SMTL ID : 8q48.1

Outward-facing, closed proteoliposome complex I at 2.5 A. Initially purified in LMNG.

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

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

PC1.1: 13 residues within 4Å: Chain A: T.15, V.18, I.19, F.22, W.23, L.27 Chain H: R.62, I.72 Chain P: W.222 Ligands: PC1.3, PLC.9, CDL.19, 3PE.50 Ligand excluded by PLIP PC1.2: 11 residues within 4Å: Chain 4: V.12, L.14 Chain A: N.83, T.86, M.90 Chain J: S.148, Y.149, T.151, W.152 Ligands: 3PE.5, PLC.6 Ligand excluded by PLIP PC1.3: 16 residues within 4Å: Chain A: I.19, I.20, W.23, L.24, P.25, Q.26 Chain P: L.304, F.305, I.307, S.308, F.310, W.313 Ligands: PC1.1, PC1.8, PLC.9, PLC.52 Ligand excluded by PLIP PC1.8: 14 residues within 4Å: Chain A: L.24, Q.26 Chain B: I.74, R.209, L.210, W.213, R.216 Chain H: F.56 Chain P: D.90, F.310, E.311 Ligands: PC1.3, PLC.9, U10.11 Ligand excluded by PLIP PC1.10: 15 residues within 4Å: Chain B: D.72, L.73, W.76, R.79, K.205 Chain H: L.46, I.49 Ligands: PLC.9, U10.11, PC1.88 Chain g: F.28, R.29, N.31, W.75, V.77 Ligand excluded by PLIP PC1.20: 23 residues within 4Å: Chain 0: A.39 Chain A: M.1, L.3, M.4, F.11 Chain H: M.98, N.99, L.100, F.104, M.108, L.111 Chain J: I.34, G.38, V.39, L.45, S.50, L.54, F.57 Chain Z: F.140, I.141, Y.143, T.144 Ligands: CDL.19 Ligand excluded by PLIP PC1.21: 9 residues within 4Å: Chain 0: F.29, R.59 Chain H: M.1, M.3, I.4, L.7, M.8, I.11 Ligands: 3PE.4 Ligand excluded by PLIP PC1.22: 18 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, L.265, L.266, S.269, W.272 Chain I: L.70 Ligands: PC1.25, 3PE.69 Ligand excluded by PLIP PC1.25: 26 residues within 4Å: Chain 1: K.15, E.16, V.18 Chain D: R.266, I.267 Chain H: W.179, M.183, F.186, I.187, T.238, L.266, Y.277, L.288, N.292, F.293, L.296 Chain I: T.60, L.61, W.63, L.66 Chain Z: I.40 Ligands: PC1.22, 3PE.26, PC1.66, 3PE.67, 3PE.71 Ligand excluded by PLIP PC1.34: 18 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, G.228, S.235, F.529, M.533, H.534, A.537, P.538, L.542 Chain M: V.398, L.405 Ligands: 3PE.38 Chain b: N.115, R.116 Ligand excluded by PLIP PC1.40: 13 residues within 4Å: Chain M: N.188, S.189, W.190 Chain Y: D.86, P.87, L.88, L.91, L.120, A.123, M.127 Ligands: 3PE.37, PC1.85, 3PE.86 Ligand excluded by PLIP PC1.66: 18 residues within 4Å: Chain H: M.183, W.272 Chain I: D.55, L.62, T.64, E.65, I.67, R.68, G.71, L.74 Chain Z: R.28, G.29, L.30, G.32, M.35 Ligands: PC1.25, 3PE.69 Chain h: W.14 Ligand excluded by PLIP PC1.74: 19 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, I.206, V.345, L.346, E.347 Ligands: CDL.44, 3PE.73 Ligand excluded by PLIP PC1.80: 18 residues within 4Å: Chain 6: V.98, L.99, V.106, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, L.68, W.71, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: 3PE.32, CDL.81 Ligand excluded by PLIP PC1.82: 14 residues within 4Å: Chain 6: L.101 Chain 7: P.81, V.82, G.85, I.89, I.93, W.110, P.116, I.117, R.119, W.120, R.123 Ligands: PLC.79 Chain f: Y.61 Ligand excluded by PLIP PC1.85: 20 residues within 4Å: Chain L: A.560, L.562, T.565, L.568, A.569 Chain N: F.281 Chain Y: G.109, I.110, A.112, A.113, A.116, Y.117 Ligands: 3PE.37, 3PE.39, PC1.40, 3PE.43, 3PE.59 Chain c: Y.77, F.80, P.82 Ligand excluded by PLIP PC1.88: 10 residues within 4Å: Chain H: F.19, P.42, L.45, L.46, I.49 Ligands: PC1.10, 3PE.89 Chain g: F.28, F.74, W.75 Ligand excluded by PLIP

