SMTL ID : 8q0a.1

Inward-facing, closed proteoliposome complex I at 3.1 A. Initially purified in DDM.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

3PE.1: 4 residues within 4Å: Chain A: L.5, T.9, L.13 Chain H: M.3 Ligand excluded by PLIP 3PE.2: 13 residues within 4Å: Chain A: I.96, L.97, Y.104, T.107, Q.108 Chain J: W.159, L.162 Chain N: N.2, I.4, I.8 Ligands: PC1.4, PLC.6, 3PE.65 Ligand excluded by PLIP 3PE.23: 6 residues within 4Å: Chain 1: K.10, W.13 Chain I: D.49, M.50 Chain Z: Y.33, F.36 Ligand excluded by PLIP 3PE.26: 7 residues within 4Å: Chain J: K.87, A.88, G.91, T.95 Chain Y: F.49 Ligands: 3PE.27, 3PE.33 Ligand excluded by PLIP 3PE.27: 20 residues within 4Å: Chain J: S.21, K.23, A.88, A.92, T.95, G.96, M.99 Chain K: M.10, T.13, V.14, V.17, G.18, M.21, Y.22, R.23 Chain L: K.585, L.596 Ligands: 3PE.26, 3PE.30, 3PE.33 Ligand excluded by PLIP 3PE.30: 12 residues within 4Å: Chain J: V.115, V.116, F.117, F.119 Chain K: M.6, T.13 Chain L: M.599, I.600, H.605, E.606 Chain N: M.93 Ligands: 3PE.27 Ligand excluded by PLIP 3PE.31: 18 residues within 4Å: Chain 8: Y.84, Y.85, H.89, K.93 Chain L: N.65, W.66, H.67, W.68, L.76, S.77, L.78, F.138, I.142 Chain M: P.371, L.449 Ligands: CDL.29, PC1.43, CDL.73 Ligand excluded by PLIP 3PE.32: 11 residues within 4Å: Chain 9: W.71, R.75 Chain L: M.88, P.91, F.334, I.459, F.463, Y.466, I.467 Chain e: F.77, L.78 Ligand excluded by PLIP 3PE.33: 9 residues within 4Å: Chain L: K.585, L.589 Chain Y: V.41, P.46, S.48, F.49, G.52 Ligands: 3PE.26, 3PE.27 Ligand excluded by PLIP 3PE.34: 19 residues within 4Å: Chain L: L.568, A.569, K.572, A.573, L.576 Chain N: W.167 Chain Y: I.110, A.114, Y.117, L.120, T.121, L.124 Ligands: 3PE.35, 3PE.36, 3PE.42, 3PE.46, 3PE.58, 3PE.59, PC1.60 Ligand excluded by PLIP 3PE.35: 16 residues within 4Å: Chain D: K.56 Chain L: L.576, S.598, F.602 Chain N: L.160 Chain Y: A.2, A.31, A.32, V.36, Y.39, S.40, K.44, Y.59 Ligands: 3PE.34, 3PE.36, 3PE.58 Ligand excluded by PLIP 3PE.36: 10 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, W.167 Chain Y: K.3, L.6, F.136 Ligands: 3PE.34, 3PE.35, 3PE.59 Ligand excluded by PLIP 3PE.41: 14 residues within 4Å: Chain 5: H.10, H.13, V.14, P.17 Chain 6: V.82, W.85, V.89, F.93 Chain M: M.22, V.25, N.26, H.30, L.33 Ligands: PLC.70 Ligand excluded by PLIP 3PE.42: 14 residues within 4Å: Chain L: L.562 Chain M: P.159, Y.166, S.191, F.194, M.195, L.197, A.198 Chain N: I.276, I.277 Chain Y: