SMTL ID : 8zsk.1

Complex I from respirasome closed state 1 bound by metformin and CoQ10, alternative orientation (SC-MetC1-ii)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

13 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 26 residues within 4Å: Chain 6: K.585, L.592 Chain 7: S.20, K.22, T.87, A.91, G.95 Chain A: M.10, A.13, I.14, L.16, A.17, G.18, M.21, Y.22, R.23 Chain M: L.33, A.37, I.40, P.45, S.47, F.48, G.51, V.52, T.55, G.56 12 PLIP interactions: 3 interactions with chain 7, 2 interactions with chain 6, 3 interactions with chain M, 4 interactions with chain A Hydrophobic interactions: 7:T.87, 6:L.592, M:A.37, M:I.40, M:V.52, A:I.14, A:L.16, A:A.17 Hydrogen bonds: 7:T.87 Salt bridges: 7:K.22, 6:K.585, A:R.23 CDL.9: 27 residues within 4Å: Chain 3: P.110, T.156, M.157, L.160, I.164 Chain 6: M.576, V.577, Q.580, T.594 Chain M: A.1, S.24, I.27, G.28, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, T.61, S.62, G.66, F.69 Ligands: CDL.11, PEE.42 26 PLIP interactions: 18 interactions with chain M, 3 interactions with chain 6, 5 interactions with chain 3 Hydrophobic interactions: M:A.1, M:I.27, M:T.31, M:I.34, M:I.34, M:V.35, M:V.35, M:V.35, M:Y.38, M:Y.38, M:Y.38, M:Y.38, M:T.61, M:F.69, M:F.69, 6:V.577, 6:T.594, 3:P.110, 3:P.110, 3:T.156, 3:L.160, 3:I.164 Hydrogen bonds: M:Y.58, M:Y.58, 6:Q.580 Salt bridges: M:K.43 CDL.11: 17 residues within 4Å: Chain 3: N.152, T.156, L.160, I.277 Chain 6: L.601, F.602 Chain M: K.2, L.123, V.124, G.127, Q.128, W.132, Q.133, V.134, F.135 Ligands: CDL.9, PEE.43 12 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain 6, 8 interactions with chain M Hydrophobic interactions: 3:L.160, 3:I.277, 6:L.601, 6:F.602, M:L.123, M:L.123, M:V.124, M:V.134, M:V.134, M:F.135 Hydrogen bonds: M:K.2 Salt bridges: M:K.2 CDL.12: 18 residues within 4Å: Chain 2: Y.43, L.45 Chain B: M.1, W.2, F.3, L.6, P.7, V.11 Chain G: S.2, A.3, T.4, I.7 Chain N: L.2, V.5, L.6, R.8, G.9, Y.22 12 PLIP interactions: 4 interactions with chain G, 2 interactions with chain N, 4 interactions with chain B, 2 interactions with chain 2 Hydrophobic interactions: G:I.7, N:V.5, B:W.2, B:F.3, B:L.6, B:V.11, 2:Y.43, 2:L.45 Hydrogen bonds: G:S.2, G:T.4, G:T.4 Salt bridges: N:R.8 CDL.13: 20 residues within 4Å: Chain 2: M.31, I.175, F.176, W.179, M.183, I.268, T.269, W.272 Chain O: R.26, M.33, V.36, G.37, T.40, F.43 Ligands: PEE.59 Chain f: L.26, T.28, V.31, R.32, L.38 11 PLIP interactions: 5 interactions with chain 2, 2 interactions with chain O, 4 interactions with chain f Hydrophobic interactions: 2:I.175, 2:F.176, 2:W.179, 2:I.268, 2:W.272, f:V.31, f:V.31, f:R.32, f:L.38 Hydrogen bonds: O:G.37, O:T.40 CDL.15: 22 residues within 4Å: Chain 1: T.28, P.30, R.31, V.33, Y.34, F.37 Chain 3: P.256, L.335, P.338 Chain 5: L.2, I.5, T.9, T.55, F.56, L.101 Chain H: F.168, W.169, T.170, M.171 Chain P: L.25, K.32 Ligands: CDL.41 21 PLIP interactions: 5 interactions with chain 5, 5 interactions with chain 1, 3 interactions with chain H, 3 interactions with chain P, 5 interactions with chain 3 Hydrophobic interactions: 5:L.2, 5:I.5, 5:T.9, 5:F.56, 5:L.101, 1:R.31, 1:V.33, 1:F.37, 1:F.37, H:F.168, H:F.168, 3:P.256, 3:P.256, 3:L.335, 3:P.338, 3:P.338 Hydrogen bonds: 1:T.28, H:T.170, P:K.32, P:K.32 Salt bridges: P:K.32 CDL.16: 22 residues within 4Å: Chain 5: Y.210, G.211, L.264 Chain 6: L.553, W.557, L.558 Chain M: Y.107, G.108, A.111 Chain S: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97 Ligands: PEE.10, PC1.17, PEE.43 12 PLIP interactions: 3 interactions