SMTL ID : 8zsl.1

Complex I from respirasome closed state 1 bound by metformin and CoQ10 (SC-MetC1-i)

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

12 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 29 residues within 4Å: Chain 6: K.585, L.589, L.592, I.593 Chain 7: S.20, K.22, T.87, A.91, G.95, M.98 Chain A: A.13, I.14, L.16, A.17, M.21, Y.22, R.23 Chain M: L.33, A.37, I.40, P.44, P.45, A.46, S.47, F.48, G.51, V.52, T.55, G.56 17 PLIP interactions: 4 interactions with chain 7, 5 interactions with chain M, 3 interactions with chain 6, 5 interactions with chain A Hydrophobic interactions: 7:T.87, 7:A.91, M:I.40, M:P.44, M:F.48, M:V.52, M:T.55, 6:L.589, 6:I.593, A:I.14, 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.2: 20 residues within 4Å: Chain 2: Y.43 Chain B: M.1, W.2, F.3, L.6, P.7, A.10, A.13, A.14, F.17 Chain G: A.3, T.4, I.7 Chain N: L.2, V.5, L.6, R.8, G.9, Q.12, Y.22 12 PLIP interactions: 8 interactions with chain B, 2 interactions with chain N, 1 interactions with chain 2, 1 interactions with chain G Hydrophobic interactions: B:W.2, B:F.3, B:F.3, B:L.6, B:A.10, B:A.13, B:A.14, B:F.17, N:L.2, 2:Y.43 Salt bridges: N:R.8 Hydrogen bonds: G:T.4 CDL.4: 23 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: I.5, T.9, T.55, F.56, M.108, L.117 Chain H: F.168, T.170, M.171 Chain P: L.25, R.28, K.32 Ligands: 3PE.27, CDL.43 18 PLIP interactions: 4 interactions with chain P, 5 interactions with chain 1, 3 interactions with chain 5, 3 interactions with chain 3, 3 interactions with chain H Hydrophobic interactions: P:L.25, 1:R.31, 1:V.33, 1:F.37, 1:F.37, 1:F.37, 5:I.5, 5:F.56, 5:L.117, 3:P.256, 3:L.335, 3:P.338, H:F.168, H:F.168 Salt bridges: P:R.28, P:K.32, P:K.32 Hydrogen bonds: H:T.170 CDL.11: 35 residues within 4Å: Chain 3: P.110, H.112, L.153, M.157, L.160 Chain 6: M.576, V.577, Q.580, I.597, S.598 Chain M: A.1, S.24, I.27, A.30, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, T.61, S.62, I.65, G.66, F.69, T.104, I.109, M.117, T.120, A.121, V.124 Ligands: CDL.13, PEE.14 24 PLIP interactions: 17 interactions with chain M, 3 interactions with chain 6, 4 interactions with chain 3 Hydrophobic interactions: M:A.1, M:I.27, M:A.30, M:T.31, M:I.34, M:I.34, M:V.35, M:Y.38, M:T.61, M:I.65, M:F.69, M:F.69, M:T.120, M:A.121, M:V.124, 6:V.577, 6:I.597, 3:P.110, 3:P.110, 3:L.153, 3:L.160 Hydrogen bonds: M:Y.58, 6:Q.580 Salt bridges: M:K.43 CDL.13: 18 residues within 4Å: Chain 3: N.152, T.156, M.159, L.160, L.281 Chain 6: F.602 Chain M: K.2, L.5, H.6, Y.8, L.123, V.124, G.127, Q.128, W.132, V.134, F.135 Ligands: CDL.11 14 PLIP interactions: 5 interactions with chain 3, 8 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: 3:M.159, 3:L.160, 3:L.160, 3:L.281, M:Y.8, M:L.123, M:L.123, M:Q.128, M:V.134, M:V.134, 6:F.602 Hydrogen bonds: 3:N.152 Salt bridges: M:K.2, M:K.2 CDL.19: 19 residues within 4Å: Chain 5: Y.210, L.264 Chain 6: W.557, L.558 Chain M: Y.107, G.108 Chain S: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97 Ligands: PEE.14, PEE.18, 3PE.44 9 PLIP interactions: 2 interactions with chain 5, 3 interactions with chain S, 2 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: 5:Y.210, 5:L.264, S:L.87, S:I.94, S:L.97, M:Y.107, 6:W.557, 6:L.558 Hydrogen bonds: M:Y.107 CDL.21: 32 residues within 4Å: Chain 5: L.446, L.449 Chain 6: L.12, T.13, T.16, F.80, I.126, M.129, I.130 