W.133 Ligands: 3PE.34, 3PE.46, PC1.60 Ligand excluded by PLIP 3PE.46: 25 residues within 4Å: Chain D: M.52, Y.53 Chain L: P.563, I.566, S.567, Q.570, M.571 Chain M: N.144, F.151, Y.152, A.155, G.156, M.201, V.205 Chain N: L.163, W.167, I.284, T.285, L.287, L.288, Y.291, R.295 Ligands: 3PE.34, 3PE.42, PC1.60 Ligand excluded by PLIP 3PE.51: 11 residues within 4Å: Chain P: Y.216, N.219, W.222, F.223, P.227, F.305, W.313, T.314, R.355 Ligands: PC1.3, CDL.25 Ligand excluded by PLIP 3PE.52: 7 residues within 4Å: Chain P: K.233, F.274, Q.278, L.289, P.290, Y.291, P.292 Ligand excluded by PLIP 3PE.58: 17 residues within 4Å: Chain Y: Y.9, W.10, I.28, G.29, V.36, Y.59, T.62, A.63, I.66, G.67, F.70, M.118, A.122, V.125 Ligands: 3PE.34, 3PE.35, 3PE.59 Ligand excluded by PLIP 3PE.59: 14 residues within 4Å: Chain N: V.159, I.277, F.281 Chain Y: L.6, W.10, A.32, G.128, Q.129, W.133, V.135, F.136 Ligands: 3PE.34, 3PE.36, 3PE.58 Ligand excluded by PLIP 3PE.61: 12 residues within 4Å: Chain H: W.179 Chain I: L.62 Chain Z: R.27, R.28, G.29, M.35, V.38, G.39, A.42 Ligands: PC1.20, PC1.62 Chain h: W.14 Ligand excluded by PLIP 3PE.63: 13 residues within 4Å: Chain 1: L.32, L.35, S.36, Y.38, R.83, L.84 Chain H: W.303, L.310 Chain Z: L.44, Y.47, W.48, R.55 Ligands: PC1.24 Ligand excluded by PLIP 3PE.64: 13 residues within 4Å: Chain 1: E.16, L.19, S.22, F.23, A.26, V.30 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295 Ligands: 3PE.65 Ligand excluded by PLIP 3PE.65: 9 residues within 4Å: Chain 1: F.8, F.23, A.24, G.27 Chain A: V.100, A.103 Ligands: 3PE.2, PLC.6, 3PE.64 Ligand excluded by PLIP 3PE.69: 17 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, Y.74 Chain 4: R.9 Chain N: L.203, I.210, M.261, L.332, L.339, M.342, L.343, V.345, L.346 Ligands: CDL.66, PC1.67 Ligand excluded by PLIP 3PE.74: 15 residues within 4Å: Chain M: W.190, V.193, L.197, Y.210, G.211, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.44, 3PE.75 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.75: 13 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: Y.108, A.112 Ligands: 3PE.74 Chain c: P.82, N.83, T.84, S.87, L.88, G.90, A.91 Ligand excluded by PLIP 3PE.76: 11 residues within 4Å: Chain L: F.227, F.529, M.533, L.536, Y.539, M.540 Chain b: W.126, N.127, F.134 Chain c: S.9, R.10 Ligand excluded by PLIP 3PE.78: 7 residues within 4Å: Ligands: PC1.79 Chain g: R.21, L.24, R.25, F.28, F.74, W.75 Ligand excluded by PLIP