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

3PE.4: 9 residues within 4Å: Chain A: M.1, L.5, T.9, T.12, L.13 Chain H: M.3, L.7, I.11 Ligands: PC1.21 Ligand excluded by PLIP 3PE.5: 15 residues within 4Å: Chain A: L.97, V.100, Y.104, T.107, Q.108 Chain J: W.159, L.162 Chain N: N.2, I.4, I.5 Chain O: Y.31, K.36, R.277 Ligands: PC1.2, 3PE.72 Ligand excluded by PLIP 3PE.26: 11 residues within 4Å: Chain 1: L.9, K.10, W.13, V.20 Chain I: D.49, M.50 Chain Z: Y.33, F.36, I.40 Ligands: PC1.25, 3PE.71 Ligand excluded by PLIP 3PE.27: 8 residues within 4Å: Chain J: K.87, A.88, G.91, T.95 Chain Y: F.49 Ligands: 3PE.30, 3PE.58, 3PE.65 Ligand excluded by PLIP 3PE.28: 14 residues within 4Å: Chain J: E.114, V.115, V.116, F.117 Chain K: M.9, M.10, F.12, T.13, L.16 Chain L: M.599, I.600, H.605 Chain N: M.93 Ligands: 3PE.30 Ligand excluded by PLIP 3PE.30: 20 residues within 4Å: Chain J: S.21, K.23, A.88, A.92, G.96, M.99, M.103 Chain K: T.13, V.14, V.17, G.18, M.21, Y.22, R.23 Chain L: K.585, L.596 Ligands: 3PE.27, 3PE.28, 3PE.58, 3PE.65 Ligand excluded by PLIP 3PE.32: 16 residues within 4Å: Chain 8: I.81, 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 Ligands: CDL.31, PC1.80, CDL.81 Ligand excluded by PLIP 3PE.36: 11 residues within 4Å: Chain 5: F.20, V.21, Y.24 Chain 6: F.105 Chain 7: F.125 Chain M: F.36, T.37, L.40 Ligands: 3PE.77, 3PE.78, PLC.79 Ligand excluded by PLIP 3PE.37: 16 residues within 4Å: Chain M: N.188, W.190, V.193, G.211, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.40, 3PE.57, PC1.85, 3PE.86 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.38: 14 residues within 4Å: Chain L: I.177, I.180, M.211, L.218, N.541 Chain M: W.267, N.390, I.391, I.393, I.394 Ligands: PC1.34 Chain c: W.101, V.104, D.108 Ligand excluded by PLIP 3PE.39: 17 residues within 4Å: Chain M: P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: N.274, I.276, I.277, T.280 Chain Y: L.124, W.133 Ligands: 3PE.43, 3PE.59, PC1.85 Ligand excluded by PLIP 3PE.43: 23 residues within 4Å: Chain D: Q.46, M.52, Y.53 Chain L: L.562, P.563, S.567, Q.570, M.571 Chain M: N.144, Y.148, F.151, A.155, G.156, V.205 Chain N: L.163, W.167, I.284, L.288, Y.291, R.295 Ligands: 3PE.39, 3PE.59, PC1.85 Ligand excluded by PLIP 3PE.45: 15 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, L.160, I.164, W.167 Chain Y: K.3, L.6, V.135, F.136, E.138 Ligands: 3PE.59, 3PE.60, 3PE.61, 3PE.62 Ligand excluded by PLIP 3PE.50: 11 residues within 4Å: Chain A: W.23 Chain P: Y.216, N.219, I.220, W.222, F.223, P.227, I.301, W.313, R.355 Ligands: PC1.1 Ligand excluded by PLIP 3PE.53: 8 residues within 4Å: Chain P: K.233, F.274, Q.278, F.288, L.289, P.290, Y.291, P.292 Ligand excluded by PLIP 3PE.57: 14 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: Y.108, A.112 Ligands: 3PE.37, PLC.64 Chain c: P.82, N.83, T.84, S.87, G.90, A.91, G.94 Ligand excluded by PLIP 3PE.58: 12 residues within 4Å: Chain L: L.589 Chain Y: V.41, P.46, T.47, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.27, 3PE.30, 3PE.65 Ligand excluded by PLIP 3PE.59: 18 