with chain 5, 3 interactions with chain S, 3 interactions with chain M, 3 interactions with chain 6 Hydrophobic interactions: 5:Y.210, 5:Y.210, 5:L.264, S:L.87, S:A.90, S:L.97, M:Y.107, M:Y.107, 6:L.553, 6:W.557, 6:W.557 Hydrogen bonds: M:Y.107 CDL.18: 35 residues within 4Å: Chain 6: L.12, T.13, T.16, N.65, F.80, I.126, I.130 Chain T: R.21, I.24, L.25, G.28, A.32, I.35, T.36, N.39, V.40, E.44, H.64 Chain U: W.79, I.81, Y.83, H.88 Chain Y: L.39, L.40, P.44, A.48, R.49, I.52, H.56 Chain Z: S.51, T.52, Y.56 Ligands: PEE.21, PLX.24, CDL.44 25 PLIP interactions: 10 interactions with chain T, 2 interactions with chain Z, 6 interactions with chain Y, 4 interactions with chain U, 3 interactions with chain 6 Hydrophobic interactions: T:R.21, T:I.24, T:L.25, T:A.32, T:I.35, T:I.35, Z:Y.56, Y:L.40, Y:P.44, Y:P.44, Y:A.48, U:W.79, U:W.79, U:Y.83, 6:F.80, 6:I.126, 6:I.130 Hydrogen bonds: T:N.39, T:N.39, T:E.44, Z:Y.56 Salt bridges: T:H.64, Y:R.49, Y:H.56, U:H.88 CDL.28: 21 residues within 4Å: Chain 2: R.62, S.67, I.68, S.69, I.73, I.76, L.77 Chain 7: G.15, Y.27, L.30, G.31, V.34, V.81, W.82, V.83, F.92 Chain I: W.187, R.251, T.323 Ligands: PEE.32, PC1.33 12 PLIP interactions: 6 interactions with chain 2, 5 interactions with chain 7, 1 interactions with chain I Hydrophobic interactions: 2:I.68, 2:I.73, 2:L.77, 7:Y.27, 7:L.30, 7:V.34, 7:W.82, 7:F.92 Hydrogen bonds: 2:S.69, 2:S.69 Salt bridges: 2:R.62, I:R.251 CDL.34: 17 residues within 4Å: Chain 3: Y.6, T.7, M.11, M.14, Q.125, L.128, L.129, T.132, W.133, L.206, I.209, L.213, M.217, K.321, L.325 Chain L: P.6, L.7 9 PLIP interactions: 8 interactions with chain 3, 1 interactions with chain L Hydrophobic interactions: 3:L.129, 3:T.132, 3:L.206, 3:I.209, 3:I.209, 3:L.325, L:L.7 Hydrogen bonds: 3:Y.6, 3:Q.125 CDL.41: 32 residues within 4Å: Chain 1: Y.40, C.41, L.44, I.45, A.48, V.54, V.55 Chain 3: P.238, V.239, S.242, L.243, M.245, V.246, L.257, S.301, T.334, L.335 Chain 5: L.12, P.13, W.16, M.17, T.90, R.91, L.94, M.98, L.101, V.127, I.131, R.135 Chain L: Y.305 Ligands: CDL.15, 3PE.27 19 PLIP interactions: 9 interactions with chain 5, 5 interactions with chain 1, 3 interactions with chain 3, 2 interactions with chain L Hydrophobic interactions: 5:L.12, 5:P.13, 5:P.13, 5:W.16, 5:W.16, 5:L.94, 5:L.101, 5:V.127, 5:I.131, 1:L.44, 1:L.44, 1:I.45, 1:V.55, 3:V.246, 3:L.257, 3:L.335 Hydrogen bonds: 1:V.54, L:Y.305, L:Y.305 CDL.44: 34 residues within 4Å: Chain 5: L.354, T.357, W.358, L.360, V.361, L.364, T.365, L.369, P.371, L.445, L.446, T.448, L.449 Chain 6: T.16, I.19, M.20, S.22, N.23, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, G.146, I.149, M.150, L.153 Chain T: L.17 Ligands: CDL.18, PEE.21, PLX.24 28 PLIP interactions: 15 interactions with chain 5, 13 interactions with chain 6 Hydrophobic interactions: 5:W.358, 5:L.360, 5:V.361, 5:L.364, 5:L.364, 5:T.365, 5:L.369, 5:P.371, 5:L.445, 5:L.445, 5:L.446, 5:T.448, 5:L.449, 6:T.16, 6:I.19, 6:L.78, 6:I.126, 6:I.130, 6:I.149, 6:L.153 Hydrogen bonds: 5:T.357, 5:T.357, 6:N.23 Salt bridges: 6:K.28, 6:R.116, 6:K.119, 6:K.119, 6:K.119 CDL.45: 18 residues within 4Å: Chain 6: L.290, I.293, L.410, L.413, I.414, S.417, L.418, A.421, R.425, M.496, L.500, L.504, S.517, Q.518, T.519, Y.520 Chain W: F.106, F.109 16 PLIP interactions: 13 interactions with chain 6, 3 interactions with chain W Hydrophobic interactions: 6:L.290, 6:L.410, 6:L.413, 6:I.414, 6:A.421, 6:L.500, 6:L.504, 6:Q.518, 6:T.519, W:F.106, W:F.109, W:F.109 Hydrogen bonds: 6:T.294, 6:S.517, 6:Y.520 Salt bridges: 6:R.425

