SMTL ID : 8q0m.1

Outward-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

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

3PE.1: 14 residues within 4Å: Chain 1: E.16, L.19, F.23, A.26, V.30 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295 Ligands: 3PE.3, PC1.24, 3PE.67 Ligand excluded by PLIP 3PE.2: 8 residues within 4Å: Chain A: M.1, L.5, L.8, T.9, T.12 Chain H: M.3, L.7 Ligands: PC1.19 Ligand excluded by PLIP 3PE.3: 7 residues within 4Å: Chain 1: F.23 Chain A: V.100, A.103, T.107 Ligands: 3PE.1, PLC.6, 3PE.46 Ligand excluded by PLIP 3PE.26: 8 residues within 4Å: Chain J: N.86, K.87, A.88, G.91, T.95 Ligands: 3PE.30, 3PE.56, 3PE.62 Ligand excluded by PLIP 3PE.27: 12 residues within 4Å: Chain J: E.114, V.115, V.116 Chain K: M.9, F.12, T.13 Chain L: M.599, I.600, H.605 Chain N: M.93, L.97 Ligands: 3PE.30 Ligand excluded by PLIP 3PE.30: 18 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, R.23 Chain L: K.585 Ligands: 3PE.26, 3PE.27, 3PE.56, 3PE.62 Ligand excluded by PLIP 3PE.31: 13 residues within 4Å: Chain L: I.177, M.211, L.218, N.541 Chain M: I.391, I.393, I.394, V.398, I.402 Ligands: PC1.33 Chain c: W.101, V.104, R.111 Ligand excluded by PLIP 3PE.40: 23 residues within 4Å: Chain D: M.52, Y.53 Chain L: L.562, P.563, S.567, Q.570, M.571 Chain M: N.144, L.147, F.151, Y.152, G.156, V.205 Chain N: L.163, W.167, I.284, L.287, L.288, Y.291, R.295 Ligands: 3PE.41, 3PE.57, PC1.83 Ligand excluded by PLIP 3PE.41: 15 residues within 4Å: Chain M: P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: I.276, I.277 Chain Y: L.120, L.124, W.133 Ligands: 3PE.40, 3PE.57 Ligand excluded by PLIP 3PE.42: 12 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, L.160, W.167 Chain Y: K.3, L.6, V.135, F.136 Ligands: 3PE.57, 3PE.59, 3PE.60 Ligand excluded by PLIP 3PE.46: 17 residues within 4Å: Chain A: L.97, V.100, A.103, Y.104, T.107, Q.108 Chain J: I.155, W.159, L.162 Chain N: N.2, I.4, I.5, I.8 Chain O: K.36, R.277 Ligands: 3PE.3, PC1.28 Ligand excluded by PLIP 3PE.49: 10 residues within 4Å: Chain A: W.23, V.29 Chain P: Y.216, N.219, I.220, W.222, F.223, P.227, W.313, R.355 Ligand excluded by PLIP 3PE.56: 11 residues within 4Å: Chain L: L.589 Chain Y: V.41, P.46, T.47, F.49, G.52, V.53, T.56 Ligands: 3PE.26, 3PE.30, 3PE.62 Ligand excluded by PLIP 3PE.57: 16 residues within 4Å: Chain L: K.572, A.573, L.576 Chain N: W.167 Chain Y: I.110, A.114, Y.117, T.121, L.124 Ligands: 3PE.40, 3PE.41, 3PE.42, 3PE.58, 3PE.59, 3PE.60, PC1.83 Ligand excluded by PLIP 3PE.58: 13 residues within 4Å: Chain Y: Y.9, W.10, R.58, Y.59, T.62, A.63, I.66, G.67, F.70, T.105 Ligands: 3PE.57, 3PE.59, 3PE.60 Ligand excluded by PLIP 3PE.59: 