SMTL ID : 6jb1.1

Structure of pancreatic ATP-sensitive potassium channel bound with repaglinide and ATPgammaS at 3.3A resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

POV.1: 10 residues within 4Å: Chain A: L.85, V.89, L.92, I.93, A.96, H.97, N.107, L.144, I.148 Ligands: POV.11 Ligand excluded by PLIP POV.6: 7 residues within 4Å: Chain B: I.93, D.96, G.97, R.102, Y.107 Ligands: POV.7, POV.8 Ligand excluded by PLIP POV.7: 6 residues within 4Å: Chain B: R.102, M.112 Ligands: POV.6, POV.8, POV.9, POV.10 Ligand excluded by PLIP POV.8: 13 residues within 4Å: Chain B: V.86, I.89, A.90, I.93, G.111, F.114, M.115, N.354, Y.356, V.357 Ligands: POV.6, POV.7, POV.13 Ligand excluded by PLIP POV.9: 10 residues within 4Å: Chain A: L.80, S.118 Chain B: P.2 Chain C: P.143, L.147, I.150, V.151, I.154 Ligands: POV.7, POV.10 Ligand excluded by PLIP POV.10: 17 residues within 4Å: Chain A: L.84, M.88, W.91, H.115, S.116, F.117 Chain B: L.3, A.4, F.5, S.12, Y.15, V.37, F.41, M.108, M.112 Ligands: POV.7, POV.9 Ligand excluded by PLIP POV.11: 4 residues within 4Å: Chain B: G.20, V.21, L.31 Ligands: POV.1 Ligand excluded by PLIP POV.12: 6 residues within 4Å: Chain B: L.318, F.321, L.358, L.361, A.365, Y.454 Ligand excluded by PLIP POV.13: 7 residues within 4Å: Chain B: Y.356, V.360, F.363, L.364, L.1261, A.1265 Ligands: POV.8 Ligand excluded by PLIP POV.19: 10 residues within 4Å: Chain C: L.85, V.89, L.92, I.93, A.96, H.97, N.107, L.144, I.148 Ligands: POV.28 Ligand excluded by PLIP POV.23: 7 residues within 4Å: Chain D: I.93, D.96, G.97, R.102, Y.107 Ligands: POV.24, POV.25 Ligand excluded by PLIP POV.24: 6 residues within 4Å: Chain D: R.102, M.112 Ligands: POV.23, POV.25, POV.26, POV.27 Ligand excluded by PLIP POV.25: 13 residues within 4Å: Chain D: V.86, I.89, A.90, I.93, G.111, F.114, M.115, N.354, Y.356, V.357 Ligands: POV.23, POV.24, POV.30 Ligand excluded by PLIP POV.26: 10 residues within 4Å: Chain C: L.80, S.118 Chain D: P.2 Chain E: P.143, L.147, I.150, V.151, I.154 Ligands: POV.24, POV.27 Ligand excluded by PLIP POV.27: 17 residues within 4Å: Chain C: L.84, M.88, W.91, H.115, S.116, F.117 Chain D: L.3, A.4, F.5, S.12, Y.15, V.37, F.41, M.108, M.112 Ligands: POV.24, POV.26 Ligand excluded by PLIP POV.28: 4 residues within 4Å: Chain D: G.20, V.21, L.31 Ligands: POV.19 Ligand excluded by PLIP POV.29: 6 residues within 4Å: Chain D: L.318, F.321, L.358, L.361, A.365, Y.454 Ligand excluded by PLIP POV.30: 7 residues within 4Å: Chain D: Y.356, V.360, F.363, L.364, L.1261, A.1265 Ligands: POV.25 Ligand excluded by PLIP POV.36: 10 residues within 4Å: Chain E: L.85, V.89, L.92, I.93, A.96, H.97, N.107, L.144, I.148 Ligands: POV.45 Ligand excluded by PLIP POV.40: 7 residues within 4Å: Chain F: I.93, D.96, G.97, R.102, Y.107 Ligands: POV.41, POV.42 Ligand excluded by PLIP POV.41: 6 residues within 4Å: Chain F: R.102, M.112 Ligands: POV.40, POV.42, POV.43, POV.44 Ligand excluded by PLIP POV.42: 13 residues within 4Å: Chain F: V.86, I.89, A.90, I.93, G.111, F.114, M.115, N.354, Y.356, V.357 Ligands: POV.40, POV.41, POV.47 Ligand excluded by PLIP POV.43: 10 residues within 4Å: Chain E: L.80, S.118 Chain F: P.2 Chain G: P.143, L.147, I.150, V.151, I.154 Ligands: POV.41, POV.44 Ligand excluded by PLIP POV.44: 17 residues within 4Å: Chain E: L.84, M.88, W.91, H.115, S.116, F.117 Chain F: L.3, A.4, F.5, S.12, Y.15, V.37, F.41, M.108, M.112 Ligands: POV.41, POV.43 Ligand excluded by PLIP POV.45: 4 residues within 4Å: Chain F: G.20, V.21, L.31 Ligands: POV.36 Ligand excluded by PLIP POV.46: 6 residues within 4Å: Chain F: L.318, F.321, L.358, L.361, A.365, Y.454 Ligand excluded by PLIP POV.47: 7 residues within 4Å: Chain F: Y.356, V.360, F.363, L.364, L.1261, A.1265 Ligands: POV.42 Ligand excluded by PLIP POV.53: 10 residues within 4Å: Chain G: L.85, V.89, L.92, I.93, A.96, H.97, N.107, L.144, I.148 Ligands: POV.62 Ligand excluded by PLIP POV.57: 7 residues within 4Å: Chain H: I.93, D.96, G.97, R.102, Y.107 Ligands: POV.58, POV.59 Ligand excluded by PLIP POV.58: 6 residues within 4Å: Chain H: R.102, M.112 Ligands: POV.57, POV.59, POV.60, POV.61 Ligand excluded by PLIP POV.59: 13 residues within 4Å: Chain H: V.86, I.89, A.90, I.93, G.111, F.114, M.115, N.354, Y.356, V.357 Ligands: POV.57, POV.58, POV.64 Ligand excluded by PLIP POV.60: 10 residues within 4Å: Chain A: P.143, L.147, I.150, V.151, I.154 Chain G: L.80, S.118 Chain H: P.2 Ligands: POV.58, POV.61 Ligand excluded by PLIP POV.61: 17 residues within 4Å: Chain G: L.84, M.88, W.91, H.115, S.116, F.117 Chain H: L.3, A.4, F.5, S.12, Y.15, V.37, F.41, M.108, M.112 Ligands: POV.58, POV.60 Ligand excluded by PLIP POV.62: 4 residues within 4Å: Chain H: G.20, V.21, L.31 Ligands: POV.53 Ligand excluded by PLIP POV.63: 6 residues within 4Å: Chain H: L.318, F.321, L.358, L.361, A.365, Y.454 Ligand excluded by PLIP POV.64: 7 residues within 4Å: Chain H: Y.356, V.360, F.363, L.364, L.1261, A.1265 Ligands: POV.59 Ligand excluded by PLIP