8 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 12 residues within 4Å: Chain D: A.5, L.8, K.9, W.12, V.19, L.27 Chain O: A.35, I.38, L.42 Ligands: PEE.31, PEE.59 Chain f: M.14 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain O Hydrophobic interactions: D:W.12, D:W.12, D:V.19, D:L.27, O:I.38, O:I.38, O:L.42 PC1.3: 9 residues within 4Å: Chain 2: M.310, T.311 Chain D: L.31, L.34, S.35 Chain O: L.42, Y.45, W.46, M.49 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain 2 Hydrophobic interactions: D:L.31, D:L.34, 2:T.311 PC1.17: 17 residues within 4Å: Chain 5: L.197, G.211, L.212, Y.256, M.257, Y.259, P.260, L.264 Chain 6: L.562 Chain S: I.94, L.97, F.98, Y.101, K.105 Ligands: CDL.16, PLX.40, PEE.43 9 PLIP interactions: 4 interactions with chain 5, 4 interactions with chain S, 1 interactions with chain 6 Hydrophobic interactions: 5:L.197, 5:L.212, 5:P.260, 5:L.264, S:L.97, S:F.98, S:Y.101, 6:L.562 Salt bridges: S:K.105 PC1.19: 10 residues within 4Å: Chain T: F.41, I.42, W.59, R.68, W.69, R.72 Chain Y: N.59 Chain Z: L.49 Ligands: PLX.14, PC1.20 8 PLIP interactions: 7 interactions with chain T, 1 interactions with chain Z Hydrophobic interactions: T:F.41, T:I.42, T:W.69, T:W.69, Z:L.49 Salt bridges: T:R.68, T:R.72, T:R.72 PC1.20: 8 residues within 4Å: Chain T: Y.23, L.26 Chain Z: R.36, F.40, I.45 Ligands: PLX.14, PC1.19, PEE.23 6 PLIP interactions: 6 interactions with chain Z Hydrophobic interactions: Z:R.36, Z:F.40, Z:F.40, Z:I.45, Z:I.45 Salt bridges: Z:R.36 PC1.33: 28 residues within 4Å: Chain 2: N.97, M.98, N.99, L.100, F.104, L.111, W.118 Chain 4: M.1, I.3, M.4 Chain 7: I.7, L.8, I.11, V.34, G.37, V.38, G.41, L.44, N.45, S.49 Chain B: A.39, H.40 Chain O: F.138, I.139, W.140, Y.141, T.142 Ligands: CDL.28 12 PLIP interactions: 6 interactions with chain 2, 5 interactions with chain 7, 1 interactions with chain 4 Hydrophobic interactions: 2:F.104, 2:F.104, 2:L.111, 2:W.118, 7:I.7, 7:V.34, 7:V.38, 4:I.3 Hydrogen bonds: 2:N.99, 2:L.100, 7:S.49, 7:S.49 PC1.36: 13 residues within 4Å: Chain 4: W.23, L.24, P.25, Q.26 Chain I: F.188, L.269, F.270, S.273, F.275, W.278 Ligands: PEE.5, PEE.32, PC1.38 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain 4 Hydrophobic interactions: I:F.188, I:L.269, I:F.270, I:F.270, I:W.278, 4:W.23, 4:L.24 pi-Cation interactions: I:F.275 PC1.38: 19 residues within 4Å: Chain 2: A.52, L.53, F.56 Chain 4: L.24, P.25, Q.26 Chain I: D.55, F.275 Ligands: PLX.29, U10.30, PC1.36, PLX.56 Chain e: V.6, K.9, L.10, V.14, L.150, W.153, R.156 13 PLIP interactions: 8 interactions with chain e, 2 interactions with chain 4, 2 interactions with chain 2, 1 interactions with chain I Hydrophobic interactions: e:V.6, e:K.9, e:L.10, e:L.10, e:V.14, e:L.150, e:W.153, 2:L.53, 2:F.56 Salt bridges: e:R.156, I:D.55 Hydrogen bonds: 4:Q.26, 4:Q.26

