SMTL ID : 8ti2.1

Cryo-EM structure of a SUR1/Kir6.2-Q52R ATP-sensitive potassium channel in the presence of PIP2 in the open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

8 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.1: 18 residues within 4Å: Chain A: K.67, W.68, P.69, L.72, T.76, L.80, R.176 Chain E: L.85, F.86, L.92, I.93, L.147, I.150, V.151, I.154, V.155, M.158 Ligands: PT5.14 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain E Hydrophobic interactions: A:L.72, A:T.76, A:L.80, E:L.85, E:F.86, E:L.92, E:I.93, E:I.150, E:V.151, E:I.154, E:V.155, E:V.155 Hydrogen bonds: A:W.68 Salt bridges: A:K.67, A:R.176 PT5.6: 15 residues within 4Å: Chain A: G.53, L.56, Q.57, S.82, L.85, M.163 Chain B: F.38, F.41, I.42, F.132, P.133, K.134, L.135, I.137 Ligands: PT5.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.38, B:K.134, B:L.135, B:I.137, A:L.85 Hydrogen bonds: B:K.134 PT5.11: 18 residues within 4Å: Chain A: L.85, F.86, L.92, I.93, L.147, I.150, V.151, I.154, V.155, M.158 Chain C: K.67, W.68, P.69, L.72, T.76, L.80, R.176 Ligands: PT5.6 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:L.72, C:T.76, C:L.80, A:L.85, A:F.86, A:L.92, A:I.93, A:I.150, A:V.151, A:I.154, A:V.155, A:V.155 Hydrogen bonds: C:W.68 Salt bridges: C:K.67, C:R.176 PT5.12: 18 residues within 4Å: Chain C: L.85, F.86, L.92, I.93, L.147, I.150, V.151, I.154, V.155, M.158 Chain D: K.67, W.68, P.69, L.72, T.76, L.80, R.176 Ligands: PT5.24 15 PLIP interactions: 6 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:L.72, D:T.76, D:L.80, C:L.85, C:F.86, C:L.92, C:I.93, C:I.150, C:V.151, C:I.154, C:V.155, C:V.155 Hydrogen bonds: D:W.68 Salt bridges: D:K.67, D:R.176 PT5.13: 18 residues within 4Å: Chain D: L.85, F.86, L.92, I.93, L.147, I.150, V.151, I.154, V.155, M.158 Chain E: K.67, W.68, P.69, L.72, T.76, L.80, R.176 Ligands: PT5.19 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.85, D:F.86, D:L.92, D:I.93, D:I.150, D:V.151, D:I.154, D:V.155, D:V.155, E:L.72, E:T.76, E:L.80 Hydrogen bonds: E:W.68 Salt bridges: E:K.67, E:R.176 PT5.14: 15 residues within 4Å: Chain E: G.53, L.56, Q.57, S.82, L.85, M.163 Chain F: F.38, F.41, I.42, F.132, P.133, K.134, L.135, I.137 Ligands: PT5.1 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.85, F:F.38, F:F.38, F:K.134, F:L.135, F:I.137 Hydrogen bonds: E:Q.57, F:K.134 PT5.19: 15 residues within 4Å: Chain D: G.53, L.56, Q.57, S.82, L.85, M.163 Chain G: F.38, F.41, I.42, F.132, P.133, K.134, L.135, I.137 Ligands: PT5.13 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain G Hydrophobic interactions: D:L.85, G:F.38, G:F.38, G:K.134, G:L.135, G:I.137 Hydrogen bonds: D:Q.57, G:K.134 PT5.24: 15 residues within 4Å: Chain C: G.53, L.56, Q.57, S.82, L.85, M.163 Chain H: F.38, F.41, I.42, F.132, P.133, K.134, L.135, I.137 Ligands: PT5.12 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain H Hydrophobic interactions: C:L.85, H:F.38, H:F.38, H:K.134, H:L.135, H:I.137 Hydrogen bonds: C:Q.57, H:K.134