Chain T: A.32, T.36, N.39, V.40, E.44, H.64 Chain U: W.79, I.80, Y.83, Y.84, H.88 Chain Y: P.44, A.48, R.49, I.52, H.56 Chain Z: V.48, S.51, A.55, Y.56 Ligands: PEE.23, PLX.42, CDL.45 27 PLIP interactions: 4 interactions with chain Y, 4 interactions with chain Z, 6 interactions with chain 6, 5 interactions with chain T, 6 interactions with chain U, 2 interactions with chain 5 Hydrophobic interactions: Y:P.44, Y:A.48, Z:V.48, Z:A.55, Z:Y.56, 6:L.12, 6:T.16, 6:F.80, 6:I.126, 6:M.129, 6:I.130, T:A.32, U:W.79, U:W.79, U:I.80, U:Y.83, U:Y.84, 5:L.446, 5:L.449 Salt bridges: Y:R.49, Y:H.56, T:H.64, U:H.88 Hydrogen bonds: Z:Y.56, T:N.39, T:N.39, T:E.44 CDL.28: 22 residues within 4Å: Chain 2: R.62, S.67, I.68, S.69, I.73, L.111, W.118 Chain 7: I.11, 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: PC1.17, PEE.31 18 PLIP interactions: 9 interactions with chain 7, 8 interactions with chain 2, 1 interactions with chain I Hydrophobic interactions: 7:L.30, 7:V.34, 7:W.82, 7:W.82, 7:W.82, 7:V.83, 7:F.92, 2:I.68, 2:I.73, 2:L.111, 2:W.118 Hydrogen bonds: 7:W.82, 7:V.83, 2:I.68, 2:S.69, 2:S.69 Salt bridges: 2:R.62, I:R.251 CDL.34: 22 residues within 4Å: Chain 3: P.3, Y.6, T.7, I.10, M.11, M.14, Q.125, L.128, L.129, T.132, W.133, L.136, I.209, L.213, M.217, I.220, K.321, K.324, M.329 Chain L: P.6, L.7, H.258 12 PLIP interactions: 11 interactions with chain 3, 1 interactions with chain L Hydrophobic interactions: 3:I.10, 3:L.129, 3:T.132, 3:W.133, 3:L.136, 3:I.209, 3:L.213, L:L.7 Hydrogen bonds: 3:Q.125 Salt bridges: 3:K.46, 3:K.321, 3:K.321 CDL.43: 29 residues within 4Å: Chain 1: C.41, L.44, I.45, A.48, V.54, V.55 Chain 3: P.238, S.242, L.243, M.245, V.246, L.335 Chain 5: L.12, W.16, M.17, T.88, T.90, R.91, L.94, M.98, F.105, V.127, I.131 Chain L: Q.295, K.304, Y.305 Chain P: V.17 Ligands: CDL.4, 3PE.27 23 PLIP interactions: 1 interactions with chain P, 3 interactions with chain L, 10 interactions with chain 5, 5 interactions with chain 1, 4 interactions with chain 3 Hydrophobic interactions: P:V.17, 5:L.12, 5:W.16, 5:W.16, 5:L.94, 5:L.94, 5:F.105, 5:V.127, 5:I.131, 1:L.44, 1:L.44, 1:I.45, 1:A.48, 1:V.55, 3:L.243, 3:V.246, 3:V.246, 3:L.335 Hydrogen bonds: L:Q.295, L:Y.305 Salt bridges: L:K.304, 5:R.91, 5:R.135 CDL.45: 33 residues within 4Å: Chain 5: L.354, T.357, W.358, V.361, L.364, L.369, P.370, P.371, L.445, L.446, T.448, L.449 Chain 6: S.22, N.23, Y.27, K.28, L.78, R.116, K.119, Y.120, L.123, I.130, I.149, M.150, L.153 Chain T: L.17, R.21, I.24, L.25, G.28 Ligands: CDL.21, PEE.23, PLX.42 22 PLIP interactions: 12 interactions with chain 5, 7 interactions with chain 6, 3 interactions with chain T Hydrophobic interactions: 5:W.358, 5:V.361, 5:V.361, 5:L.364, 5:L.369, 5:L.445, 5:L.445, 5:L.446, 5:T.448, 5:L.449, 6:N.23, 6:L.78, 6:L.153, T:R.21, T:I.24, T:L.25 Hydrogen bonds: 5:T.357, 5:T.357 Salt bridges: 6:K.28, 6:R.116, 6:K.119, 6:K.119 CDL.47: 18 residues within 4Å: Chain 6: L.290, I.293, L.413, I.414, S.417, A.421, R.425, V.493, M.496, G.497, L.500, S.517, Q.518, T.519, Y.520 Chain W: F.106, F.109, M.110 16 PLIP interactions: 13 interactions with chain 6, 3 interactions with chain W Hydrophobic interactions: 6:L.290, 6:L.413, 6:L.413, 6:I.414, 6:A.421, 6:V.493, 6:L.500, 6:Q.518, 6:T.519, W:F.106, W:F.109, W:F.109 Hydrogen bonds: 6:S.517, 6:S.517, 6:Y.520 Salt bridges: 6:R.425