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.4: 25 residues within 4Å: Chain I: G.25, A.26, T.27, G.28, F.29, L.30, R.50, C.51, W.73, L.94, V.95, G.96, R.97, F.104, F.110, I.113, I.132, S.133, H.134, Y.145, K.149, P.168, I.171, R.177 Chain e: R.156 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain e Hydrogen bonds: I:G.25, I:T.27, I:T.27, I:T.27, I:F.29, I:L.30, I:R.50, I:L.94, I:G.96, I:K.149, I:I.171 Salt bridges: I:R.50, I:R.97, I:R.97, I:R.177, e:R.156 pi-Cation interactions: I:R.50

13 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.5: 13 residues within 4Å: Chain I: Y.181, S.184, W.187, F.188, P.192, Y.256, V.266, W.278, T.279, R.320, H.321 Ligands: PEE.32, PC1.36 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:Y.181, I:W.187, I:W.187, I:F.188, I:P.192, I:V.266, I:V.266, I:T.279 Hydrogen bonds: I:S.184, I:S.184, I:W.278, I:R.320, I:R.320 PEE.10: 10 residues within 4Å: Chain M: I.91, A.95, L.98, T.99, G.101, A.102, R.105, S.106, Y.107 Ligands: CDL.16 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:I.91, M:A.95, M:A.102 Salt bridges: M:R.105, M:R.105 PEE.21: 14 residues within 4Å: Chain 5: L.449 Chain 6: W.66, W.68, S.77, L.78, N.136 Chain T: E.44, H.64 Chain U: I.80, Y.84, H.88 Ligands: CDL.18, PLX.24, CDL.44 9 PLIP interactions: 5 interactions with chain 6, 1 interactions with chain 5, 2 interactions with chain U, 1 interactions with chain T Hydrophobic interactions: 6:W.66, 6:W.68, 6:W.68, 6:L.78, 6:L.78, 5:L.449, U:I.80 Salt bridges: U:H.88 Hydrogen bonds: T:E.44 PEE.23: 12 residues within 4Å: Chain 5: N.21, M.22, L.33, I.37 Chain P: H.9, H.12 Chain Z: I.29, V.30, W.33, V.37 Ligands: PLX.14, PC1.20 3 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain P Hydrophobic interactions: Z:W.33, Z:V.37 Salt bridges: P:H.9 PEE.31: 18 residues within 4Å: Chain 2: K.291, P.295, A.299, M.302 Chain 4: A.99, L.102, A.103, W.106 Chain D: E.15, L.18, S.21, F.22, A.23, G.26, L.27, I.29 Ligands: PC1.2, PEE.37 13 PLIP interactions: 7 interactions with chain D, 3 interactions with chain 2, 3 interactions with chain 4 Hydrophobic interactions: D:L.18, D:L.18, D:F.22, D:F.22, D:A.23, D:L.27, D:I.29, 2:P.295, 2:A.299, 4:L.102, 4:W.106, 4:W.106 Salt bridges: 2:K.291 PEE.32: 10 residues within 4Å: Chain 2: R.62, I.72, I.76 Chain 4: V.18, L.19, F.22, W.23 Ligands: PEE.5, CDL.28, PC1.36 4 PLIP interactions: 2 interactions with chain 4, 2 interactions with chain 2 Hydrophobic interactions: 4:V.18, 4:W.23, 2:I.72, 2:I.76 PEE.37: 12 residues within 4Å: Chain 3: T.8 Chain 4: I.96, L.97, A.100, A.103, Y.104, T.107 Chain 7: W.158, L.161 Chain D: F.22, I.29 Ligands: PEE.31 11 PLIP interactions: 2 interactions with chain 7, 3 interactions with chain D, 6 interactions with chain 4 Hydrophobic interactions: 7:W.158, 7:L.161, D:F.22, D:F.22, D:I.29, 