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

PC1.3: 11 residues within 4Å: Chain A: T.15, I.19, F.22, W.23, L.27 Chain H: R.62, I.72 Chain P: W.222 Ligands: PC1.5, CDL.18, 3PE.51 Ligand excluded by PLIP PC1.4: 9 residues within 4Å: Chain 4: L.14 Chain A: T.86, F.93 Chain J: S.148, Y.149, T.151, W.152, I.155 Ligands: 3PE.2 Ligand excluded by PLIP PC1.5: 14 residues within 4Å: Chain A: I.19, W.23, L.24, P.25, Q.26 Chain P: L.304, I.307, S.308, F.310, W.313 Ligands: PC1.3, PC1.8, PLC.10, PLC.53 Ligand excluded by PLIP PC1.8: 12 residues within 4Å: Chain A: Q.26 Chain B: L.73, I.74, L.210, W.213, R.216 Chain P: D.90, F.310, E.311 Ligands: PC1.5, PC1.9, PLC.10 Ligand excluded by PLIP PC1.9: 15 residues within 4Å: Chain B: K.69, L.70, D.72, L.73, W.76, R.79, K.205 Chain H: L.46 Ligands: PC1.8, PC1.79 Chain g: F.28, R.29, N.31, W.75, V.77 Ligand excluded by PLIP PC1.19: 22 residues within 4Å: Chain 0: A.39 Chain A: L.3, M.4, F.11 Chain H: M.98, N.99, L.100, F.104, M.108, L.111 Chain J: G.38, V.39, C.41, L.45, N.46, S.50 Chain Z: F.140, I.141, W.142, Y.143, T.144 Ligands: CDL.18 Ligand excluded by PLIP PC1.20: 16 residues within 4Å: Chain H: Q.169, E.170, Q.171, M.172, W.173, G.244, T.245, S.246, N.258, I.261, K.262, S.269, W.272 Chain I: L.70 Ligands: PC1.24, 3PE.61 Ligand excluded by PLIP PC1.24: 24 residues within 4Å: Chain 1: K.15, E.16, V.18, I.25 Chain D: R.266 Chain H: A.182, M.183, F.186, I.187, T.238, Y.277, F.280, L.288, N.292, F.293, L.296, W.303 Chain I: T.60, L.61, W.63, L.66 Chain Z: L.43 Ligands: PC1.20, 3PE.63 Ligand excluded by PLIP PC1.37: 16 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, H.534, A.537, P.538, N.541, L.542 Chain M: V.398, L.405 Chain b: Q.84, R.114, N.115, R.116 Ligand excluded by PLIP PC1.43: 17 residues within 4Å: Chain 6: V.98, S.103, A.107 Chain L: W.66 Chain M: P.64, I.67, L.68, W.71, I.317, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: 3PE.31, CDL.73 Ligand excluded by PLIP PC1.44: 6 residues within 4Å: Chain M: N.188, S.189, W.190 Chain Y: L.91, L.120 Ligands: 3PE.74 Ligand excluded by PLIP PC1.60: 17 residues within 4Å: Chain L: I.561, T.565, A.569, Q.570 Chain N: I.277, F.281 Chain Y: G.109, A.113, A.116, Y.117 Ligands: 3PE.34, 3PE.42, 3PE.46 Chain c: Y.77, P.78, F.80, P.82 Ligand excluded by PLIP PC1.62: 19 residues within 4Å: Chain H: M.183, W.272 Chain I: D.55, Q.59, L.62, T.64, E.65, I.67, R.68, G.71, L.74 Chain Z: R.28, G.29, L.30, S.31, G.32, M.35 Ligands: 3PE.61 Chain h: W.14 Ligand excluded by PLIP PC1.67: 17 residues within 4Å: Chain 3: T.3, T.10, F.11, Q.12, F.13, R.78 Chain 4: F.3, F.4, R.9 Chain N: M.21, L.136, Y.143, L.202, V.345, L.346 Ligands: CDL.45, 3PE.69 Ligand excluded by PLIP PC1.71: 12 residues within 4Å: Chain 7: P.81, V.82, I.86, I.89, I.93, W.110, P.116, I.117, R.119, W.120, R.123 Chain f: Y.61 Ligand excluded by PLIP PC1.79: 9 residues within 4Å: Chain H: F.19, P.42, L.45, L.46 Ligands: PC1.9, 3PE.78 Chain g: F.28, F.74, W.75 Ligand excluded by PLIP