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

PC1.3: 16 residues within 4Å: Chain D: A.5, L.8, K.9, W.12, V.19, A.20, A.23, I.24 Chain O: Y.31, A.35, I.38, L.42 Ligands: PEE.16, PEE.33, PEE.35 Chain f: M.14 3 PLIP interactions: 2 interactions with chain O, 1 interactions with chain D Hydrophobic interactions: O:Y.31, O:L.42, D:I.24 PC1.7: 16 residues within 4Å: Chain 4: L.16, L.19, I.20, W.23, L.24, P.25, Q.26 Chain I: F.188, F.270, V.272, S.273, F.275, W.278 Ligands: PEE.6, PEE.31, PC1.36 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain 4 Hydrophobic interactions: I:F.188, I:F.188, I:F.270, I:F.270, I:V.272, 4:L.16, 4:W.23 pi-Cation interactions: I:F.275 PC1.17: 23 residues within 4Å: Chain 2: I.73, L.77, M.98, N.99, L.100, F.104, M.108, L.111 Chain 4: I.3, M.4, V.11 Chain 7: I.4, G.41, L.44, N.45, S.49 Chain B: A.39 Chain O: F.138, I.139, W.140, Y.141, T.142 Ligands: CDL.28 12 PLIP interactions: 1 interactions with chain O, 6 interactions with chain 2, 1 interactions with chain 4, 4 interactions with chain 7 pi-Cation interactions: O:F.138 Hydrophobic interactions: 2:I.73, 2:F.104, 2:F.104, 2:L.111, 4:V.11, 7:I.4, 7:L.44 Hydrogen bonds: 2:N.99, 2:L.100, 7:N.45, 7:S.49 PC1.22: 14 residues within 4Å: Chain T: P.30, V.31, I.33, G.34, V.38, I.42, W.59, P.65, R.68, W.69, R.72 Chain Y: Y.61 Ligands: PLX.20, PEE.39 9 PLIP interactions: 9 interactions with chain T Hydrophobic interactions: T:V.31, T:I.33, T:V.38, T:P.65, T:W.69, T:W.69, T:W.69 Salt bridges: T:R.68, T:R.72 PC1.29: 10 residues within 4Å: Chain 2: I.175, M.183, I.268, T.269, W.272 Chain G: W.13 Chain O: R.26, L.28 Chain f: V.31, L.38 4 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain f Hydrophobic interactions: 2:I.175, 2:I.268, 2:W.272, f:L.38 PC1.30: 14 residues within 4Å: Chain 2: Q.169, E.170, H.171, I.172, W.173, I.175, F.176, W.179, G.244, A.245, S.246, N.258, K.262 Chain O: G.37 10 PLIP interactions: 10 interactions with chain 2 Hydrophobic interactions: 2:W.173, 2:W.173, 2:I.175, 2:F.176, 2:W.179 Hydrogen bonds: 2:G.244, 2:S.246, 2:N.258 Salt bridges: 2:K.262, 2:K.262 PC1.36: 14 residues within 4Å: Chain 2: A.52, F.56, T.57 Chain 4: L.24, Q.26 Chain I: D.55, F.275 Ligands: PC1.7, PLX.58 Chain e: L.10, V.14, L.150, W.153, R.156 12 PLIP interactions: 4 interactions with chain 2, 3 interactions with chain e, 2 interactions with chain I, 3 interactions with chain 4 Hydrophobic interactions: 2:A.52, 2:F.56, 2:F.56, 2:T.57, e:L.10, e:W.153, I:F.275, 4:L.24, 4:L.24 Salt bridges: e:R.156, I:D.55 Hydrogen bonds: 4:Q.26 PC1.46: 13 residues within 4Å: Chain 6: F.227, G.228, M.276, C.279, I.283, Y.529, M.533 Chain W: V.107, L.111, F.114, E.118 Ligands: PEE.48, 3PE.49 5 PLIP interactions: 2 interactions with chain W, 3 interactions with chain 6 Hydrophobic interactions: W:V.107, 6:F.227, 6:I.283, 6:Y.529 Salt bridges: W:E.118