4:I.96, 4:I.96, 4:L.97, 4:A.100, 4:A.103, 4:Y.104 PEE.39: 19 residues within 4Å: Chain 3: I.276, I.277, T.280, L.281, M.284 Chain 5: A.155, P.159, V.162, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain M: L.119, E.130, W.132 Ligands: PEE.52 13 PLIP interactions: 4 interactions with chain M, 1 interactions with chain 3, 8 interactions with chain 5 Hydrophobic interactions: M:L.119, M:W.132, M:W.132, 3:I.277, 5:P.159, 5:V.162, 5:Y.166, 5:F.194, 5:F.194, 5:L.197, 5:M.201 Hydrogen bonds: M:E.130, 5:S.191 PEE.42: 10 residues within 4Å: Chain 6: I.569, K.572, M.573 Chain M: F.69, M.117, A.121, V.124 Ligands: CDL.9, PEE.43, PEE.52 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:F.69, M:A.121, M:V.124, M:V.124 PEE.43: 17 residues within 4Å: Chain 6: T.560, I.561, T.565, F.568, I.569 Chain M: G.108, I.109, A.112, A.113, A.115, Y.116, L.119, T.120 Ligands: CDL.11, CDL.16, PC1.17, PEE.42 8 PLIP interactions: 4 interactions with chain 6, 4 interactions with chain M Hydrophobic interactions: 6:T.560, 6:I.561, 6:I.561, 6:I.569, M:A.112, M:A.115, M:Y.116, M:L.119 PEE.46: 20 residues within 4Å: Chain 5: L.277, M.398, M.401, L.405 Chain 6: D.163, L.169, Q.170, L.173, Y.174, F.227, G.228, L.229, Y.529, M.533, H.534, T.538, N.541 Chain W: N.85, R.86 Ligands: 3PE.47 13 PLIP interactions: 1 interactions with chain W, 2 interactions with chain 5, 10 interactions with chain 6 Hydrophobic interactions: W:R.86, 5:L.277, 5:L.405, 6:L.169, 6:L.173, 6:Y.174, 6:L.229, 6:N.541 Hydrogen bonds: 6:D.163, 6:Q.170, 6:T.538 Salt bridges: 6:H.534, 6:H.534 PEE.52: 20 residues within 4Å: Chain 3: L.170, L.281, M.284, T.285, L.287, L.288, Y.291, R.295 Chain 5: L.147, Y.148, F.151, Y.152 Chain 6: P.563, T.566, S.567, Q.570, M.571 Chain 9: Y.20 Ligands: PEE.39, PEE.42 20 PLIP interactions: 7 interactions with chain 5, 3 interactions with chain 6, 1 interactions with chain 9, 9 interactions with chain 3 Hydrophobic interactions: 5:Y.148, 5:Y.148, 5:F.151, 5:F.151, 5:F.151, 5:F.151, 5:Y.152, 6:P.563, 6:T.566, 6:Q.570, 3:L.170, 3:L.281, 3:L.287, 3:L.288, 3:Y.291, 3:Y.291, 3:Y.291 Hydrogen bonds: 9:Y.20, 3:Y.291, 3:R.295 PEE.59: 25 residues within 4Å: Chain 2: I.175, W.179, P.180, A.182, M.183, F.186, I.187, T.238, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 Chain 9: R.233 Chain D: E.15, I.24 Chain O: L.41 Ligands: PC1.2, CDL.13 Chain f: T.24, L.25, W.27, L.30 21 PLIP interactions: 11 interactions with chain 2, 2 interactions with chain D, 5 interactions with chain f, 2 interactions with chain 9, 1 interactions with chain O Hydrophobic interactions: 2:I.175, 2:W.179, 2:P.180, 2:A.182, 2:F.186, 2:F.186, 2:T.238, 2:I.273, 2:F.293, 2:L.296, 2:W.303, D:I.24, f:L.25, f:W.27, f:W.27, f:W.27, f:L.30, O:L.41 Hydrogen bonds: D:E.15 Salt bridges: 9:R.233, 9:R.233