residues within 4Å: Chain L: A.569, K.572, A.573, L.576 Chain N: W.167, F.281 Chain Y: I.110, A.114, Y.117, T.121, L.124 Ligands: 3PE.39, 3PE.43, 3PE.45, 3PE.60, 3PE.61, 3PE.62, PC1.85 Ligand excluded by PLIP 3PE.60: 19 residues within 4Å: Chain Y: Y.9, W.10, I.28, G.29, R.58, Y.59, T.62, A.63, I.66, G.67, F.70, T.105, M.118, A.122, V.125 Ligands: 3PE.45, 3PE.59, 3PE.61, 3PE.62 Ligand excluded by PLIP 3PE.61: 18 residues within 4Å: Chain D: E.57 Chain L: L.576, T.594, S.598, L.601, F.602 Chain N: L.160 Chain Y: A.32, V.35, V.36, Y.39, S.40, K.44, Y.59 Ligands: 3PE.45, 3PE.59, 3PE.60, 3PE.62 Ligand excluded by PLIP 3PE.62: 17 residues within 4Å: Chain N: V.159, I.277, F.281 Chain Y: L.6, W.10, I.28, L.124, V.125, G.128, Q.129, W.133, V.135, F.136 Ligands: 3PE.45, 3PE.59, 3PE.60, 3PE.61 Ligand excluded by PLIP 3PE.63: 9 residues within 4Å: Chain Y: V.53, A.54, G.57, R.58, F.61, A.64, R.104, R.106 Ligands: 3PE.65 Ligand excluded by PLIP 3PE.65: 18 residues within 4Å: Chain K: M.21 Chain L: L.592, I.593, L.596, I.600, L.601 Chain Y: A.2, T.4, V.5, S.27, G.30, A.31, L.34, A.38 Ligands: 3PE.27, 3PE.30, 3PE.58, 3PE.63 Ligand excluded by PLIP 3PE.67: 18 residues within 4Å: Chain 1: I.25, L.28, L.32, L.35, S.36, Y.38 Chain H: L.300, W.303, L.307, L.310, T.311 Chain Z: L.43, L.44, Y.47, W.48, K.52, R.55 Ligands: PC1.25 Ligand excluded by PLIP 3PE.69: 15 residues within 4Å: Chain H: I.175, L.176, W.179 Chain I: L.62, I.67 Chain Z: R.27, R.28, G.29, L.30, M.35, V.38, G.39 Ligands: PC1.22, PC1.66 Chain h: W.14 Ligand excluded by PLIP 3PE.70: 8 residues within 4Å: Chain 0: G.13, F.17, M.21 Chain H: M.251, E.253, L.254, I.257, L.264 Ligand excluded by PLIP 3PE.71: 16 residues within 4Å: Chain 1: E.16, L.19, S.22, F.23, A.24, A.26, V.30 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295 Ligands: PC1.25, 3PE.26, 3PE.72 Ligand excluded by PLIP 3PE.72: 9 residues within 4Å: Chain 1: F.8, F.23, A.24 Chain A: V.100, A.103, T.107 Ligands: 3PE.5, PLC.6, 3PE.71 Ligand excluded by PLIP 3PE.73: 18 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, Y.74, L.75 Chain 4: R.9 Chain N: L.203, I.210, M.261, L.332, L.339, L.343, V.345, L.346 Ligands: CDL.44, PC1.74, CDL.75 Ligand excluded by PLIP 3PE.77: 10 residues within 4Å: Chain 5: H.10, H.13, V.14, L.15, P.17, M.18, V.21 Chain M: M.10 Ligands: 3PE.36, 3PE.78 Ligand excluded by PLIP 3PE.78: 16 residues within 4Å: Chain 5: H.10, H.13, P.17 Chain 6: A.81, V.82, W.85, V.89 Chain M: K.19, M.22, V.25, A.29, H.30, L.33 Ligands: 3PE.36, 3PE.77, PLC.79 Ligand excluded by PLIP 3PE.84: 9 residues within 4Å: Chain L: F.227, F.529, L.536, M.540 Chain b: W.126, C.130, L.141 Chain c: S.9, R.10 Ligand excluded by PLIP 3PE.86: 7 residues within 4Å: Chain Y: L.91 Ligands: 3PE.37, PC1.40 Chain c: I.95, V.99, Y.102, Y.103 Ligand excluded by PLIP 3PE.89: 9 residues within 4Å: Chain H: P.42 Ligands: PC1.88 Chain g: R.21, L.24, R.25, F.28, T.66, F.74, W.75 Ligand excluded by PLIP 3PE.91: 6 residues within 4Å: Ligands: CDL.90 Chain g: M.1, E.2 Chain h: R.6, F.7, W.10 Ligand excluded by PLIP

