SMTL ID : 7u24.1

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and glibenclamide with Kir6.2-CTD in the up 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: 10 residues within 4Å: Chain A: I.182, F.183, K.185, L.205, Y.330, G.334 Chain D: N.48, I.49, R.50, R.54 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:N.48, D:R.50, D:R.50, D:R.54, A:K.185, A:G.334 Salt bridges: D:R.50, D:R.50, A:K.185, A:K.185, A:K.185 pi-Cation interactions: D:R.50 ATP.6: 13 residues within 4Å: Chain A: N.48, R.50, R.54 Chain B: K.39, I.182, F.183, S.184, K.185, H.186, L.205, Y.330, G.334 Chain E: K.205 12 PLIP interactions: 5 interactions with chain B, 1 interactions with chain E, 6 interactions with chain A Hydrogen bonds: B:K.39, B:K.39, B:K.185, B:G.334, A:N.48, A:R.50, A:R.54, A:R.54 Salt bridges: B:H.186, E:K.205, A:R.50 pi-Cation interactions: A:R.50 ATP.10: 11 residues within 4Å: Chain B: N.48, I.49, R.50 Chain C: K.39, I.182, F.183, S.184, K.185, L.205, Y.330, G.334 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:K.185, C:G.334, B:N.48, B:R.50, B:R.50 Salt bridges: C:K.185, C:K.185, B:R.50 pi-Cation interactions: B:R.50, B:R.50 ATP.14: 11 residues within 4Å: Chain C: N.48, R.50, R.54 Chain D: K.39, I.182, S.184, K.185, L.205, Y.330, F.333, G.334 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.39, D:K.185, D:Y.330, C:R.50, C:R.50, C:R.54 Salt bridges: D:K.185, D:K.185, C:R.50 pi-Cation interactions: C:R.50, C:R.50 ATP.19: 10 residues within 4Å: Chain E: T.404, N.406, W.688, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:T.404, E:N.406, E:G.716, E:C.717, E:G.718, E:K.719, E:S.720, E:S.721, E:Q.775, E:Q.775 pi-Stacking: E:W.688, E:W.688, E:W.688

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 8 residues within 4Å: Chain A: V.89, L.92, A.96, H.97, L.144 Chain E: V.17, V.21 Ligands: P5S.5 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:V.21, A:V.89, A:L.92, A:L.144 Hydrogen bonds: E:V.17 PTY.21: 8 residues within 4Å: Chain E: Q.54, L.82, I.118, V.122, H.125, N.126, L.225 Ligands: PTY.22 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.82, E:I.118, E:I.118, E:V.122, E:H.125, E:L.225 Hydrogen bonds: E:Q.54 Salt bridges: E:H.125 PTY.22: 10 residues within 4Å: Chain E: W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231, Y.1254 Ligands: PTY.21 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.225, E:W.231, E:W.231, E:Y.1254 Salt bridges: E:H.125 PTY.23: 8 residues within 4Å: Chain E: V.86, I.89, A.90, I.93, G.97, Y.356, V.357, V.360 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.86, E:I.89, E:Y.356, E:V.357, E:V.360 Hydrogen bonds: E:G.97 PTY.24: 6 residues within 4Å: Chain E: L.318, C.319, F.321, L.352, L.361, L.451 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.318, E:L.361, E:L.361, E:L.451

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.3: 12 residues within 4Å: Chain A: M.88, W.91, H.115, S.116, F.117 Chain E: L.3, A.4, F.5, Y.15, L.104, M.108, M.112 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:W.91, A:F.117, E:F.5, E:Y.15 POV.7: 8 residues within 4Å: Chain A: I.146 Chain B: L.84, M.88, W.91, H.115, S.116, F.117, S.118 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.84, B:F.117, A:I.146, A:I.146 Hydrogen bonds: B:F.117 POV.11: 7 residues within 4Å: Chain B: P.143 Chain C: M.88, W.91, H.115, S.116, F.117, S.118 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.117 POV.15: 6 residues within 4Å: Chain D: L.84, W.91, H.115, S.116, F.117, S.118 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.84, D:F.117, D:F.117 Hydrogen bonds: D:F.117