2 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)

ZMP.6: 18 residues within 4Å: Chain F: K.16, V.19, W.26, G.46, V.50, M.53, F.54, M.55, N.57, A.58, V.60, V.66, V.70, G.73, I.90, F.93 Chain J: S.43, L.44 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain J Hydrophobic interactions: F:W.26, F:W.26, F:V.50, F:F.54, F:F.54, F:V.60, F:V.66, F:I.90, F:F.93, J:L.44 Hydrogen bonds: F:N.57, F:A.58, J:S.43 ZMP.7: 18 residues within 4Å: Chain K: D.42, S.43 Chain X: H.11, Q.12, V.15, A.22, L.26, W.29, M.43, R.46, F.47, H.50, K.51, A.59, A.66, E.69, F.70, G.73 13 PLIP interactions: 12 interactions with chain X, 1 interactions with chain K Hydrophobic interactions: X:Q.12, X:A.22, X:L.26, X:F.47, X:F.47, X:A.59, X:A.66, X:E.69, X:F.70 Hydrogen bonds: X:K.51, X:A.59, K:S.43 Salt bridges: X:K.51

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 14 residues within 4Å: Chain L: I.32, C.33, S.34, K.36, E.54, L.80, Y.84, Q.98, L.101, R.105, R.127, D.132, F.135, M.139 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:C.33, L:S.34, L:S.34, L:S.34, L:Y.84, L:Q.98, L:Q.98, L:R.105, L:R.127, L:E.192 Salt bridges: L:K.36, L:K.36 pi-Stacking: L:F.135, L:F.135

7 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.14: 14 residues within 4Å: Chain 5: L.36, S.40 Chain P: F.19, C.23, R.27 Chain T: R.72, T.73, F.74, Y.75, D.76 Chain Z: F.53 Ligands: PC1.19, PC1.20, PEE.23 9 PLIP interactions: 3 interactions with chain P, 1 interactions with chain Z, 3 interactions with chain 5, 2 interactions with chain T Hydrophobic interactions: P:F.19, P:F.19, Z:F.53, 5:L.36, T:F.74 Salt bridges: P:R.27, T:D.76 Hydrogen bonds: 5:S.40, 5:S.40 PLX.24: 20 residues within 4Å: Chain 5: L.39, V.67, W.71, P.443, L.446, L.447, L.449, N.450 Chain 6: I.19, M.20, S.22, N.23, W.66 Chain Z: S.51, V.54, A.55, Y.56 Ligands: CDL.18, PEE.21, CDL.44 11 PLIP interactions: 10 interactions with chain 5, 1 interactions with chain 6 Hydrophobic interactions: 5:L.39, 5:W.71, 5:W.71, 5:P.443, 5:L.446, 5:L.447, 5:L.447, 5:L.449, 5:N.450, 6:N.23 Hydrogen bonds: 5:N.450 PLX.26: 18 residues within 4Å: Chain 1: S.4, R.9, L.12, Q.13, F.14, M.35, F.72, L.76, R.79 Chain 3: L.203, I.207, T.210, M.261, M.339, A.342, S.345 Chain c: P.1, F.2 11 PLIP interactions: 3 interactions with chain 3, 8 interactions with chain 1 Hydrophobic interactions: 3:L.203, 3:I.207, 3:M.339, 1:F.14, 1:F.72, 1:L.76, 1:L.76 Hydrogen bonds: 1:L.12, 1:L.12 Salt bridges: 1:R.9, 1:R.79 PLX.29: 13 residues within 4Å: Chain 2: L.15, A.18, F.19, P.42, L.45, L.46, I.49 Chain B: A.14, C.15 Chain N: W.74 Ligands: U10.30, PC1.38, PLX.56 8 PLIP interactions: 7 interactions with chain 2, 1 interactions with chain B Hydrophobic interactions: 2:L.15, 2:A.18, 2:P.42, 2:L.45, 2:L.46, 2:I.49, 2:I.49, B:A.14 PLX.35: 10 residues within 4Å: Chain 3: S.15 Chain 4: N.83, M.90, F.93 Chain 7: S.147, Y.148, T.150, W.151, I.154 Chain c: D.12 6 PLIP interactions: 1 interactions with chain c, 4 interactions with chain 7, 1 interactions with chain 4 Hydrogen bonds: c:D.12 Hydrophobic interactions: 7:T.150, 7:W.151, 7:I.154, 7:I.154, 4:F.93 PLX.40: 11 residues within 4Å: Chain 5: N.188, W.190, I.193, Y.256 Chain M: D.85, L.87, F.90, L.119, M.126 Chain S: F.98 Ligands: PC1.17 6 PLIP interactions: 3 interactions with chain M, 1 interactions with chain S, 2 interactions with chain 5 Hydrophobic interactions: M:F.90, M:L.119, S:F.98 Hydrogen bonds: M:P.86, 5:Y.256 pi-Cation interactions: 5:W.190 PLX.56: 18 residues within 4Å: Chain 2: V.40, L.46, I.49, L.53 Chain N: F.27, R.28, N.30, W.74, D.75 Ligands: PLX.29, U10.30, PC1.38 Chain e: K.9, D.12, L.13, W.16, R.19, K.145 15 PLIP interactions: 3 interactions with chain 2, 12 interactions with chain e Hydrophobic interactions: 2:I.49, 2:L.53, 2:L.53, e:L.13, e:L.13, e:L.13, e:W.16, e:W.16, e:W.16, e:W.16, e:W.16 Salt bridges: e:R.19, e:R.19, e:K.145, e:K.145