8 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.6: 10 residues within 4Å: Chain 1: V.30, P.33, T.34, S.36, T.39 Chain A: N.85, L.88, T.89 Ligands: 3PE.2, 3PE.65 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.88 PLC.10: 7 residues within 4Å: Chain B: L.70, Y.214 Chain P: Q.137, P.309 Ligands: PC1.5, PC1.8, PLC.53 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:P.309, B:L.70 PLC.28: 9 residues within 4Å: Chain J: M.1, Y.4, F.7, I.8, V.11, M.15, F.101, V.104, L.108 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:F.7, J:V.11, J:V.11, J:F.101, J:F.101, J:V.104 PLC.38: 11 residues within 4Å: Chain L: L.293, T.294, F.418, I.421, R.425, L.500, I.504, A.519, F.520, S.523 Chain d: W.30 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:T.294, L:F.418, L:F.520 Hydrogen bonds: L:R.425 PLC.49: 12 residues within 4Å: Chain N: I.4, I.7, L.11, K.322 Chain O: L.24, Q.25, G.27, P.28, L.29, A.30 Ligands: CDL.45, CDL.66 8 PLIP interactions: 5 interactions with chain N, 3 interactions with chain O Hydrophobic interactions: N:I.4, N:I.7, N:L.11, O:L.29 Salt bridges: N:K.322, N:K.322 Hydrogen bonds: O:L.29, O:A.30 PLC.53: 8 residues within 4Å: Chain P: E.135, Q.137, R.303, E.306, I.307, P.309 Ligands: PC1.5, PLC.10 1 PLIP interactions: 1 interactions with chain P Salt bridges: P:R.303 PLC.68: 9 residues within 4Å: Chain 3: Y.39, L.54, L.55, L.62, I.65 Chain 5: W.11 Chain M: L.17, S.18 Ligands: CDL.57 4 PLIP interactions: 1 interactions with chain 5, 3 interactions with chain 3 Hydrophobic interactions: 5:W.11, 3:Y.39, 3:L.62, 3:I.65 PLC.70: 8 residues within 4Å: Chain 6: M.87, R.88, F.92, F.93 Chain 7: L.70, Y.74, L.77 Ligands: 3PE.41 5 PLIP interactions: 5 interactions with chain 6 Hydrophobic interactions: 6:F.92, 6:F.92, 6:F.93, 6:F.93 Salt bridges: 6:R.88

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

SF4.7: 13 residues within 4Å: Chain B: A.90, C.91, C.92, G.127, T.128, G.154, S.155, C.156, C.186, P.187 Chain D: R.118, R.138, H.223 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.91, B:C.92, B:C.156, B:C.186 SF4.13: 13 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.14: 11 residues within 4Å: Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, V.228, G.229 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.127 Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.15: 13 residues within 4Å: Chain G: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, C.226, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.21: 12 residues within 4Å: Chain I: H.101, C.123, P.124, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:C.123, I:C.152, I:C.155, I:C.158 SF4.22: 12 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, C.119, I.130, Y.145, C.162, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.113, I:C.116, I:C.119, I:C.162

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

FES.11: 10 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, C.176, L.177, G.178, A.179, C.180, M.185 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.135, E:C.140, E:C.176, E:C.180 FES.16: 9 residues within 4Å: Chain G: R.62, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.12: 19 residues within 4Å: Chain F: G.87, R.88, G.89, A.91, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:Y.204, F:Y.204, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:G.89, F:N.116, F:E.119, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.17: 5 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:I.223, G:C.226, G:V.228, G:L.231