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

PLC.6: 12 residues within 4Å: Chain 1: V.30, P.33, T.34, L.35, S.36 Chain A: N.85, L.88, T.89, L.92, F.93 Ligands: PC1.2, 3PE.72 5 PLIP interactions: 1 interactions with chain 1, 4 interactions with chain A Hydrophobic interactions: 1:V.30, A:L.92, A:L.92, A:F.93, A:F.93 PLC.9: 13 residues within 4Å: Chain B: G.63, L.70, W.213, Y.214, R.216 Chain P: Q.137, P.309, F.310 Ligands: PC1.1, PC1.3, PC1.8, PC1.10, PLC.52 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:F.310, B:L.70 PLC.29: 8 residues within 4Å: Chain J: M.1, Y.4, V.11, M.15, L.97, F.101, V.104, L.108 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.11, J:L.97, J:F.101, J:F.101, J:F.101, J:L.108 PLC.33: 12 residues within 4Å: Chain L: M.290, L.293, S.417, F.418, I.421, R.425, L.500, I.504, A.519, F.520, F.522 Chain d: W.30 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:F.418, L:I.421, L:L.500, L:A.519, L:F.522 Salt bridges: L:R.425 PLC.42: 7 residues within 4Å: Chain 3: L.54, L.55 Chain 5: W.11 Chain M: W.16, L.17, S.18, K.19 2 PLIP interactions: 1 interactions with chain 5, 1 interactions with chain M Hydrophobic interactions: 5:W.11, M:L.17 PLC.48: 9 residues within 4Å: Chain N: I.7, L.11, K.322 Chain O: Q.25, G.27, P.28, L.29, I.32 Ligands: CDL.44 5 PLIP interactions: 2 interactions with chain O, 3 interactions with chain N Hydrophobic interactions: O:I.32, N:I.7, N:L.11 Hydrogen bonds: O:L.29 Salt bridges: N:K.322 PLC.52: 9 residues within 4Å: Chain P: E.135, T.136, Q.137, R.303, E.306, I.307, P.309 Ligands: PC1.3, PLC.9 1 PLIP interactions: 1 interactions with chain P Salt bridges: P:R.303 PLC.64: 14 residues within 4Å: Chain Y: I.69, L.72, A.96, L.99, I.100, G.102, A.103, R.106, S.107, Y.108, G.111, A.112, C.115 Ligands: 3PE.57 8 PLIP interactions: 8 interactions with chain Y Hydrophobic interactions: Y:I.69, Y:L.72, Y:A.96, Y:L.99, Y:L.99, Y:I.100, Y:Y.108 Hydrogen bonds: Y:S.107 PLC.68: 7 residues within 4Å: Chain H: L.176 Chain Z: L.30, S.31, S.34, A.37, V.38, F.45 3 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain H Hydrophobic interactions: Z:F.45, H:L.176 Hydrogen bonds: Z:S.34 PLC.79: 13 residues within 4Å: Chain 6: M.87, R.88, F.92, F.93, L.101 Chain 7: L.70, F.73, Y.74, L.77, T.78 Ligands: 3PE.36, 3PE.78, PC1.82 7 PLIP interactions: 5 interactions with chain 6, 2 interactions with chain 7 Hydrophobic interactions: 6:F.92, 6:F.93, 6:F.93, 6:L.101, 7:L.77, 7:T.78 Salt bridges: 6:R.88

