SMTL ID : 7tys.1

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with Kir6.2-CTD in the up 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: 14 residues within 4Å: Chain A: K.39, I.182, F.183, K.185, L.205, Y.330, S.331, F.333, G.334, N.335 Chain D: N.48, I.49, R.50, R.54 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:K.39, A:K.39, A:K.185, A:G.334, A:N.335, D:N.48, D:R.50, D:R.54, D:R.54 Salt bridges: A:K.185, A:K.185, D:R.50 pi-Cation interactions: D:R.50 ATP.8: 11 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, G.334 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.48, A:R.50, A:R.50, A:R.50, A:R.54, B:K.39, B:K.39, B:K.185, B:G.334 Salt bridges: A:R.50, A:R.50, B:K.185, B:K.185 pi-Cation interactions: A:R.50 ATP.11: 13 residues within 4Å: Chain B: N.48, I.49, R.50, R.54 Chain C: I.182, F.183, S.184, K.185, L.205, Y.330, S.331, F.333, G.334 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:N.48, B:R.50, B:R.54, C:K.39, C:K.185, C:K.185, C:K.185, C:G.334 Salt bridges: B:R.50, B:R.50, C:K.185, C:K.185 pi-Cation interactions: B:R.50 ATP.14: 10 residues within 4Å: Chain C: N.48, I.49, R.50 Chain D: K.39, I.182, F.183, K.185, L.205, Y.330, G.334 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.39, D:K.185, D:G.334, C:N.48, C:R.50, C:R.50, C:R.50 Salt bridges: D:K.185, C:R.50 pi-Cation interactions: C:R.50 ATP.19: 13 residues within 4Å: Chain E: T.404, N.406, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775, D.855 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:T.404, E:N.406, E:N.406, E:G.716, E:G.718, E:K.719, E:S.720, E:S.720, E:S.721, E:Q.775, E:Q.775 Salt bridges: E:K.719, E:K.719 pi-Stacking: E:W.688, E:W.688

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: F.133 Chain B: F.133 Chain C: F.133 Chain D: F.133 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:F.133, B:F.133, A:F.133, C:F.133 K.4: 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: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Metal complexes: C:T.130, C:I.131, A:T.130, D:T.130, B:T.130

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

POV.5: 15 residues within 4Å: Chain A: L.84, W.91, L.100, H.115, S.116, F.117 Chain E: L.3, A.4, F.5, S.12, Y.15, V.37, F.41, L.104, M.112 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.84, A:L.84, A:F.117, A:F.117, A:F.117, E:V.37, E:F.41 Hydrogen bonds: A:F.117, E:F.5, E:Y.15, E:Y.15 POV.9: 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 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.146, A:I.146, B:F.117, B:F.121, B:F.121 Hydrogen bonds: B:S.116, B:F.117 POV.12: 10 residues within 4Å: Chain B: I.146, L.147 Chain C: M.88, W.91, L.100, H.115, S.116, F.117, S.118, F.121 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.146, B:L.147, C:F.121 Hydrogen bonds: C:F.117 POV.16: 9 residues within 4Å: Chain C: P.143, I.146 Chain D: M.88, W.91, H.115, S.116, F.117, S.118, F.121 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:P.143, C:P.143, C:I.146, D:F.117, D:F.121 Hydrogen bonds: D:S.116, D:F.117 POV.24: 10 residues within 4Å: Chain E: H.67, G.70, H.71, N.72, L.73, L.184, N.188, P.220, F.221 Ligands: P5S.23 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:N.72, E:L.73, E:L.184, E:L.184 Hydrogen bonds: 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.6: 13 residues within 4Å: Chain A: K.67, W.68, P.69, H.70, L.72, L.80, H.175, R.176 Chain D: I.150, I.154, V.155, M.158, I.162 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:I.150, D:I.154, D:I.154, D:V.155, D:M.158, D:I.162, A:W.68, A:L.72, A:L.80 Hydrogen bonds: A:R.176 Salt bridges: A:K.170, A:H.175, A:R.176 P5S.7: 17 residues within 4Å: Chain A: L.56, Q.57, V.59, L.63, S.78, I.159 Chain B: R.176 Chain E: F.41, I.42, P.45, I.46, F.132, K.134, I.137, A.138, I.141 Ligands: P5S.10 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:I.42, E:P.45, E:I.46, E:I.137, E:A.138, E:I.141, A:V.59, A:L.63, A:I.159 Hydrogen bonds: A:Q.57 P5S.10: 19 residues within 4Å: Chain A: Q.57, V.59, F.60, I.154, M.158, I.162 Chain B: V.64, D.65, L.66, K.67, W.68, P.69, L.72, T.76, K.170, Q.173, H.175, R.176 Ligands: P5S.7 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.68, B:W.68, B:P.69, B:L.72, B:L.72, A:F.60, A:I.162 Hydrogen bonds: B:L.66, B:W.68, B:Q.173 Salt bridges: B:K.170, B:H.175, B:H.175, B:R.176, B:R.176 P5S.13: 13 residues within 4Å: Chain B: Q.57, V.59, F.60, I.154, V.155, I.159, I.162 Chain C: K.67, W.68, P.69, L.72, L.73, R.176 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.60, B:V.155, B:I.159, B:I.162, C:W.68, C:P.69, C:L.72, C:L.73, C:L.73 Hydrogen bonds: C:W.68 Salt bridges: C:R.176, C:R.176, C:R.176 P5S.15: 14 residues within 4Å: Chain C: F.60, V.151, I.154, V.155, M.158, I.162 Chain D: L.66, K.67, W.68, P.69, L.72, K.170, H.175, R.176 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.68, D:L.72, C:F.60, C:V.151, C:I.154, C:I.154 Hydrogen bonds: D:W.68, D:W.68, D:K.170 Salt bridges: D:K.170, D:H.175, D:R.176, D:R.176 P5S.23: 16 residues within 4Å: Chain E: I.76, F.79, I.80, F.83, L.224, K.227, G.228, R.298, L.301, F.305, L.364, L.368, T.371, F.372 Ligands: POV.24, 65I.26 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.79, E:F.79, E:I.80, E:I.80, E:L.224, E:K.227, E:K.227, E:F.305, E:F.305, E:L.364, E:L.368, E:T.371, E:F.372, E:F.372 Salt bridges: E:R.298

