SMTL ID : 7u1s.1

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with SUR1-out conformation

Coordinates

PDB Format

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 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.10

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

ATP.2: 11 residues within 4Å: Chain A: I.182, F.183, K.185, L.205, Y.330, S.331, G.334, N.335 Chain D: N.48, I.49, R.50 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.48, D:R.50, D:R.50, A:G.334, A:N.335 Salt bridges: D:R.50, D:R.50, A:K.185 pi-Cation interactions: D:R.50 ATP.6: 11 residues within 4Å: Chain A: N.48, I.49, R.50, Q.52, R.54 Chain B: I.182, F.183, K.185, L.205, Y.330, G.334 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.48, A:R.50, A:R.50, A:Q.52, A:R.54, B:K.185 Salt bridges: A:R.50 pi-Cation interactions: A:R.50 ATP.10: 10 residues within 4Å: Chain B: N.48, I.49, R.50 Chain C: I.182, F.183, K.185, L.205, Y.330, F.333, 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, B:R.50 pi-Cation interactions: B:R.50 ATP.13: 8 residues within 4Å: Chain C: N.48, I.49, R.50 Chain D: I.182, K.185, L.205, Y.330, G.334 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.185, C:N.48, C:R.50 Salt bridges: D:K.185, D:K.185, D:K.185, C:R.50 ATP.25: 10 residues within 4Å: Chain E: N.406, W.688, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:N.406, E:G.716, E:G.716, E:G.718, E:K.719, E:S.720, E:S.720, E:S.721, E:S.721, E:Q.775, E:Q.775 Salt bridges: E:K.719

1 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: T.130, I.131 Chain B: T.130, I.131 Chain C: T.130, I.131 Chain D: T.130, I.131 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Metal complexes: A:T.130, C:T.130, B:T.130, B:I.131, D:T.130

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

POV.4: 16 residues within 4Å: Chain A: L.84, M.88, W.91, L.100, H.115, S.116, F.117, S.118 Chain D: P.143, I.146 Chain E: L.3, A.4, F.5, Y.15, L.104, M.112 10 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: A:L.84, A:F.117, D:P.143, D:I.146, D:I.146, E:F.5 Hydrogen bonds: A:F.117, E:L.3, E:F.5, E:Y.15 POV.8: 9 residues within 4Å: Chain A: I.146 Chain B: L.84, M.88, W.91, L.100, H.115, S.116, F.117, F.121 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.84, B:F.121, A:I.146 Hydrogen bonds: B:F.117 POV.11: 6 residues within 4Å: Chain C: L.84, M.88, W.91, L.100, H.115, F.117 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.84, C:F.117 Hydrogen bonds: C:W.91, C:F.117 POV.14: 7 residues within 4Å: Chain C: I.146 Chain D: M.88, W.91, H.115, S.116, F.117, S.118 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.146, D:F.117 Hydrogen bonds: D:F.117 POV.19: 12 residues within 4Å: Chain E: H.67, F.68, P.69, G.70, H.71, N.72, L.73, M.181, L.184, N.188, K.227 Ligands: P5S.24 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:N.72, E:L.73, E:L.184 Hydrogen bonds: E:G.70, E:H.71, E:N.72, E:N.72

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

P5S.5: 11 residues within 4Å: Chain A: K.67, W.68, P.69, H.70, L.72, T.76, R.176 Chain D: Q.57, I.154, V.155, I.162 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.68, A:P.69, A:L.72, D:I.154, D:V.155, D:I.162 Hydrogen bonds: A:W.68 P5S.7: 14 residues within 4Å: Chain A: L.56, Q.57, V.59, L.85, F.86, V.151 Chain B: R.176 Chain E: F.41, I.42, F.132, K.134, I.137, A.138 Ligands: P5S.9 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E, 2 interactions with chain A Salt bridges: B:R.176 Hydrophobic interactions: E:I.42, E:I.137, E:A.138, A:L.85, A:V.151 P5S.9: 13 residues within 4Å: Chain A: F.60, I.154, V.155, I.162 Chain B: K.67, W.68, P.69, H.70, L.72, T.76, H.175, R.176 Ligands: P5S.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.72, A:F.60, A:V.155 Hydrogen bonds: B:W.68, B:R.176 Salt bridges: B:H.175, B:R.176, B:R.176 P5S.12: 9 residues within 4Å: Chain B: Q.57, V.151, V.155, I.162 Chain C: K.67, W.68, P.69, H.175, R.176 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:P.69, C:P.69, B:V.151, B:I.162 Salt bridges: C:R.176 P5S.15: 14 residues within 4Å: Chain C: Q.57, F.60, V.151, V.155, I.162 Chain D: D.65, L.66, K.67, W.68, P.69, H.70, K.170, H.175, R.176 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:W.68, D:W.68, D:R.176, D:R.176 Salt bridges: D:K.170, D:H.175, D:R.176 Hydrophobic interactions: C:F.60, C:V.151, C:V.155 P5S.24: 17 residues within 4Å: Chain E: I.76, F.79, I.80, L.82, F.83, L.225, K.227, G.228, R.298, L.301, F.305, L.368, T.371, F.372, A.375 Ligands: PTY.18, POV.19 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.79, E:F.79, E:L.82, E:F.83, E:F.83, E:K.227, E:F.305, E:F.305, E:L.368, E:L.368, E:T.371, E:A.375 Salt bridges: E:K.227, E:K.227, E:R.298

6 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.16: 7 residues within 4Å: Chain A: V.89, L.92, L.144, I.148 Chain E: G.20, V.21, L.22 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:V.89, A:L.92, A:L.144, A:I.148, E:L.22, E:L.22 Hydrogen bonds: E:V.21 PTY.18: 14 residues within 4Å: Chain E: F.44, L.47, F.48, W.51, W.75, L.82, V.121, V.122, H.125, N.126, T.129, L.225 Ligands: PTY.20, P5S.24 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.44, E:L.47, E:F.48, E:W.51, E:W.51, E:W.75, E:L.82 Hydrogen bonds: E:T.129, E:N.223 Salt bridges: E:H.125, E:H.125 PTY.20: 9 residues within 4Å: Chain E: W.65, H.125, V.222, N.223, L.225, S.226, W.231 Ligands: PTY.18, PTY.22 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.225, E:W.231, E:W.231 Hydrogen bonds: E:I.60, E:N.223, E:N.223, E:S.226 Salt bridges: E:H.125 PTY.21: 10 residues within 4Å: Chain E: I.89, A.90, I.93, D.96, G.97, Y.107, N.354, Y.356, V.357, V.360 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.89, E:A.90, E:I.93, E:Y.356, E:V.357, E:V.360 Hydrogen bonds: E:G.97, E:N.354 PTY.22: 6 residues within 4Å: Chain E: W.231, N.234, K.238, Y.1181, Y.1254 Ligands: PTY.20 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.231, E:Y.1254 Salt bridges: E:K.238, E:K.238 PTY.23: 5 residues within 4Å: Chain E: L.318, F.321, L.352, L.361, I.450 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.318, E:L.361, E:I.450

1 x BJX: Repaglinide(Non-covalent)

BJX.17: 14 residues within 4Å: Chain A: S.3, K.5 Chain E: R.306, Y.377, I.381, L.434, M.441, L.592, S.595, V.596, N.1245, R.1246, W.1297, R.1300 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain E Hydrophobic interactions: A:S.3, A:K.5, E:I.381, E:L.434, E:L.434, E:L.592, E:V.596, E:W.1297 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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