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 21 residues within 4Å: Chain H: R.62, S.66, A.68, S.69, M.70, I.72, L.73, I.76 Chain J: I.12, M.15, V.35, I.82, W.83, L.84, F.93 Chain P: W.222, R.286, T.358 Ligands: PC1.3, PC1.19, CDL.25 17 PLIP interactions: 8 interactions with chain H, 7 interactions with chain J, 2 interactions with chain P Hydrophobic interactions: H:L.73, H:L.73, H:I.76, J:M.15, J:V.35, J:W.83, J:W.83, J:F.93, P:W.222 Hydrogen bonds: H:A.68, H:S.69, H:S.69, J:W.83, J:L.84 Salt bridges: H:R.62, H:R.62, P:R.286 CDL.25: 11 residues within 4Å: Chain J: L.84, K.87, L.90 Chain P: F.223, G.224, G.225, R.286, P.287, L.289 Ligands: CDL.18, 3PE.51 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain J Hydrophobic interactions: P:L.289 Hydrogen bonds: P:R.286 Salt bridges: J:K.87 CDL.29: 22 residues within 4Å: Chain 6: V.100, T.104 Chain 7: L.68, R.72, I.75 Chain L: S.23, L.78, K.116, K.119, Y.120, L.123, T.127, I.130, M.150 Chain M: T.357, L.360, L.364, L.442, L.445, L.446 Ligands: 3PE.31, CDL.73 16 PLIP interactions: 2 interactions with chain 7, 9 interactions with chain L, 4 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: 7:I.75, L:L.78, L:L.123, L:L.123, L:T.127, L:I.130, M:L.360, M:L.364, M:L.445, M:L.446, 6:V.100 Salt bridges: 7:R.72, L:K.119, L:K.119, L:K.119, L:K.119 CDL.40: 31 residues within 4Å: Chain 3: F.36, C.40, L.43, V.53, L.54 Chain M: I.9, M.12, W.16, T.90, R.91, L.94, T.97, M.98, L.104, F.105, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, L.245, A.246, L.249, P.256, L.257, T.301, M.335 Chain O: K.326, Y.327 Ligands: CDL.57 25 PLIP interactions: 6 interactions with chain N, 2 interactions with chain 3, 13 interactions with chain M, 4 interactions with chain O Hydrophobic interactions: N:V.242, N:L.245, N:L.249, N:P.256, N:L.257, N:M.335, 3:L.43, 3:V.53, M:I.9, M:W.16, M:W.16, M:R.91, M:L.94, M:L.94, M:L.104, M:F.105, M:V.127, M:I.131, M:I.131 Hydrogen bonds: M:N.88, M:T.90, O:K.326, O:K.326, O:Y.327 Salt bridges: O:K.326 CDL.45: 22 residues within 4Å: Chain N: P.3, F.6, I.7, I.13, M.14, K.46, S.125, L.128, I.129, T.132, W.133, I.209, I.210, T.217, M.323, T.324, F.325, M.329 Chain O: P.28, H.280 Ligands: PLC.49, PC1.67 15 PLIP interactions: 14 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.7, N:I.13, N:L.128, N:L.128, N:I.129, N:I.129, N:W.133, N:W.133, N:I.210, N:F.325, N:F.325 Hydrogen bonds: N:S.125, N:T.324 Salt bridges: N:K.46, O:H.280 CDL.57: 27 residues within 4Å: Chain 3: K.25, L.26, T.27, P.29, R.30, A.32, F.33, G.35, F.36, Y.39 Chain 5: F.22, L.26, N.30, K.33 Chain M: L.2, I.5, L.55, F.56, F.105 Chain N: P.256, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.40, PLC.68 24 PLIP interactions: 3 interactions with chain N, 4 interactions with chain 5, 4 interactions with chain M, 11 interactions with chain 3, 2 interactions with chain X Hydrophobic interactions: N:P.256, N:P.338, N:P.338, 5:F.22, 5:L.26, M:I.5, M:L.55, M:F.56, M:F.105, 3:R.30, 3:A.32, 3:F.33, 3:F.33, 3:F.36, 3:F.36, 3:F.36, 3:Y.39, 3:Y.39, 3:Y.39 Hydrogen bonds: 5:K.33, X:T.171, X:T.171 Salt bridges: 5:K.33, 3:K.25 CDL.66: 20 residues within 4Å: Chain 2: K.43, T.47, T.50 Chain 3: V.34, D.45, R.49, R.60, L.63, Y.64, S.67, F.68, L.75 Chain N: M.323, T.324, F.325, T.328, L.332, M.342 Ligands: PLC.49, 3PE.69 12 PLIP interactions: 2 interactions with chain N, 8 interactions with chain 3, 2 interactions with chain 2 Hydrophobic interactions: N:L.332, 3:V.34, 3:Y.64, 3:Y.64, 3:F.68, 3:L.75 Hydrogen bonds: N:F.325, 3:R.49, 3:R.60 Salt bridges: 3:R.60, 2:K.43, 2:K.43 CDL.73: 19 residues within 4Å: Chain 6: A.107, Y.108 Chain 7: I.86, T.87, N.90, V.91, E.95, H.115 Chain 8: W.80, Y.84, H.89 Chain L: L.12 Ligands: CDL.29, 3PE.31, PC1.43 Chain f: P.44, L.47, V.48, R.49 15 PLIP interactions: 3 interactions with chain 7, 4 interactions with chain f, 5 interactions with chain 8, 2 interactions with chain 6, 1 interactions with chain L Hydrogen bonds: 7:N.90, 7:N.90, 8:Y.84, 6:Y.108 Salt bridges: 7:H.115, f:R.49, 8:H.89 Hydrophobic interactions: f:P.44, f:L.47, f:V.48, 8:W.80, 8:Y.84, 8:Y.84, 6:A.107, L:L.12 CDL.80: 18 residues within 4Å: Chain 0: M.1, W.2, F.3, L.6, P.7, A.10 Chain H: Y.43 Chain g: L.3, V.6, L.7, R.9, G.10, Q.13 Chain h: S.3, A.4, T.5, F.7, I.8 11 PLIP interactions: 7 interactions with chain 0, 2 interactions with chain g, 2 interactions with chain h Hydrophobic interactions: 0:W.2, 0:F.3, 0:F.3, 0:L.6, 0:L.6, 0:P.7, 0:A.10, h:F.7 Hydrogen bonds: g:R.9, h:T.5 Salt bridges: g:R.9

