SMTL ID : 7tyt.1

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with Kir6.2-CTD in the down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

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

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

ATP.2: 10 residues within 4Å: Chain A: I.182, F.183, K.185, L.205, Y.330, F.333, G.334 Chain D: N.48, I.49, R.50 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:Y.330, A:F.333, A:G.334, D:R.50, D:R.50 Salt bridges: A:K.185, A:K.185, D:R.50, D:R.50 pi-Cation interactions: D:R.50 ATP.5: 8 residues within 4Å: Chain A: I.49, R.50 Chain B: F.183, K.185, L.205, Y.330, S.331, G.334 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.185, B:G.334, A:N.48, A:R.50 Salt bridges: B:K.185, B:K.185, B:K.185, A:R.50, A:R.50 pi-Stacking: B:F.333 pi-Cation interactions: A:R.50, A:R.50 ATP.8: 9 residues within 4Å: Chain B: N.48, I.49, R.50 Chain C: I.182, F.183, K.185, Y.330, F.333, G.334 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:R.50, B:R.50, C:K.185, C:Y.330, C:G.334 Salt bridges: B:R.50, B:R.50, B:R.50, C:K.185, C:K.185 pi-Cation interactions: B:R.50, B:R.50 ATP.10: 8 residues within 4Å: Chain C: N.48, I.49, R.50, E.51 Chain D: F.183, K.185, Y.330, G.334 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.50, C:R.50, C:E.51, D:K.185, D:Y.330 Salt bridges: C:R.50, C:R.50, D:K.185, D:K.185 pi-Cation interactions: C:R.50 ATP.14: 11 residues within 4Å: Chain E: N.406, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.406, E:G.716, E:C.717, E:G.718, E:K.719, E:S.720, E:S.720, E:S.721, E:Q.775 pi-Stacking: E:W.688

1 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.130 Chain B: T.130 Chain C: T.130 Chain D: T.130 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: D:T.130, B:T.130, C:T.130, A:T.130

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

POV.4: 14 residues within 4Å: Chain A: L.84, W.91, L.100, H.115, S.116, F.117, S.118 Chain D: I.146 Chain E: L.3, A.4, F.5, S.12, Y.15, M.108 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 3 interactions with chain E Hydrogen bonds: A:F.117, E:F.5, E:Y.15, E:Y.15 Hydrophobic interactions: D:I.146 POV.6: 7 residues within 4Å: Chain B: L.84, M.88, W.91, L.100, H.115, S.116, F.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.117 POV.9: 8 residues within 4Å: Chain B: P.143 Chain C: L.84, M.88, W.91, L.100, H.115, S.116, F.117 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:P.143, C:L.84, C:L.84, C:W.91, C:F.117 Hydrogen bonds: C:F.117 POV.11: 8 residues within 4Å: Chain C: I.146 Chain D: L.84, W.91, L.100, H.115, S.116, F.117, S.118 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.84 Hydrogen bonds: D:F.117 POV.19: 10 residues within 4Å: Chain E: H.67, F.68, P.69, G.70, H.71, N.72, I.76, P.220, K.227 Ligands: P5S.18 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:N.72, E:I.76, E:I.76 Hydrogen bonds: E:G.70, E:H.71, E:N.72, E:N.72

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

P5S.7: 10 residues within 4Å: Chain A: F.55, L.56, V.151, I.154 Chain B: W.68, P.69, L.72, L.80 Chain E: K.134, I.137 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: E:I.137, B:L.80, A:V.151, A:I.154 Hydrogen bonds: A:L.56 P5S.18: 20 residues within 4Å: Chain E: I.76, F.79, I.80, F.83, V.84, L.174, L.224, K.227, G.228, R.298, L.301, F.305, L.364, L.368, T.371, F.372, A.375 Ligands: PTY.15, POV.19, PTY.21 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:I.76, E:F.79, E:I.80, E:V.84, E:L.174, E:K.227, E:F.305, E:L.364, E:L.368, E:F.372 Salt bridges: E:K.227, E:K.227, E:R.298

6 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.12: 6 residues within 4Å: Chain A: V.89, L.92, A.96, L.144 Chain E: G.20, V.21 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:V.89, A:L.92, A:A.96, A:L.144 Hydrogen bonds: E:V.21 PTY.15: 12 residues within 4Å: Chain E: W.65, H.125, T.129, V.222, N.223, L.225, S.226, W.231, Y.1254 Ligands: PTY.17, P5S.18, PTY.21 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.225, E:W.231, E:W.231 Hydrogen bonds: E:N.223, E:S.226 Salt bridges: E:H.125, E:H.125 PTY.16: 9 residues within 4Å: Chain E: I.89, I.93, L.94, H.326, N.354, Y.356, V.357, V.360, L.1272 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.89, E:I.93, E:L.94, E:V.357 Hydrogen bonds: E:H.326, E:N.354 PTY.17: 7 residues within 4Å: Chain E: W.231, N.234, A.235, K.238, V.1174, Y.1254 Ligands: PTY.15 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.231, E:V.1174, E:Y.1254 PTY.20: 9 residues within 4Å: Chain E: F.83, L.311, F.314, L.318, F.321, D.325, L.358, A.365, Y.454 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.83, E:F.314, E:A.365 Hydrogen bonds: E:D.325, E:Y.454 PTY.21: 14 residues within 4Å: Chain E: F.44, L.47, F.79, L.82, I.118, T.119, V.121, V.122, H.125, N.126, T.129, L.225 Ligands: PTY.15, P5S.18 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:F.44, E:L.47, E:F.79, E:F.79, E:L.82, E:T.119, E:V.121, E:V.122, E:V.122 Hydrogen bonds: E:T.129 Salt bridges: E:H.125, E:H.125

1 x BJX: Repaglinide(Non-covalent)

BJX.13: 18 residues within 4Å: Chain A: M.1, S.3, K.5, G.6 Chain E: R.306, Y.377, I.381, W.430, L.434, N.437, T.588, L.592, S.595, V.596, N.1245, R.1246, W.1297, R.1300 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.377, E:I.381, E:L.434, E:T.588, E:L.592, E:L.592, E:L.592, E:V.596, E:W.1297, E:W.1297, A:S.3, A:K.5 Hydrogen bonds: E:N.1245 Salt bridges: E:R.1246, E:R.1300

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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