17 residues within 4Å: Chain L: L.576, T.594, S.598, L.601, F.602 Chain N: L.160 Chain Y: A.31, V.35, V.36, Y.39, S.40, K.44, Y.59 Ligands: 3PE.42, 3PE.57, 3PE.58, 3PE.60 Ligand excluded by PLIP 3PE.60: 15 residues within 4Å: Chain N: V.159, I.277, F.281 Chain Y: W.10, A.32, L.124, V.125, G.128, Q.129, V.135, F.136 Ligands: 3PE.42, 3PE.57, 3PE.58, 3PE.59 Ligand excluded by PLIP 3PE.61: 8 residues within 4Å: Chain Y: V.53, A.54, G.57, R.58, F.61, A.64, R.104 Ligands: 3PE.62 Ligand excluded by PLIP 3PE.62: 17 residues within 4Å: Chain K: M.21 Chain L: 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.26, 3PE.30, 3PE.56, 3PE.61 Ligand excluded by PLIP 3PE.64: 13 residues within 4Å: Chain H: I.175, L.176, W.179 Chain I: I.67 Chain Z: R.28, G.29, L.30, M.35, V.38, G.39 Ligands: PC1.20, PC1.25 Chain h: W.14 Ligand excluded by PLIP 3PE.65: 17 residues within 4Å: Chain 1: I.25, 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: PC1.24 Ligand excluded by PLIP 3PE.67: 12 residues within 4Å: Chain 1: A.6, L.9, K.10, W.13, V.20, A.21 Chain I: D.49, M.50 Chain Z: Y.33, F.36 Ligands: 3PE.1, PC1.24 Ligand excluded by PLIP 3PE.70: 14 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, Y.74, L.75 Chain 4: R.9 Chain N: I.210, M.261, L.332, L.339, V.345 Ligands: CDL.68, PC1.71 Ligand excluded by PLIP 3PE.72: 13 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, H.30 Ligands: 3PE.73, PLC.74 Ligand excluded by PLIP 3PE.73: 10 residues within 4Å: Chain 5: V.6, V.7, H.10, W.11, H.13, V.14, P.17, M.18 Chain M: M.10 Ligands: 3PE.72 Ligand excluded by PLIP 3PE.78: 16 residues within 4Å: Chain 8: I.81, Y.85, H.89, K.93 Chain L: W.66, H.67, W.68, L.76, S.77, L.78, F.138, I.142 Chain M: P.371 Ligands: PC1.32, CDL.35, CDL.76 Ligand excluded by PLIP 3PE.79: 9 residues within 4Å: Chain L: F.227, F.529, L.536, M.540 Chain b: W.126, C.130, F.134 Chain c: S.9, R.10 Ligand excluded by PLIP 3PE.80: 7 residues within 4Å: Chain Y: L.91 Ligands: PC1.37, 3PE.81 Chain c: I.95, V.99, Y.102, Y.103 Ligand excluded by PLIP 3PE.81: 15 residues within 4Å: Chain M: W.190, V.193, G.211, L.212, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.37, 3PE.80, 3PE.82 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.82: 14 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: Y.108, A.112 Ligands: PLC.63, 3PE.81 Chain c: P.82, N.83, S.87, L.88, G.90, A.91, G.94 Ligand excluded by PLIP 3PE.85: 11 residues within 4Å: Chain H: P.42, L.45 Ligands: PC1.86, CDL.88 Chain g: R.21, L.24, R.25, F.28, T.66, F.74, W.75 Ligand excluded by PLIP 3PE.87: 8 residues within 4Å: Ligands: CDL.88 Chain g: M.1, E.2, L.3 Chain h: R.6, F.7, Q.9, W.10 Ligand excluded by PLIP