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

NDP.5: 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, V.109, F.110, I.113, I.132, S.133, H.134, Y.145, K.149, P.168, I.171 Chain e: R.156 19 PLIP interactions: 18 interactions with chain I, 1 interactions with chain e Hydrophobic interactions: I:P.168 Hydrogen bonds: I:G.25, I:T.27, I:T.27, I:T.27, I:F.29, I:L.30, I:R.50, I:C.51, I:L.94, I:G.96, I:K.149, I:I.171 Salt bridges: I:R.50, I:R.97, I:R.97, e:R.156 pi-Cation interactions: I:R.50, I:R.50

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

PEE.6: 13 residues within 4Å: Chain I: Y.181, S.184, M.185, W.187, F.188, P.192, Y.256, Y.263, F.270, W.278, T.279 Ligands: PC1.7, PEE.31 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:Y.181, I:Y.181, I:W.187, I:F.188, I:F.188, I:F.188, I:F.188, I:F.270, I:W.278, I:T.279 Hydrogen bonds: I:S.184 PEE.12: 7 residues within 4Å: Chain M: A.95, T.99, G.101, A.102, R.105, S.106, Y.107 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:A.95, M:A.102, M:Y.107 PEE.14: 19 residues within 4Å: Chain 6: T.560, I.561, L.562, T.565, F.568, I.569 Chain M: S.106, G.108, I.109, A.112, A.113, A.115, Y.116, L.119, T.120 Chain S: P.81 Ligands: CDL.11, CDL.19, 3PE.44 10 PLIP interactions: 8 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: M:I.109, M:A.112, M:A.113, M:A.115, M:Y.116, M:Y.116, M:L.119, 6:I.561, 6:L.562 Hydrogen bonds: M:S.106 PEE.16: 10 residues within 4Å: Chain 2: M.310, T.311 Chain D: L.27, L.31, S.35 Chain O: L.42, F.43, W.46, M.49 Ligands: PC1.3 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain O, 1 interactions with chain 2 Hydrophobic interactions: D:L.27, D:L.31, O:L.42, 2:T.311 PEE.18: 6 residues within 4Å: Chain S: P.83, K.84, L.87, L.88, L.91 Ligands: CDL.19 4 PLIP interactions: 4 interactions with chain S Hydrophobic interactions: S:L.87, S:L.88 Hydrogen bonds: S:K.84 Salt bridges: S:K.84 PEE.23: 15 residues within 4Å: Chain 5: P.371, L.449 Chain 6: W.66, H.67, W.68, S.77, N.136, F.138, I.142 Chain U: I.80, Y.84, H.88 Ligands: CDL.21, PLX.42, CDL.45 13 PLIP interactions: 8 interactions with chain 6, 3 interactions with chain U, 2 interactions with chain 5 Hydrophobic interactions: 6:W.66, 6:W.66, 6:W.68, 6:W.68, 6:W.68, 6:F.138, 6:I.142, U:I.80, U:Y.84, 5:P.371, 5:P.371 Hydrogen bonds: 6:H.67 Salt bridges: U:H.88 PEE.31: 10 residues within 4Å: Chain 2: R.62 Chain 4: S.15, L.19, F.22, W.23, L.27 Chain I: W.187 Ligands: PEE.6, PC1.7, CDL.28 3 PLIP interactions: 1 interactions with chain 2, 2 interactions with chain 4 Hydrogen bonds: 2:R.62, 4:F.22 Hydrophobic interactions: 4:L.19 PEE.33: 22 residues within 4Å: Chain 2: A.182, M.183, F.186, I.187, P.197, T.238, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 Chain 9: R.233 Chain D: V.17, I.24 Chain O: L.41 Ligands: PC1.3 Chain f: T.24, L.25, W.27, L.30 17 PLIP interactions: 10 interactions with chain 2, 4 interactions with chain f, 1 interactions with chain D, 2 interactions with chain 9 Hydrophobic interactions: 2:F.186, 2:I.187, 2:P.197, 2:T.238, 2:I.273, 