8 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 14 residues within 4Å: Chain A: N.48, I.49, R.50, R.54 Chain B: E.203, K.205 Chain G: K.39, I.182, F.183, K.185, L.205, Y.330, F.333, G.334 11 PLIP interactions: 6 interactions with chain A, 4 interactions with chain G, 1 interactions with chain B Hydrogen bonds: A:N.48, A:R.50, A:R.54, A:R.54, G:K.39, G:K.185, G:G.334 Salt bridges: A:R.50, G:K.185, B:K.205 pi-Cation interactions: A:R.50 AGS.4: 12 residues within 4Å: Chain B: T.404, S.405, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.404, B:G.716, B:C.717, B:G.718, B:K.719, B:K.719, B:S.720, B:S.720, B:S.721, B:S.721, B:Q.775 Salt bridges: B:K.719 pi-Stacking: B:W.688, B:W.688, B:W.688, B:W.688 AGS.18: 14 residues within 4Å: Chain A: K.39, I.182, F.183, K.185, L.205, Y.330, F.333, G.334 Chain C: N.48, I.49, R.50, R.54 Chain D: E.203, K.205 11 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:N.48, C:R.50, C:R.54, C:R.54, A:K.39, A:K.185, A:G.334 Salt bridges: C:R.50, A:K.185, D:K.205 pi-Cation interactions: C:R.50 AGS.21: 12 residues within 4Å: Chain D: T.404, S.405, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.404, D:G.716, D:C.717, D:G.718, D:K.719, D:K.719, D:S.720, D:S.720, D:S.721, D:S.721, D:Q.775 Salt bridges: D:K.719 pi-Stacking: D:W.688, D:W.688, D:W.688, D:W.688 AGS.35: 14 residues within 4Å: Chain C: K.39, I.182, F.183, K.185, L.205, Y.330, F.333, G.334 Chain E: N.48, I.49, R.50, R.54 Chain F: E.203, K.205 11 PLIP interactions: 4 interactions with chain C, 1 interactions with chain F, 6 interactions with chain E Hydrogen bonds: C:K.39, C:K.185, C:G.334, E:N.48, E:R.50, E:R.54, E:R.54 Salt bridges: C:K.185, F:K.205, E:R.50 pi-Cation interactions: E:R.50 AGS.38: 12 residues within 4Å: Chain F: T.404, S.405, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:T.404, F:G.716, F:C.717, F:G.718, F:K.719, F:K.719, F:S.720, F:S.720, F:S.721, F:S.721, F:Q.775 Salt bridges: F:K.719 pi-Stacking: F:W.688, F:W.688, F:W.688, F:W.688 AGS.52: 14 residues within 4Å: Chain E: K.39, I.182, F.183, K.185, L.205, Y.330, F.333, G.334 Chain G: N.48, I.49, R.50, R.54 Chain H: E.203, K.205 11 PLIP interactions: 6 interactions with chain G, 1 interactions with chain H, 4 interactions with chain E Hydrogen bonds: G:N.48, G:R.50, G:R.54, G:R.54, E:K.39, E:K.185, E:G.334 Salt bridges: G:R.50, H:K.205, E:K.185 pi-Cation interactions: G:R.50 AGS.55: 12 residues within 4Å: Chain H: T.404, S.405, W.688, Q.714, V.715, G.716, C.717, G.718, K.719, S.720, S.721, Q.775 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:T.404, H:G.716, H:C.717, H:G.718, H:K.719, H:K.719, H:S.720, H:S.720, H:S.721, H:S.721, H:Q.775 Salt bridges: H:K.719 pi-Stacking: H:W.688, H:W.688, H:W.688, H:W.688

