-EM structure of a SUR1/Kir6.2 ATP-sensitive potassium channel in the presence of Aekatperone in the closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 12 residues within 4Å: Chain A: K.39, I.182, K.185, L.205, Y.330, S.331, K.332, F.333, G.334, N.335 Chain E: N.48, R.50 14 PLIP interactions: 6 interactions with chain E, 8 interactions with chain A Hydrogen bonds: E:N.48, E:R.50, E:R.50, E:R.50, A:K.39, A:K.39, A:S.331, A:S.331, A:G.334, A:N.335, A:N.335 pi-Cation interactions: E:R.50, E:R.50 Salt bridges: A:K.185 ATP.5: 13 residues within 4Å: Chain B: T.404, S.405, N.406, W.688, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775, D.855 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.404, B:N.406, B:N.406, B:G.716, B:G.718, B:K.719, B:S.720, B:S.720, B:S.721, B:Q.775, B:Q.775 Salt bridges: B:K.719, B:K.719 pi-Stacking: B:W.688, B:W.688 ATP.8: 12 residues within 4Å: Chain A: N.48, R.50 Chain C: K.39, I.182, K.185, L.205, Y.330, S.331, K.332, F.333, G.334, N.335 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:K.39, C:K.39, C:S.331, C:S.331, C:G.334, C:N.335, C:N.335, A:N.48, A:R.50, A:R.50, A:R.50 Salt bridges: C:K.185 pi-Cation interactions: A:R.50, A:R.50 ATP.9: 12 residues within 4Å: Chain C: N.48, R.50 Chain D: K.39, I.182, K.185, L.205, Y.330, S.331, K.332, F.333, G.334, N.335 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:N.48, C:R.50, C:R.50, C:R.50, D:K.39, D:K.39, D:S.331, D:S.331, D:G.334, D:N.335, D:N.335 pi-Cation interactions: C:R.50 Salt bridges: D:K.185 ATP.13: 12 residues within 4Å: Chain D: N.48, R.50 Chain E: K.39, I.182, K.185, L.205, Y.330, S.331, K.332, F.333, G.334, N.335 14 PLIP interactions: 8 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:K.39, E:K.39, E:S.331, E:S.331, E:G.334, E:N.335, E:N.335, D:N.48, D:R.50, D:R.50, D:R.50 Salt bridges: E:K.185 pi-Cation interactions: D:R.50, D:R.50

6 x K: POTASSIUM ION(Non-covalent)

K.2: 8 residues within 4Å: Chain A: F.133 Chain C: F.133, G.134 Chain D: F.133, G.134 Chain E: F.133 Ligands: K.3, K.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:F.133 K.3: 10 residues within 4Å: Chain A: G.132, F.133, G.134 Chain C: G.132, F.133 Chain D: G.132, F.133 Chain E: G.132 Ligands: K.2, K.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:G.132, A:F.133, C:G.132, C:F.133 K.4: 7 residues within 4Å: Chain A: T.130, I.131, G.132 Chain C: T.130, I.131 Ligands: K.11, K.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:T.130, C:I.131, A:T.130, A:I.131 K.10: 9 residues within 4Å: Chain A: G.132 Chain C: G.132 Chain D: G.132, F.133, G.134 Chain E: G.132, F.133 Ligands: K.2, K.3 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Metal complexes: D:G.132, D:F.133, E:G.132, E:F.133 K.11: 6 residues within 4Å: Chain C: T.130, I.131 Chain D: T.130, I.131 Ligands: K.4, K.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:T.130, D:I.131, C:T.130 K.12: 7 residues within 4Å: Chain A: T.130, I.131 Chain E: T.130, I.131, G.132 Ligands: K.4, K.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Metal complexes: A:T.130, A:I.131, E:T.130, E:I.131

1 x 01: N-[3-(cyclohexylmethyl)-1H-pyrazol-5-yl]-2-[(1H-imidazol-1-yl)methyl]benzene-1-sulfonamide

01.6: 5 residues within 4Å: Chain A: R.4 Chain B: Y.377, R.1246, W.1297, R.1300 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.377, B:Y.377 Hydrogen bonds: B:R.1246, B:R.1246, B:R.1300, B:R.1300

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.7: 1 residues within 4Å: Chain B: N.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

ElSheikh, A. et al., AI-Based Discovery and CryoEM Structural Elucidation of a KATP Channel Pharmacochaperone. Elife (2024)

Release Date

2025-02-12

Peptides

ATP-sensitive inward rectifier potassium channel 11: ACDE
SUR1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

B
E

Membrane

We predict this structure to be a membrane protein.
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ATP-sensitive inward rectifier potassium channel 11

SUR1

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