2:Y.277, 2:F.293, 2:L.296, 2:W.303, f:W.27, f:W.27, f:W.27, f:L.30, D:I.24 Hydrogen bonds: 2:S.292 Salt bridges: 9:R.233, 9:R.233 PEE.35: 22 residues within 4Å: Chain 2: K.291, P.295, A.299 Chain 4: A.99, L.102, A.103, W.106, T.107, K.109, E.112 Chain D: L.8, A.11, E.15, L.18, V.19, S.21, F.22, G.25, G.26, I.29 Ligands: PC1.3, PEE.37 18 PLIP interactions: 4 interactions with chain 4, 11 interactions with chain D, 3 interactions with chain 2 Hydrophobic interactions: 4:A.99, 4:L.102, 4:W.106, 4:W.106, D:L.8, D:A.11, D:L.18, D:L.18, D:L.18, D:V.19, D:F.22, D:F.22, D:F.22, D:F.22, D:I.29, 2:P.295, 2:A.299 Salt bridges: 2:K.291 PEE.37: 12 residues within 4Å: Chain 3: T.8 Chain 4: L.92, F.93, I.96, L.97, A.100, A.103, Y.104, T.107 Chain 7: W.158, L.161 Ligands: PEE.35 8 PLIP interactions: 6 interactions with chain 4, 2 interactions with chain 7 Hydrophobic interactions: 4:L.92, 4:F.93, 4:L.97, 4:A.100, 4:A.103, 4:Y.104, 7:W.158, 7:W.158 PEE.38: 9 residues within 4Å: Chain 3: S.15 Chain 4: N.83, T.86 Chain 7: T.150, W.151, I.154, V.155, W.158 Chain c: L.13 10 PLIP interactions: 7 interactions with chain 7, 2 interactions with chain 4, 1 interactions with chain c Hydrophobic interactions: 7:W.151, 7:W.151, 7:W.151, 7:I.154, 7:I.154, 7:V.155, 7:W.158, c:L.13 Hydrogen bonds: 4:N.83, 4:T.86 PEE.39: 12 residues within 4Å: Chain 5: M.22, L.33, I.37 Chain P: H.9, H.12, P.16 Chain Z: I.29, W.33, F.40, I.45 Ligands: PLX.20, PC1.22 6 PLIP interactions: 2 interactions with chain 5, 2 interactions with chain P, 2 interactions with chain Z Hydrophobic interactions: 5:L.33, 5:I.37, P:P.16, Z:F.40, Z:I.45 Hydrogen bonds: P:H.9 PEE.40: 20 residues within 4Å: Chain 3: I.276, I.277, T.280, L.281 Chain 5: Y.152, A.155, G.156, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Chain M: L.119, L.123, E.130, W.132 Ligands: PEE.54 12 PLIP interactions: 3 interactions with chain M, 6 interactions with chain 5, 3 interactions with chain 3 Hydrophobic interactions: M:L.119, M:W.132, 5:A.155, 5:F.194, 5:F.194, 5:L.197, 5:A.198, 3:I.276, 3:T.280, 3:L.281 Hydrogen bonds: M:E.130, 5:S.191 PEE.48: 21 residues within 4Å: Chain 5: M.398, M.401 Chain 6: Q.170, L.173, Y.174, I.177, I.180, L.217, L.218, G.228, L.229, L.280, Y.529, M.533, H.534, T.538, N.541, L.542 Chain W: N.85 Ligands: PC1.46, 3PE.49 14 PLIP interactions: 14 interactions with chain 6 Hydrophobic interactions: 6:L.173, 6:Y.174, 6:I.177, 6:I.180, 6:L.217, 6:L.218, 6:L.229, 6:L.229, 6:L.280, 6:N.541, 6:L.542 Hydrogen bonds: 6:Q.170 Salt bridges: 6:H.534, 6:H.534 PEE.54: 17 residues within 4Å: Chain 3: L.163, L.170, M.284, L.287, L.288, Y.291, R.295 Chain 5: N.144, Y.148, F.151, Y.152 Chain 6: L.562, P.563, S.567, Q.570 Chain 9: Y.20 Ligands: PEE.40 17 PLIP interactions: 7 interactions with chain 5, 2 interactions with chain 6, 7 interactions with chain 3, 1 interactions with chain 9 Hydrophobic interactions: 5:Y.148, 5:Y.148, 5:F.151, 5:F.151, 5:F.151, 5:Y.152, 5:Y.152, 6:L.562, 6:Q.570, 3:L.163, 3:L.170, 3:L.287, 3:L.287, 3:Y.291, 3:Y.291 Hydrogen bonds: 3:R.295, 9:Y.20