2 x ZN: ZINC ION(Non-covalent)

ZN.39: 4 residues within 4Å: Chain 6: D.63 Chain M: H.82, E.335, H.338 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:H.82, M:H.338 ZN.54: 5 residues within 4Å: Chain R: C.87, G.89, H.96, C.112, C.115 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.87, R:H.96, R:C.112, R:C.115

1 x MG: MAGNESIUM ION(Non-covalent)

MG.47: 2 residues within 4Å: Chain O: S.59 Ligands: DGT.48 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.59

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.48: 21 residues within 4Å: Chain O: I.54, C.55, S.56, G.57, K.58, S.59, E.76, L.102, F.105, Y.106, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214, Y.221 Ligands: MG.47 17 PLIP interactions: 17 interactions with chain O Hydrophobic interactions: O:I.54 Hydrogen bonds: O:C.55, O:S.56, O:G.57, O:K.58, O:S.59, O:S.59, O:Q.120, O:Q.120, O:R.127, O:E.214, O:Y.221 Salt bridges: O:K.58, O:R.149, O:K.209 pi-Stacking: O:F.157, O:F.157

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

NDP.50: 28 residues within 4Å: Chain B: R.216 Chain P: G.60, A.61, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, V.130, G.131, R.132, F.139, V.144, F.145, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, A.204, E.205, I.206, R.212 21 PLIP interactions: 20 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:P.203 Hydrogen bonds: P:G.60, P:T.62, P:T.62, P:T.62, P:F.64, P:L.65, P:R.85, P:V.130, P:G.131, P:R.132, P:R.132, P:Y.180, P:K.184, P:E.205, P:I.206 Salt bridges: P:R.85, P:R.132, P:R.212, B:R.216 pi-Cation interactions: P:R.85

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)

EHZ.55: 13 residues within 4Å: Chain T: S.112, L.113 Chain W: V.32, W.39, T.46, K.62, V.63, M.66, F.67, N.70, A.71, I.73, V.79 11 PLIP interactions: 9 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:V.32, W:W.39, W:T.46, W:K.62, W:F.67, W:F.67, W:I.73, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 EHZ.56: 19 residues within 4Å: Chain L: Y.513, H.514 Chain U: D.111, S.112 Chain d: H.12, Q.13, W.30, L.44, R.47, F.48, H.51, K.52, E.54, M.57, A.60, L.63, A.67, E.70, G.74 8 PLIP interactions: 7 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:L.44, d:F.48, d:A.60, d:A.67 Hydrogen bonds: d:H.12, d:R.47, U:S.112

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.72: 10 residues within 4Å: Chain 8: K.63, R.66, H.67, F.70 Chain L: Y.27, K.28, N.31, L.34, Y.35, T.38 10 PLIP interactions: 5 interactions with chain 8, 5 interactions with chain L Hydrophobic interactions: 8:F.70, 8:F.70, L:Y.27, L:L.34, L:Y.35, L:Y.35 Salt bridges: 8:K.63, 8:R.66, 8:H.67 Hydrogen bonds: L:K.28

1 x MYR: MYRISTIC ACID(Covalent)

MYR.77: 7 residues within 4Å: Chain L: Y.485, L.486 Chain b: Y.153, Q.154 Chain e: G.2, A.3, L.5 4 PLIP interactions: 2 interactions with chain e, 1 interactions with chain b, 1 interactions with chain L Hydrophobic interactions: e:A.3, e:L.5, L:Y.485 Hydrogen bonds: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grba, D.N. et al., Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science (2024)

Release Date

2024-06-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

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

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

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

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

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

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

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

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

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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