6 x SF4: IRON/SULFUR CLUSTER(Non-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 SF4.14: 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 SF4.15: 11 residues within 4Å: Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.16: 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 SF4.23: 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 SF4.24: 13 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, L.118, 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

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

U10.11: 39 residues within 4Å: Chain B: W.83, T.86, F.87, G.88, L.89, A.90, A.93, M.96, M.97, A.100, D.107, F.113, R.114 Chain D: H.92, G.93, Y.141, M.185, T.189, L.192, M.197, F.200, F.201, V.457 Chain H: L.14, A.18, E.24, R.25, L.28, R.34, D.51, A.52, L.55, A.221, F.224, M.225, Y.228, R.274 Ligands: PC1.8, PC1.10 25 PLIP interactions: 6 interactions with chain B, 11 interactions with chain H, 8 interactions with chain D Hydrophobic interactions: B:W.83, B:W.83, B:T.86, B:A.93, B:A.100, B:F.113, H:A.18, H:E.24, H:L.28, H:D.51, H:A.52, H:L.55, H:A.221, H:F.224, H:F.224, H:F.224, H:F.224, D:L.192, D:L.192, D:F.200, D:F.200, D:F.200, D:F.201, D:F.201 Water bridges: D:H.92

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

FES.12: 9 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, C.176, L.177, G.178, A.179, C.180 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.135, E:C.140, E:C.176, E:C.180 FES.17: 10 residues within 4Å: Chain G: R.62, F.63, 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.13: 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 18 PLIP interactions: 18 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:N.116, F:E.119, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244 Water bridges: F:D.127, F:D.127 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.18: 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.19: 24 residues within 4Å: Chain A: F.11 Chain H: R.62, S.66, S.67, A.68, S.69, L.73, I.76 Chain J: I.12, M.15, G.16, Y.28, L.31, V.35, I.82, W.83, L.84, F.93 Chain P: W.222, R.286, T.358 Ligands: PC1.1, PC1.20, CDL.51 18 PLIP interactions: 8 interactions with chain J, 1 interactions with chain A, 6 interactions with chain H, 3 interactions with chain P Hydrophobic interactions: J:I.12, J:M.15, J:L.31, J:V.35, J:W.83, J:W.83, J:F.93, A:F.11, H:I.76, P:W.222 Hydrogen bonds: J:W.83, H:A.68, H:S.69, H:S.69 Water bridges: H:M.70, P:Y.359 Salt bridges: H:R.62, P:R.286 CDL.31: 26 residues within 4Å: Chain 7: L.68, L.71, R.72, I.75 Chain L: I.19, M.22, F.24, L.78, K.116, K.119, Y.120, L.123, T.127, I.130, I.149, M.150, L.153 Chain M: P.353, T.357, L.360, L.361, P.371, L.442, L.445 Ligands: 3PE.32, CDL.81 18 PLIP interactions: 4 interactions with chain M, 4 interactions with chain 7, 10 interactions with chain L Hydrophobic interactions: M:L.360, M:L.361, M:L.442, M:L.445, 7:L.71, 7:R.72, 7:I.75, L:L.78, L:L.123, L:T.127, L:I.149, L:L.153 Salt bridges: 7:R.72, L:K.116, L:K.119, L:K.119, L:K.119, L:K.119 CDL.41: 31 residues within 4Å: Chain 3: C.40, L.43, I.44, V.53 Chain M: I.9, M.12, P.13, W.16, T.90, R.91, L.94, T.97, M.98, S.101, L.104, F.105, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, L.243, A.246, P.256, L.257, T.301, T.334, M.335, P.338 