SMTL ID : 7u1q.1

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with SUR1-in 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, Y.330, S.331, F.333, G.334, N.335 Chain D: N.48, R.50 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:K.185, A:Y.330, A:S.331, A:F.333, A:G.334, A:N.335, D:R.50 Salt bridges: A:K.185, A:K.185, D:R.50, D:R.50 pi-Cation interactions: D:R.50, D:R.50 ATP.6: 12 residues within 4Å: Chain A: N.48, I.49, R.50, R.54 Chain B: K.39, I.182, F.183, K.185, L.205, Y.330, F.333, G.334 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.48, A:R.50, A:R.50, A:R.54, B:K.185, B:G.334 pi-Cation interactions: A:R.50, A:R.50 ATP.9: 12 residues within 4Å: Chain B: N.48, I.49, R.50 Chain C: I.182, F.183, K.185, L.205, Y.330, S.331, F.333, G.334, N.335 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Y.330, C:S.331, C:F.333, C:G.334, C:N.335, C:N.335, B:R.50, B:R.50 Salt bridges: C:K.185, B:R.50, B:R.50 pi-Cation interactions: B:R.50 ATP.12: 11 residues within 4Å: Chain C: N.48, I.49, R.50 Chain D: I.182, F.183, K.185, L.205, Y.330, S.331, F.333, G.334 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:N.48, C:R.50, C:R.50, D:K.185, D:G.334 Salt bridges: D:K.185, D:K.185 ATP.18: 12 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, D.855 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 Salt bridges: E:K.719, E:K.719

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 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:T.130, D:T.130

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

P5S.4: 13 residues within 4Å: Chain A: K.67, W.68, P.69, H.70, L.72, T.76, R.176 Chain D: F.60, L.147, V.151, I.154, M.158, I.162 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:L.147, D:V.151, D:I.162, A:L.72, A:T.76 Hydrogen bonds: A:W.68, A:R.176 Salt bridges: A:H.175, A:R.176 P5S.8: 17 residues within 4Å: Chain A: Q.57, F.60, I.154, V.155, I.162 Chain B: V.64, K.67, W.68, P.69, H.70, L.72, T.76, K.170, Q.173, H.175, R.176 Ligands: P5S.16 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.67, B:P.69, B:L.72, A:F.60, A:I.154, A:V.155 Hydrogen bonds: B:W.68, B:Q.173 Salt bridges: B:K.67, B:K.170, B:R.176, B:R.176 P5S.10: 9 residues within 4Å: Chain B: Q.57, F.60, I.154, V.155, I.162 Chain C: W.68, P.69, H.70, L.73 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.60, B:I.154, C:W.68, C:L.73 Hydrogen bonds: B:Q.57, C:W.68 P5S.13: 10 residues within 4Å: Chain C: F.60, V.151, I.154, I.162 Chain D: L.66, K.67, W.68, P.69, T.76, R.176 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:P.69, D:P.69, D:T.76, C:F.60, C:V.151, C:I.154, C:I.162 Hydrogen bonds: D:W.68, D:W.68 Salt bridges: D:R.176, D:R.176 P5S.16: 11 residues within 4Å: Chain A: V.59, L.85 Chain B: R.176 Chain E: F.41, I.42, P.45, I.46, F.132, K.134, L.135 Ligands: P5S.8 9 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: E:I.42, E:P.45, E:I.46, A:V.59, A:L.85 Salt bridges: E:K.134, E:K.134, B:R.176 Hydrogen bonds: B:R.176 P5S.24: 16 residues within 4Å: Chain E: N.72, I.76, F.79, I.80, F.83, V.84, L.224, K.227, G.228, L.301, F.305, L.364, T.371, F.372, A.375 Ligands: PTY.19 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.76, E:F.79, E:F.83, E:V.84, E:L.224, E:K.227, E:F.305, E:F.305, E:L.364, E:F.372, E:F.372, E:A.375 Salt bridges: E:K.227, E:R.298

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

POV.5: 13 residues within 4Å: Chain A: L.84, M.88, W.91, L.100, H.115, S.116, F.117 Chain E: L.3, A.4, F.5, Y.15, L.104, M.112 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:L.3, A:L.84, A:F.117 Hydrogen bonds: E:F.5, E:Y.15, A:F.117 POV.7: 9 residues within 4Å: Chain A: P.143, I.146 Chain B: L.84, M.88, W.91, L.100, H.115, S.116, F.117 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.143, A:I.146, B:L.84 Hydrogen bonds: B:F.117 POV.11: 7 residues within 4Å: Chain C: L.84, M.88, W.91, H.115, S.116, F.117, S.118 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.84, C:L.84, C:F.117 Hydrogen bonds: C:S.116, C:F.117 POV.14: 8 residues within 4Å: Chain C: P.143 Chain D: M.88, W.91, L.100, H.115, S.116, F.117, S.118 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.117, D:F.117, C:P.143 Hydrogen bonds: D:H.115, D:F.117 POV.20: 8 residues within 4Å: Chain E: H.67, F.68, G.70, H.71, N.72, L.73, N.188, P.220 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.73 Hydrogen bonds: E:G.70, E:H.71, E:N.72, E:N.72

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.15: 6 residues within 4Å: Chain A: V.89, L.92, L.144 Chain E: V.21, L.22, I.148 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:V.89, A:L.144, E:I.148 PTY.19: 14 residues within 4Å: Chain E: L.47, F.48, W.51, Q.54, W.75, F.79, L.82, V.121, V.122, H.125, N.126, T.129 Ligands: PTY.21, P5S.24 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.47, E:F.48, E:W.75, E:F.79, E:L.82, E:V.121 Hydrogen bonds: E:T.129 Salt bridges: E:H.125, E:H.125 PTY.21: 8 residues within 4Å: Chain E: W.65, H.125, V.222, N.223, L.225, S.226, W.231 Ligands: PTY.19 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.231, E:W.231 Hydrogen bonds: E:N.223, E:S.226 Salt bridges: E:H.125 PTY.22: 6 residues within 4Å: Chain E: I.89, A.90, I.93, F.114, N.354, Y.356 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.89, E:A.90, E:F.114 Hydrogen bonds: E:N.354, E:Y.356 PTY.23: 9 residues within 4Å: Chain E: L.311, A.315, L.318, C.319, F.321, L.352, L.361, A.365, L.451 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.315, E:L.361, E:L.451

1 x BJX: Repaglinide(Non-covalent)

BJX.17: 14 residues within 4Å: Chain A: M.1, S.3 Chain E: Y.377, W.430, L.434, N.437, T.588, L.592, S.595, V.596, N.1245, R.1246, W.1297, R.1300 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:Y.377, E:L.434, E:L.434, E:T.588, E:L.592, E:L.592, E:V.596, E:W.1297, E:W.1297, A:S.3 Hydrogen bonds: E:N.437 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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