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

P5S.4: 16 residues within 4Å: Chain A: K.67, W.68, P.69, L.72, T.76, H.175, R.176 Chain D: V.59, F.60, L.147, V.151, I.154, V.155, M.158, I.162 Ligands: P5S.13 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:L.72, A:L.72, A:T.76, D:L.147, D:L.147, D:I.154, D:V.155, D:I.162 Hydrogen bonds: A:W.68, A:R.176 Salt bridges: A:K.67, A:R.176 P5S.5: 14 residues within 4Å: Chain A: L.56, Q.57, F.86, V.151 Chain B: K.67, R.176 Chain E: I.46, F.132, K.134, L.135, I.137, A.138 Ligands: PTY.2, P5S.8 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E, 3 interactions with chain A Salt bridges: B:K.67, B:R.176 Hydrophobic interactions: E:I.46, A:F.86, A:V.151 Hydrogen bonds: A:Q.57 P5S.8: 20 residues within 4Å: Chain A: Q.57, V.59, F.60, I.154, V.155, M.158, I.162 Chain B: V.64, D.65, L.66, K.67, W.68, P.69, L.72, L.73, T.76, K.170, H.175, R.176 Ligands: P5S.5 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:V.59, A:F.60, A:I.154, A:I.162, B:W.68, B:W.68, B:W.68, B:L.72, B:L.73, B:T.76 Hydrogen bonds: B:K.67, B:W.68 Salt bridges: B:K.67, B:K.170, B:H.175, B:R.176 P5S.9: 6 residues within 4Å: Chain B: L.56, Q.57, V.59, L.85 Chain C: R.176 Ligands: P5S.12 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.176, C:R.176, B:Q.57 Salt bridges: C:R.176 Hydrophobic interactions: B:L.56, B:V.59 P5S.12: 12 residues within 4Å: Chain B: V.151, V.155, M.158, I.159, I.162 Chain C: K.67, W.68, P.69, L.72, L.73, R.176 Ligands: P5S.9 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:V.151, B:V.155, B:M.158, B:I.159, B:I.162, C:P.69, C:L.72, C:L.73, C:L.73 Hydrogen bonds: C:K.67, C:R.176 Salt bridges: C:H.175, C:R.176, C:R.176 P5S.13: 7 residues within 4Å: Chain A: R.176 Chain D: L.56, Q.57, V.59, F.86, V.151 Ligands: P5S.4 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.59, D:F.86, D:V.151 Hydrogen bonds: D:Q.57 Salt bridges: A:K.67, A:R.176 P5S.16: 17 residues within 4Å: Chain C: L.147, I.150, V.151, I.154, V.155, M.158, I.162 Chain D: K.67, W.68, P.69, L.72, L.73, T.76, M.77, H.175, R.176 Ligands: P5S.17 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.147, C:I.150, C:I.154, C:V.155, C:M.158, D:L.72, D:L.72, D:T.76 Hydrogen bonds: D:W.68, D:R.176 Salt bridges: D:R.176 P5S.17: 10 residues within 4Å: Chain C: L.56, Q.57, V.59, S.82, L.85 Chain D: P.69, H.70, L.73, R.176 Ligands: P5S.16 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.69, D:L.73, C:L.56, C:L.85 Salt bridges: D:R.176, D:R.176 P5S.25: 18 residues within 4Å: Chain E: N.72, I.76, F.79, I.80, L.224, L.225, K.227, G.228, R.298, L.301, F.305, L.364, L.368, T.371, F.372, A.375, V.379, Y.1254 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:I.76, E:F.79, E:F.79, E:F.79, E:I.80, E:L.224, E:K.227, E:F.305, E:L.364, E:L.368, E:T.371, E:F.372, E:F.372, E:A.375 Hydrogen bonds: E:R.298 Salt bridges: E:K.227, E:R.298

1 x GBM: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide(Non-covalent)

GBM.18: 17 residues within 4Å: Chain A: R.4 Chain E: R.306, Y.377, I.381, W.430, F.433, L.434, N.437, P.589, L.592, D.1193, S.1238, L.1241, T.1242, N.1245, R.1246, R.1300 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.377, E:Y.377, E:I.381, E:F.433, E:L.592, E:L.1241 Hydrogen bonds: E:R.306, E:N.437, E:T.1242, E:N.1245, E:R.1246, E:R.1246 pi-Stacking: E:Y.377

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

NAG.20: 1 residues within 4Å: Chain E: N.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sung, M.W. et al., Ligand-mediated Structural Dynamics of a Mammalian Pancreatic K ATP Channel. J.Mol.Biol. (2022)

Release Date

2022-08-31

Peptides

ATP-sensitive inward rectifier potassium channel 11: ABCD
ATP-binding cassette sub-family C member 8: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

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

ATP-binding cassette sub-family C member 8

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