4 x AJP: Digitonin(Non-covalent)

AJP.3: 17 residues within 4Å: Chain B: N.426, W.430, N.547, T.548, P.551, H.584, V.587, T.588, F.591, K.602, L.1027, M.1290, Y.1294, W.1297, R.1300, D.1304 Ligands: BJX.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.548, B:P.551, B:V.587, B:V.587, B:V.587, B:F.591, B:L.1027, B:W.1297 Hydrogen bonds: B:N.426, B:N.547, B:N.547, B:R.598, B:K.602, B:K.602, B:R.1300 AJP.20: 17 residues within 4Å: Chain D: N.426, W.430, N.547, T.548, P.551, H.584, V.587, T.588, F.591, K.602, L.1027, M.1290, Y.1294, W.1297, R.1300, D.1304 Ligands: BJX.22 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.548, D:P.551, D:V.587, D:V.587, D:V.587, D:F.591, D:L.1027, D:W.1297 Hydrogen bonds: D:N.426, D:N.547, D:N.547, D:R.598, D:K.602, D:K.602, D:R.1300 AJP.37: 17 residues within 4Å: Chain F: N.426, W.430, N.547, T.548, P.551, H.584, V.587, T.588, F.591, K.602, L.1027, M.1290, Y.1294, W.1297, R.1300, D.1304 Ligands: BJX.39 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:T.548, F:P.551, F:V.587, F:V.587, F:V.587, F:F.591, F:L.1027, F:W.1297 Hydrogen bonds: F:N.426, F:N.547, F:N.547, F:R.598, F:K.602, F:K.602, F:R.1300 AJP.54: 17 residues within 4Å: Chain H: N.426, W.430, N.547, T.548, P.551, H.584, V.587, T.588, F.591, K.602, L.1027, M.1290, Y.1294, W.1297, R.1300, D.1304 Ligands: BJX.56 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:T.548, H:P.551, H:V.587, H:V.587, H:V.587, H:F.591, H:L.1027, H:W.1297 Hydrogen bonds: H:N.426, H:N.547, H:N.547, H:R.598, H:K.602, H:K.602, H:R.1300

4 x BJX: Repaglinide(Non-covalent)