6 x 65I: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate(Non-covalent)

65I.17: 9 residues within 4Å: Chain A: V.89, L.92, I.93, A.96, L.144, I.148 Chain E: G.20, V.21, F.27 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:F.27, A:V.89, A:L.92, A:I.93, A:A.96, A:L.144, A:I.148 Hydrogen bonds: E:V.21 65I.20: 10 residues within 4Å: Chain E: W.65, H.125, T.129, V.222, N.223, L.225, S.226, W.231 Ligands: 65I.22, 65I.26 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.225, E:W.231, E:W.231 Hydrogen bonds: E:N.223, E:N.223, E:N.223, E:S.226 Salt bridges: E:H.125 65I.21: 8 residues within 4Å: Chain E: V.86, I.89, A.90, I.93, G.97, F.114, N.354, Y.356 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.89, E:A.90, E:F.114 Hydrogen bonds: E:N.354 65I.22: 7 residues within 4Å: Chain E: W.231, N.234, F.1177, I.1178, Y.1181, Y.1254 Ligands: 65I.20 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.231, E:W.231, E:F.1177, E:F.1177, E:I.1178, E:Y.1181, E:Y.1254 Hydrogen bonds: E:W.231 65I.25: 10 residues within 4Å: Chain E: F.83, L.311, A.315, L.318, C.319, F.321, L.361, L.364, A.365, L.451 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.83, E:A.315, E:L.364, E:A.365 65I.26: 14 residues within 4Å: Chain E: L.47, F.48, W.51, Q.54, W.75, L.82, V.121, V.122, H.125, N.126, T.129, L.225 Ligands: 65I.20, P5S.23 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:L.47, E:F.48, E:W.51, E:W.51, E:W.75, E:L.82, E:V.121, E:V.122, E:L.225 Salt bridges: E:H.125, E:H.125

1 x BJX: Repaglinide(Non-covalent)

BJX.18: 16 residues within 4Å: Chain A: M.1, S.3, K.5, G.6 Chain E: R.306, Y.377, I.381, L.434, N.437, T.588, L.592, V.596, N.1245, R.1246, W.1297, R.1300 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.377, E:Y.377, E:I.381, E:L.434, E:T.588, E:L.592, E:L.592, E:V.596, E:W.1297, E:W.1297, A:M.1, A:S.3 Hydrogen bonds: E:R.306, E:N.437, 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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