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

ZMP.8: 18 residues within 4Å: Chain F: M.11, K.15, V.18, L.21, W.25, V.49, M.52, F.53, M.54, N.56, A.57, V.59, V.65, V.69, E.75, I.89, F.92 Chain J: S.43 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:L.21, F:W.25, F:M.52, F:F.53, F:F.53, F:I.89, F:F.92 Hydrogen bonds: F:K.15, F:N.56, F:A.57 Salt bridges: F:K.15 ZMP.9: 19 residues within 4Å: Chain 6: F.513 Chain K: D.42, S.43 Chain X: H.11, Q.12, V.15, H.25, L.26, W.29, M.43, R.46, F.47, H.50, K.51, A.59, A.66, E.69, F.70, G.73 15 PLIP interactions: 2 interactions with chain K, 12 interactions with chain X, 1 interactions with chain 6 Hydrogen bonds: K:D.42, K:S.43, X:Q.12, X:K.51, X:A.59 Hydrophobic interactions: X:Q.12, X:V.15, X:H.25, X:L.26, X:F.47, X:F.47, X:A.59, X:E.69, X:F.70, 6:F.513

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

ADP.10: 15 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, K.187 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:N.31, L:C.33, L:S.34, L:S.34, L:S.34, L:Y.84, L:Q.98, L:Q.98, L:R.105 Salt bridges: L:K.36, L:K.36, L:R.127, L:K.187 pi-Stacking: L:F.135, L:F.135