Ligands: CDL.76 21 PLIP interactions: 12 interactions with chain M, 3 interactions with chain 3, 6 interactions with chain N Hydrophobic interactions: M:I.9, M:M.12, M:P.13, M:W.16, M:W.16, M:R.91, M:L.94, M:T.97, M:L.104, M:F.105, M:V.127, M:R.135, 3:L.43, 3:I.44, 3:V.53, N:L.243, N:A.246, N:P.256, N:L.257, N:T.301, N:P.338 CDL.44: 29 residues within 4Å: Chain N: P.3, F.6, L.10, L.11, I.13, M.14, I.18, K.46, S.125, L.128, I.129, T.132, W.133, I.209, I.210, T.217, M.220, K.322, M.323, T.324, F.325, M.329, L.332 Chain O: P.28, H.280 Ligands: PLC.48, 3PE.73, PC1.74, CDL.75 21 PLIP interactions: 20 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:L.10, N:L.11, N:I.13, N:I.18, N:L.128, N:I.129, N:W.133, N:W.133, N:W.133, N:I.209, N:I.210, N:I.210, N:K.322, N:F.325, N:F.325, N:L.332 Hydrogen bonds: N:S.125, N:M.323, N:T.324 Salt bridges: N:K.46, O:H.280 CDL.51: 7 residues within 4Å: Chain J: L.84, K.87, L.90, V.94 Chain P: R.286, L.289 Ligands: CDL.19 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain P Hydrophobic interactions: J:L.84, J:K.87, J:L.90, J:V.94, P:L.289 Salt bridges: J:K.87, P:R.286 CDL.75: 24 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, F.70, V.71, L.75 Chain N: M.323, T.324, F.325, T.328, L.332, M.336, L.339, M.342 Ligands: CDL.44, 3PE.73 15 PLIP interactions: 11 interactions with chain 3, 3 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:L.63, 3:Y.64, 3:Y.64, 3:F.68, 3:F.68, 3:F.70, 3:V.71, 3:V.71, 3:L.75, N:L.332, N:L.339 Salt bridges: 3:R.60, 2:K.43 Hydrogen bonds: N:F.325 CDL.76: 23 residues within 4Å: Chain 3: T.27, P.29, R.30, A.32, F.33, F.36 Chain 5: K.29, K.33 Chain M: L.2, I.5, I.6, I.9, L.55, L.104, F.105, M.108 Chain N: P.256, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.41 18 PLIP interactions: 5 interactions with chain 3, 3 interactions with chain N, 2 interactions with chain 5, 7 interactions with chain M, 1 interactions with chain X Hydrophobic interactions: 3:T.27, 3:A.32, 3:F.33, 3:F.36, 3:F.36, N:P.256, N:P.338, N:P.338, M:L.2, M:I.5, M:I.6, M:I.6, M:I.9, M:L.104, M:F.105 Salt bridges: 5:K.29, 5:K.33 Hydrogen bonds: X:T.171 CDL.81: 21 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, Y.85, H.89 Chain L: L.12, F.80 Chain M: L.446 Ligands: CDL.31, 3PE.32, PC1.80 Chain f: V.48, R.49, I.52 20 PLIP interactions: 2 interactions with chain 6, 3 interactions with chain 7, 2 interactions with chain L, 8 interactions with chain 8, 4 interactions with chain f, 1 interactions with chain M Hydrophobic interactions: 6:A.107, L:L.12, L:F.80, 8:W.80, 8:W.80, 8:W.80, 8:W.80, 8:Y.84, 8:Y.85, f:V.48, f:V.48, f:I.52, M:L.446 Hydrogen bonds: 6:Y.108, 7:N.90, 7:E.95, 8:Y.84 Salt bridges: 7:H.115, 8:H.89, f:R.49 CDL.90: 19 residues within 4Å: Chain 0: W.2, F.3, L.6, P.7, A.10 Chain H: Y.43 Ligands: 3PE.91 Chain g: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 Chain h: S.3, A.4, T.5, F.7, I.8 15 PLIP interactions: 7 interactions with chain 0, 5 interactions with chain g, 2 interactions with chain h, 1 interactions with chain I Hydrophobic interactions: 0:W.2, 0:F.3, 0:F.3, 0:L.6, 0:L.6, 0:P.7, 0:A.10, g:L.3, h:F.7 Hydrogen bonds: g:R.9, h:T.5 Water bridges: g:Q.13, g:Q.13, I:F.78 Salt bridges: g:R.9