BJX.5: 14 residues within 4Å: Chain B: Y.377, I.381, W.430, F.433, L.434, N.437, L.592, S.595, V.596, N.1245, R.1246, E.1249, R.1300 Ligands: AJP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.377, B:I.381, B:W.430, B:L.434, B:L.434, B:L.592, B:L.592, B:V.596 Hydrogen bonds: B:N.437, B:N.1245, B:R.1246 Salt bridges: B:R.1246 BJX.22: 14 residues within 4Å: Chain D: Y.377, I.381, W.430, F.433, L.434, N.437, L.592, S.595, V.596, N.1245, R.1246, E.1249, R.1300 Ligands: AJP.20 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.377, D:I.381, D:W.430, D:L.434, D:L.434, D:L.592, D:L.592, D:V.596 Hydrogen bonds: D:N.437, D:N.1245, D:R.1246 Salt bridges: D:R.1246 BJX.39: 14 residues within 4Å: Chain F: Y.377, I.381, W.430, F.433, L.434, N.437, L.592, S.595, V.596, N.1245, R.1246, E.1249, R.1300 Ligands: AJP.37 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Y.377, F:I.381, F:W.430, F:L.434, F:L.434, F:L.592, F:L.592, F:V.596 Hydrogen bonds: F:N.437, F:N.1245, F:R.1246 Salt bridges: F:R.1246 BJX.56: 14 residues within 4Å: Chain H: Y.377, I.381, W.430, F.433, L.434, N.437, L.592, S.595, V.596, N.1245, R.1246, E.1249, R.1300 Ligands: AJP.54 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:Y.377, H:I.381, H:W.430, H:L.434, H:L.434, H:L.592, H:L.592, H:V.596 Hydrogen bonds: H:N.437, H:N.1245, H:R.1246 Salt bridges: H:R.1246

16 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.14: 7 residues within 4Å: Chain B: I.118, V.121, V.122, H.125, N.126, L.225 Ligands: PTY.16 Ligand excluded by PLIP PTY.15: 9 residues within 4Å: Chain B: N.72, I.76, I.80, L.224, F.305, L.308, L.368, F.372 Ligands: PTY.17 Ligand excluded by PLIP PTY.16: 10 residues within 4Å: Chain B: W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231, Y.1254 Ligands: PTY.14 Ligand excluded by PLIP PTY.17: 13 residues within 4Å: Chain B: F.79, L.224, K.227, G.228, L.301, F.305, L.367, T.371, F.372, A.375, V.379, Y.1254 Ligands: PTY.15 Ligand excluded by PLIP PTY.31: 7 residues within 4Å: Chain D: I.118, V.121, V.122, H.125, N.126, L.225 Ligands: PTY.33 Ligand excluded by PLIP PTY.32: 9 residues within 4Å: Chain D: N.72, I.76, I.80, L.224, F.305, L.308, L.368, F.372 Ligands: PTY.34 Ligand excluded by PLIP PTY.33: 10 residues within 4Å: Chain D: W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231, Y.1254 Ligands: PTY.31 Ligand excluded by PLIP PTY.34: 13 residues within 4Å: Chain D: F.79, L.224, K.227, G.228, L.301, F.305, L.367, T.371, F.372, A.375, V.379, Y.1254 Ligands: PTY.32 Ligand excluded by PLIP PTY.48: 7 residues within 4Å: Chain F: I.118, V.121, V.122, H.125, N.126, L.225 Ligands: PTY.50 Ligand excluded by PLIP PTY.49: 9 residues within 4Å: Chain F: N.72, I.76, I.80, L.224, F.305, L.308, L.368, F.372 Ligands: PTY.51 Ligand excluded by PLIP PTY.50: 10 residues within 4Å: Chain F: W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231, Y.1254 Ligands: PTY.48 Ligand excluded by PLIP PTY.51: 13 residues within 4Å: Chain F: F.79, L.224, K.227, G.228, L.301, F.305, L.367, T.371, F.372, A.375, V.379, Y.1254 Ligands: PTY.49 Ligand excluded by PLIP PTY.65: 7 residues within 4Å: Chain H: I.118, V.121, V.122, H.125, N.126, L.225 Ligands: PTY.67 Ligand excluded by PLIP PTY.66: 9 residues within 4Å: Chain H: N.72, I.76, I.80, L.224, F.305, L.308, L.368, F.372 Ligands: PTY.68 Ligand excluded by PLIP PTY.67: 10 residues within 4Å: Chain H: W.65, H.125, V.222, N.223, L.225, S.226, T.229, W.231, Y.1254 Ligands: PTY.65 Ligand excluded by PLIP PTY.68: 13 residues within 4Å: Chain H: F.79, L.224, K.227, G.228, L.301, F.305, L.367, T.371, F.372, A.375, V.379, Y.1254 Ligands: PTY.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, D. et al., The Structural Basis for the Binding of Repaglinide to the Pancreatic KATPChannel. Cell Rep (2019)

Release Date

2019-05-22

Peptides

ATP-sensitive inward rectifier potassium channel 11: ACEG
ATP-binding cassette sub-family C member 8 isoform X2: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

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 isoform X2

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