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.22: 5 residues within 4Å: Chain 6: A.406 Chain V: L.10 Chain W: F.112, V.116, Y.120 8 PLIP interactions: 1 interactions with chain V, 1 interactions with chain 6, 6 interactions with chain W Hydrophobic interactions: V:L.10, 6:A.406, W:F.112, W:V.116, W:Y.120, W:Y.120, W:Y.120 Hydrogen bonds: W:Y.120 3PE.27: 12 residues within 4Å: Chain 0: W.28, I.32 Chain 1: L.27, T.28, G.36, F.37, Y.40, Q.62, L.63, V.66, V.70 Ligands: CDL.41 6 PLIP interactions: 5 interactions with chain 1, 1 interactions with chain 0 Hydrophobic interactions: 1:Y.40, 1:L.63, 1:V.66, 1:V.66, 1:V.70, 0:W.28 3PE.47: 8 residues within 4Å: Chain 5: I.394 Chain 6: L.184, P.209, N.210, M.211, I.214, M.276 Ligands: PEE.46 7 PLIP interactions: 5 interactions with chain 6, 2 interactions with chain 5 Hydrophobic interactions: 6:L.184, 6:I.214, 5:I.394, 5:I.394 Hydrogen bonds: 6:N.210, 6:N.210, 6:M.211

1 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.25: 11 residues within 4Å: Chain 0: K.16, L.19, T.20, T.23, F.26 Chain 1: R.61, L.64, Y.65, S.68, F.72 Chain 3: K.324 11 PLIP interactions: 5 interactions with chain 0, 2 interactions with chain 3, 4 interactions with chain 1 Hydrophobic interactions: 0:L.19, 0:T.23, 0:F.26, 1:Y.65, 1:Y.65, 1:F.72 Salt bridges: 0:K.16, 0:K.16, 3:K.324, 3:K.324, 1:R.61

1 x U10: UBIQUINONE-10(Non-covalent)

U10.30: 32 residues within 4Å: Chain 2: I.11, L.14, L.15, T.21, R.25, Q.32, R.34, P.48, D.51, A.52, F.56, F.224, M.225 Chain 9: P.56, L.159, M.164, F.167, F.168 Ligands: PLX.29, PC1.38, MF8.53, PLX.56 Chain e: W.23, T.26, G.28, A.33, M.36, M.37, A.40, V.52, F.53, R.54 16 PLIP interactions: 10 interactions with chain 2, 2 interactions with chain 9, 4 interactions with chain e Hydrophobic interactions: 2:I.11, 2:L.14, 2:L.15, 2:T.21, 2:D.51, 2:A.52, 2:F.56, 2:F.224, 2:F.224, 2:F.224, 9:L.159, 9:F.167, e:W.23, e:A.40, e:V.52, e:F.53