6 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.15: 11 residues within 4Å: Chain 2: F.19, P.42, L.46, I.49 Chain B: V.11, A.14, I.18 Chain N: F.27, W.74 Ligands: U10.32, PLX.58 6 PLIP interactions: 3 interactions with chain 2, 3 interactions with chain B Hydrophobic interactions: 2:F.19, 2:P.42, 2:I.49, B:V.11, B:A.14, B:I.18 PLX.20: 23 residues within 4Å: Chain 5: K.3, L.33, L.36, I.37, S.40 Chain P: F.19, C.23, R.27 Chain T: I.35, I.66, R.72, T.73, F.74, Y.75, D.76 Chain Z: F.40, F.41, I.45, L.49, T.52, F.53 Ligands: PC1.22, PEE.39 17 PLIP interactions: 6 interactions with chain T, 4 interactions with chain Z, 3 interactions with chain P, 4 interactions with chain 5 Hydrophobic interactions: T:I.35, T:I.66, T:F.74, T:F.74, Z:F.40, Z:F.41, Z:I.45, Z:F.53, P:F.19, P:F.19, 5:L.36 Hydrogen bonds: T:T.73, 5:S.40, 5:S.40 Salt bridges: T:D.76, P:R.27, 5:K.3 PLX.25: 20 residues within 4Å: Chain 1: S.4, R.9, L.12, Q.13, F.14, M.35, S.68, F.71, F.72, L.76, R.79 Chain 3: M.261, L.332, M.339, A.342, S.345, L.346 Ligands: 3PE.26 Chain c: P.1, F.2 12 PLIP interactions: 10 interactions with chain 1, 2 interactions with chain 3 Hydrophobic interactions: 1:F.14, 1:F.14, 1:F.14, 1:F.71, 1:F.72, 1:L.76, 3:L.332, 3:M.339 Hydrogen bonds: 1:L.12, 1:R.79 Salt bridges: 1:R.9, 1:R.79 PLX.41: 10 residues within 4Å: Chain 5: N.188, W.190, Y.256 Chain M: D.85, P.86, L.87, F.90, L.119 Chain S: F.98 Ligands: 3PE.44 9 PLIP interactions: 6 interactions with chain M, 2 interactions with chain 5, 1 interactions with chain S Hydrophobic interactions: M:P.86, M:F.90, M:F.90, M:F.90, M:L.119, 5:W.190, S:F.98 Hydrogen bonds: M:L.87, 5:Y.256 PLX.42: 17 residues within 4Å: Chain 5: L.39, V.67, W.71, P.443, L.446, L.449, N.450 Chain 6: I.19, M.20, W.66 Chain Z: V.46, S.51, A.55, Y.56 Ligands: CDL.21, PEE.23, CDL.45 10 PLIP interactions: 9 interactions with chain 5, 1 interactions with chain Z Hydrophobic interactions: 5:L.39, 5:L.39, 5:W.71, 5:W.71, 5:P.443, 5:L.446, 5:L.449, 5:N.450, Z:V.46 Hydrogen bonds: 5:N.450 PLX.58: 19 residues within 4Å: Chain 2: I.49, A.52, L.53 Chain N: F.27, R.28, N.30, W.74, D.75, V.76 Ligands: PLX.15, U10.32, PC1.36 Chain e: V.6, K.9, D.12, L.13, W.16, R.19, K.145 16 PLIP interactions: 3 interactions with chain 2, 12 interactions with chain e, 1 interactions with chain N Hydrophobic interactions: 2:I.49, 2:A.52, 2:L.53, e:V.6, e:K.9, e:L.13, e:L.13, e:L.13, e:W.16, e:W.16, e:W.16 Salt bridges: e:R.19, e:R.19, e:K.145, e:K.145 Hydrogen bonds: N:D.75