2 x ZN: ZINC ION(Non-covalent)

ZN.35: 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 DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.46: 22 residues within 4Å: Chain O: N.53, I.54, C.55, S.56, G.57, K.58, S.59, E.76, L.102, F.105, Y.106, L.119, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214 Ligands: MG.47 17 PLIP interactions: 17 interactions with chain O Hydrogen bonds: O:C.55, O:S.56, O:G.57, O:K.58, O:S.59, O:Q.120, O:Q.120, O:Q.120, O:R.127, O:R.149, O:E.214 Salt bridges: O:K.58, O:K.58, O:R.149, O:K.209 pi-Stacking: O:F.157, O:F.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.47: 2 residues within 4Å: Chain O: S.59 Ligands: DGT.46 No protein-ligand interaction detected (PLIP)

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

NDP.49: 27 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, F.145, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, A.204, E.205, I.206, R.212 22 PLIP interactions: 21 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:I.206 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:K.184, P:E.205, P:I.206 Water bridges: P:R.132, P:R.212, P:R.212 Salt bridges: P:R.85, P:R.132, 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: 17 residues within 4Å: Chain T: S.112, L.113 Chain W: M.25, K.29, V.32, R.33, W.39, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, V.103, F.106 15 PLIP interactions: 13 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:R.33, W:W.39, W:W.39, W:M.66, W:F.67, W:F.67, W:V.103, W:F.106, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:L.82, T:S.112 Salt bridges: W:K.29 EHZ.56: 20 residues within 4Å: Chain L: Y.513 Chain U: D.111, S.112 Chain d: H.12, Q.13, V.16, A.23, H.26, L.27, W.30, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67, G.74 13 PLIP interactions: 12 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:V.16, d:H.26, d:L.27, d:L.44, d:F.48, d:A.60 Hydrogen bonds: d:R.47, d:H.51, d:K.52, d:K.52, U:S.112 Salt bridges: d:K.52

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.83: 11 residues within 4Å: Chain 8: K.63, R.66, H.67, F.70, H.74 Chain L: T.26, K.28, N.31, L.34, Y.35, T.38 12 PLIP interactions: 5 interactions with chain 8, 7 interactions with chain L Hydrophobic interactions: 8:R.66, L:T.26, L:N.31, L:Y.35, L:Y.35 Hydrogen bonds: 8:R.66, L:K.28, L:K.28, L:N.31 Salt bridges: 8:K.63, 8:R.66, 8:H.67

1 x MYR: MYRISTIC ACID(Covalent)

MYR.87: 5 residues within 4Å: Chain L: Y.485, L.486 Chain b: Y.153, Q.154 Chain e: G.2 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain b Hydrophobic interactions: L:Y.485, L:L.486 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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