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.48: 12 residues within 4Å: Chain 8: H.95, D.98, C.99, C.102, G.105, C.108, L.110, Q.111, V.199, G.200 Chain 9: M.342, I.346 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:H.95, 8:C.99, 8:C.102, 8:C.108 SF4.49: 11 residues within 4Å: Chain 8: C.147, I.148, Q.149, C.150, T.151, R.152, C.153, C.197, P.198, V.199, L.202 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.147, 8:C.150, 8:C.153, 8:C.197 SF4.55: 14 residues within 4Å: Chain 9: R.85, R.105, H.190 Chain e: A.30, C.31, C.32, G.67, T.68, G.94, S.95, C.96, G.125, C.126, P.127 4 PLIP interactions: 4 interactions with chain e, Metal complexes: e:C.31, e:C.32, e:C.96, e:C.126 SF4.57: 12 residues within 4Å: Chain f: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, V.128, I.131 4 PLIP interactions: 4 interactions with chain f, Metal complexes: f:C.77, f:C.80, f:C.83, f:C.126 SF4.58: 12 residues within 4Å: Chain f: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 5 PLIP interactions: 5 interactions with chain f, Salt bridges: f:E.133 Metal complexes: f:C.87, f:C.116, f:C.119, f:C.122 SF4.60: 13 residues within 4Å: Chain g: I.176, P.194, S.349, C.350, G.351, Q.352, C.353, C.356, T.394, I.395, C.396, L.398, G.399 4 PLIP interactions: 4 interactions with chain g, Metal complexes: g:C.350, g:C.353, g:C.356, g:C.396

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.50: 9 residues within 4Å: Chain 8: R.33, C.35, Y.36, G.44, N.45, C.46, R.47, C.49, C.63 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.35, 8:C.46, 8:C.49, 8:C.63 FES.62: 9 residues within 4Å: Chain h: C.103, T.105, P.107, C.108, C.144, L.145, G.146, A.147, C.148 4 PLIP interactions: 4 interactions with chain h, Metal complexes: h:C.103, h:C.108, h:C.144, h:C.148

1 x MG: MAGNESIUM ION(Non-covalent)

MG.51: 5 residues within 4Å: Chain 8: Q.104, I.194, C.197, V.199, L.202 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:I.194, 8:C.197, 8:L.202

1 x MF8: Metformin(Non-covalent)

MF8.53: 4 residues within 4Å: Chain 9: H.59, Y.108, T.156 Ligands: U10.30 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.54: 5 residues within 4Å: Chain d: C.59, G.61, H.68, C.84, C.87 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.59, d:H.68, d:C.84, d:C.87

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.61: 17 residues within 4Å: Chain g: G.58, R.59, G.60, K.69, N.87, D.89, E.90, D.98, Y.175, G.178, E.179, E.180, V.213, A.214, N.215, A.397, L.398 9 PLIP interactions: 9 interactions with chain g Hydrophobic interactions: g:N.87, g:N.215 Hydrogen bonds: g:G.60, g:N.87, g:E.180, g:N.215, g:T.218, g:A.397 Salt bridges: g:K.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Z. et al., Hydrophilic metformin and hydrophobic biguanides inhibit mitochondrial complex I by distinct mechanisms. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-11-19

Peptides

NADH-ubiquinone oxidoreductase chain 4L: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: E
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: F
Complex I-B14.5a: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: I
Acyl carrier protein: JK
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: O
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: P
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: Q
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: R
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: S
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: Z
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 0
NADH dehydrogenase [ubiquinone] 1 subunit C2: 1
NADH-ubiquinone oxidoreductase chain 1: 2
NADH-ubiquinone oxidoreductase chain 2: 3
NADH-ubiquinone oxidoreductase chain 3: 4
NADH-ubiquinone oxidoreductase chain 4: 5
NADH-ubiquinone oxidoreductase chain 5: 6
NADH-ubiquinone oxidoreductase chain 6: 7
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: 8
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: 9
Complex I-30kD: a
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: b
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: c
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: d
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: e
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: f
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: g
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: h
NADH:ubiquinone oxidoreductase subunit V3: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4L

B
A1

C
A2

D
A3

E
A5

F
A6

G
A7

H
A8

I
A9

J
AB

K
AC

L
AK

M
AL

N
AM

O
AN

P
B1

Q
B2

R
B3

S
B4

T
B5

U
B6

V
B7

W
B8

X
B9

Y
BK

Z
BL

0
CA

1
CB

2
N1

3
N2

4
N3

5
N4

6
N5

7
N6

8
S1

9
S2

a
S3

b
S4

c
S5

d
S6

e
S7

f
S8

g
V1

h
V2

i
V3

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 4L

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

Complex I-B14.5a

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

Complex I-30kD

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH:ubiquinone oxidoreductase subunit V3

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