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.2: 4 residues within 4Å: Chain A: T.130 Chain C: T.130 Chain D: T.130 Chain E: T.130 No protein-ligand interaction detected (PLIP) K.3: 8 residues within 4Å: Chain A: G.132, F.133 Chain C: G.132, F.133 Chain D: G.132, F.133 Chain E: G.132, F.133 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Metal complexes: E:G.132, E:F.133, C:G.132, D:F.133, A:F.133 K.4: 8 residues within 4Å: Chain A: T.130, I.131 Chain C: T.130, I.131 Chain D: T.130, I.131 Chain E: T.130, I.131 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A Metal complexes: C:T.130, C:I.131, D:T.130, A:T.130, A:I.131 K.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.7: 10 residues within 4Å: Chain B: H.62, W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231 Ligands: P5S.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.225, B:W.231, B:W.231 Hydrogen bonds: B:H.62, B:N.223, B:N.223, B:S.226 Salt bridges: B:H.125 PEF.15: 10 residues within 4Å: Chain F: H.62, W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231 Ligands: P5S.16 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:L.225, F:W.231, F:W.231 Hydrogen bonds: F:H.62, F:N.223, F:N.223, F:S.226 Salt bridges: F:H.125 PEF.20: 10 residues within 4Å: Chain G: H.62, W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231 Ligands: P5S.21 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:L.225, G:W.231, G:W.231 Hydrogen bonds: G:H.62, G:N.223, G:N.223, G:S.226 Salt bridges: G:H.125 PEF.25: 10 residues within 4Å: Chain H: H.62, W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231 Ligands: P5S.26 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:L.225, H:W.231, H:W.231 Hydrogen bonds: H:H.62, H:N.223, H:N.223, H:S.226 Salt bridges: H:H.125

8 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.8: 12 residues within 4Å: Chain A: R.52 Chain B: H.61, H.62, W.75, L.82, I.118, V.122, H.125, N.126, L.364 Ligands: PEF.7, P5S.9 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.75, B:L.82, B:I.118, B:I.118, B:V.122, B:L.364 Hydrogen bonds: B:H.61, B:H.62, B:N.126 Salt bridges: B:H.125, B:H.125, A:R.52 P5S.9: 14 residues within 4Å: Chain B: N.72, I.76, F.79, F.83, L.224, K.227, G.228, R.298, L.301, F.305, L.368, T.371, F.372 Ligands: P5S.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.76, B:F.83, B:F.305, B:L.368, B:L.368, B:T.371, B:F.372 Salt bridges: B:R.298 P5S.16: 12 residues within 4Å: Chain E: R.52 Chain F: H.61, H.62, W.75, L.82, I.118, V.122, H.125, N.126, L.364 Ligands: PEF.15, P5S.17 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain F Salt bridges: E:R.52, F:H.125, F:H.125 Hydrophobic interactions: F:W.75, F:I.118, F:I.118, F:V.122, F:L.364 Hydrogen bonds: F:H.61, F:H.62, F:N.126 P5S.17: 14 residues within 4Å: Chain F: N.72, I.76, F.79, F.83, L.224, K.227, G.228, R.298, L.301, F.305, L.368, T.371, F.372 Ligands: P5S.16 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.76, F:F.83, F:F.305, F:L.368, F:L.368, F:T.371, F:F.372 Salt bridges: F:R.298 P5S.21: 12 residues within 4Å: Chain D: R.52 Chain G: H.61, H.62, W.75, L.82, I.118, V.122, H.125, N.126, L.364 Ligands: PEF.20, P5S.22 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:W.75, G:I.118, G:I.118, G:V.122, G:L.364 Hydrogen bonds: G:H.61, G:H.62, G:N.126 Salt bridges: G:H.125, G:H.125, D:R.52 P5S.22: 14 residues within 4Å: Chain G: N.72, I.76, F.79, F.83, L.224, K.227, G.228, R.298, L.301, F.305, L.368, T.371, F.372 Ligands: P5S.21 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.76, G:F.83, G:F.305, G:L.368, G:L.368, G:T.371, G:F.372 Salt bridges: G:R.298 P5S.26: 12 residues within 4Å: Chain C: R.52 Chain H: H.61, H.62, W.75, L.82, I.118, V.122, H.125, N.126, L.364 Ligands: PEF.25, P5S.27 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:W.75, H:I.118, H:I.118, H:V.122, H:L.364 Hydrogen bonds: H:H.61, H:H.62, H:N.126 Salt bridges: H:H.125, H:H.125, C:R.52 P5S.27: 14 residues within 4Å: Chain H: N.72, I.76, F.79, F.83, L.224, K.227, G.228, R.298, L.301, F.305, L.368, T.371, F.372 Ligands: P5S.26 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:I.76, H:F.83, H:F.305, H:L.368, H:L.368, H:T.371, H:F.372 Salt bridges: H:R.298

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 2 residues within 4Å: Chain B: N.10, Q.339 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.10, B:Q.339 NAG.18: 2 residues within 4Å: Chain F: N.10, Q.339 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.10, F:Q.339 NAG.23: 2 residues within 4Å: Chain G: N.10, Q.339 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.10, G:Q.339 NAG.28: 2 residues within 4Å: Chain H: N.10, Q.339 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.10, H:Q.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Driggers, C.M. et al., Structure of an open K ATP channel reveals tandem PIP 2 binding sites mediating the Kir6.2 and SUR1 regulatory interface. Nat Commun (2024)

Release Date

2024-04-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

B
E

F
H

G
G

H
F

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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