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

3PE.24: 6 residues within 4Å: Chain V: R.8, Y.9 Chain W: W.115, I.119, Y.120, P.121 3 PLIP interactions: 2 interactions with chain W, 1 interactions with chain V Hydrophobic interactions: W:I.119, W:Y.120, V:Y.9 3PE.26: 18 residues within 4Å: Chain 0: K.16, L.19, T.20, T.23 Chain 1: D.46, R.61, L.64, Y.65, S.68, F.69, F.72 Chain 3: Q.322, K.324, L.325, T.328, M.329, L.332 Ligands: PLX.25 12 PLIP interactions: 9 interactions with chain 1, 1 interactions with chain 3, 2 interactions with chain 0 Hydrophobic interactions: 1:R.61, 1:L.64, 1:Y.65, 1:Y.65, 1:Y.65, 1:F.69, 1:F.69, 1:F.72, 3:L.332 Salt bridges: 1:R.61, 0:K.16 Hydrogen bonds: 0:L.19 3PE.27: 12 residues within 4Å: Chain 0: W.28 Chain 1: L.27, T.28, G.36, F.37, Y.40, Q.62, L.63, V.66, V.70 Ligands: CDL.4, CDL.43 6 PLIP interactions: 5 interactions with chain 1, 1 interactions with chain 0 Hydrophobic interactions: 1:Y.40, 1:Y.40, 1:L.63, 1:V.66, 1:V.70, 0:W.28 3PE.44: 20 residues within 4Å: Chain 5: L.197, M.201, L.209, G.211, L.212, Y.256, M.257, P.260, F.261, L.264 Chain 6: L.558, I.561, L.562 Chain S: L.97, F.98, Y.101, K.105 Ligands: PEE.14, CDL.19, PLX.41 14 PLIP interactions: 7 interactions with chain 5, 3 interactions with chain 6, 4 interactions with chain S Hydrophobic interactions: 5:L.209, 5:L.212, 5:Y.256, 5:P.260, 5:P.260, 5:F.261, 5:L.264, 6:L.558, 6:I.561, 6:L.562, S:Y.101 Hydrogen bonds: S:K.105, S:K.105 Salt bridges: S:K.105 3PE.49: 10 residues within 4Å: Chain 5: I.394 Chain 6: I.180, L.184, E.207, P.209, N.210, M.211, I.214 Ligands: PC1.46, PEE.48 7 PLIP interactions: 3 interactions with chain 5, 4 interactions with chain 6 Hydrophobic interactions: 5:I.394, 5:I.394, 5:I.394, 6:I.180, 6:I.214 Hydrogen bonds: 6:E.207, 6:N.210

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

U10.32: 27 residues within 4Å: Chain 2: I.11, L.14, L.15, A.18, T.21, R.25, D.51, A.52, L.55, A.221, F.224, M.225 Chain 9: P.56, L.159, M.164, F.167 Ligands: PLX.15, MF8.55, PLX.58 Chain e: W.23, T.26, F.27, G.28, M.36, M.37, V.52, F.53 16 PLIP interactions: 10 interactions with chain 2, 4 interactions with chain e, 2 interactions with chain 9 Hydrophobic interactions: 2:L.14, 2:L.15, 2:L.15, 2:T.21, 2:D.51, 2:A.52, 2:L.55, 2:A.221, 2:F.224, 2:F.224, e:W.23, e:M.36, e:F.53, e:F.53, 9:L.159, 9:F.167

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

SF4.50: 12 residues within 4Å: Chain 8: H.95, P.96, D.98, C.99, C.102, G.105, C.108, L.110, Q.111, V.199, G.200 Chain 9: M.342 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:H.95, 8:C.99, 8:C.102, 8:C.108 SF4.51: 12 residues within 4Å: Chain 8: M.144, C.147, I.148, Q.149, C.150, T.151, R.152, C.153, C.197, V.199, A.201, L.202 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.147, 8:C.150, 8:C.153, 8:C.197 SF4.57: 13 residues within 4Å: Chain 9: 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 SF4.59: 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 SF4.60: 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 SF4.61: 12 residues within 4Å: Chain g: I.176, P.194, 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.52: 11 residues within 4Å: Chain 8: R.33, F.34, C.35, Y.36, G.44, N.45, C.46, R.47, M.48, 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.63: 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.53: 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:V.199, 8:L.202

1 x MF8: Metformin(Non-covalent)

MF8.55: 10 residues within 4Å: Chain 9: P.56, H.59, Y.108, M.152, T.156 Ligands: U10.32 Chain e: G.28, A.30, A.33, M.37 2 PLIP interactions: 2 interactions with chain 9 Hydrogen bonds: 9:P.56, 9:H.59

1 x ZN: ZINC ION(Non-covalent)

ZN.56: 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.62: 19 residues within 4Å: Chain g: G.58, R.59, G.60, A.62, K.69, N.87, D.89, E.90, D.98, Y.175, G.178, E.179, E.180, V.213, A.214, N.215, T.218, 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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