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

PC1.4: 12 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: PC1.5, CDL.21, PLC.50 Ligand excluded by PLIP PC1.5: 14 residues within 4Å: Chain A: I.20, W.23, L.24, P.25, Q.26 Chain P: L.304, F.305, S.308, F.310, W.313 Ligands: PC1.4, PC1.9, PLC.50, PLC.51 Ligand excluded by PLIP PC1.9: 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: PC1.5, PC1.10, PLC.50 Ligand excluded by PLIP PC1.10: 17 residues within 4Å: Chain B: D.72, L.73, W.76, R.79, K.205 Chain H: V.39, L.46, I.49 Ligands: U10.8, PC1.9, PLC.50, PC1.86 Chain g: F.28, R.29, N.31, W.75, V.77 Ligand excluded by PLIP PC1.18: 24 residues within 4Å: Chain 0: A.39, H.40 Chain A: M.1, L.3, M.4, L.7, 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, N.46, S.50 Chain Z: F.140, I.141, Y.143, T.144 Ligands: CDL.21 Ligand excluded by PLIP PC1.19: 7 residues within 4Å: Chain 0: F.29 Chain H: M.1, M.3, I.4, L.7, M.8 Ligands: 3PE.2 Ligand excluded by PLIP PC1.20: 17 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, W.272 Chain I: L.70 Ligands: PC1.24, 3PE.64 Ligand excluded by PLIP PC1.24: 28 residues within 4Å: Chain 1: K.15, E.16, V.18, A.24, I.25, L.28 Chain D: R.266 Chain H: W.179, M.183, F.186, I.187, I.273, Y.277, L.288, N.292, F.293, L.296 Chain I: T.60, L.61, W.63, L.66, I.67 Chain Z: I.40 Ligands: 3PE.1, PC1.20, PC1.25, 3PE.65, 3PE.67 Ligand excluded by PLIP PC1.25: 16 residues within 4Å: Chain H: M.183, W.272 Chain I: D.55, Q.59, L.62, T.64, E.65, R.68, G.71, L.74 Chain Z: R.28, L.30, M.35 Ligands: PC1.24, 3PE.64 Chain h: A.15 Ligand excluded by PLIP PC1.28: 12 residues within 4Å: Chain 4: V.12, L.14 Chain A: N.83, T.86, F.93 Chain J: S.148, Y.149, T.151, W.152, I.155 Ligands: PLC.6, 3PE.46 Ligand excluded by PLIP PC1.32: 17 residues within 4Å: Chain 6: V.98, L.99, V.106, A.107, Y.108 Chain L: W.66 Chain M: I.67, L.68, W.71, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: CDL.76, 3PE.78 Ligand excluded by PLIP PC1.33: 18 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, G.228, F.529, M.533, H.534, A.537, P.538 Chain M: V.398, L.405 Ligands: 3PE.31 Chain b: Q.84, N.115, R.116, D.118 Ligand excluded by PLIP PC1.37: 10 residues within 4Å: Chain M: N.188, S.189, W.190 Chain Y: D.86, L.88, A.123, M.127 Ligands: 3PE.80, 3PE.81, PC1.83 Ligand excluded by PLIP PC1.71: 16 residues within 4Å: Chain 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, L.202, I.206, V.345, L.346 Ligands: CDL.43, 3PE.70 Ligand excluded by PLIP PC1.75: 12 residues within 4Å: Chain 7: P.81, V.82, G.85, I.89, I.93, W.110, P.116, R.119, W.120, R.123 Ligands: PLC.74 Chain f: Y.61 Ligand excluded by PLIP PC1.83: 15 residues within 4Å: Chain L: T.565, I.566, L.568, A.569 Chain Y: G.109, A.113, A.116, Y.117 Ligands: PC1.37, 3PE.40, 3PE.57 Chain c: Y.77, P.78, F.80, P.82 Ligand excluded by PLIP PC1.86: 10 residues within 4Å: Chain H: F.19, P.42, L.45, L.46, I.49 Ligands: PC1.10, 3PE.85 Chain g: F.28, F.74, W.75 Ligand excluded by PLIP

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

PLC.6: 11 residues within 4Å: Chain 1: V.30, P.33, T.34, S.36 Chain A: N.85, L.88, T.89, L.92, F.93 Ligands: 3PE.3, PC1.28 6 PLIP interactions: 2 interactions with chain 1, 4 interactions with chain A Hydrophobic interactions: 1:V.30, 1:T.34, A:L.88, A:L.92, A:F.93, A:F.93 PLC.29: 8 residues within 4Å: Chain J: M.1, Y.4, V.11, M.15, L.97, F.101, V.104, L.108 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:V.11, J:L.97, J:F.101, J:F.101, J:L.108 PLC.34: 13 residues within 4Å: Chain L: M.290, L.293, T.294, S.417, F.418, I.421, R.425, I.504, A.519, F.520, F.522, S.523 Chain d: W.30 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:T.294, L:F.418, L:A.519, L:F.522 Hydrogen bonds: L:R.425 PLC.38: 6 residues within 4Å: Chain 3: L.54, L.55 Chain 5: W.11 Chain M: W.16, L.17, S.18 1 PLIP interactions: 1 interactions with chain 5 Hydrophobic interactions: 5:W.11 PLC.47: 8 residues within 4Å: Chain N: I.7, L.11, K.322 Chain O: G.27, P.28, L.29 Ligands: CDL.43, CDL.68 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:I.7, N:L.11, O:L.29 Salt bridges: N:K.322 Hydrogen bonds: O:L.29 PLC.50: 12 residues within 4Å: Chain B: V.66, W.213, Y.214, R.216 Chain P: Q.137, P.309, F.310 Ligands: PC1.4, PC1.5, PC1.9, PC1.10, PLC.51 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:P.309, P:F.310, B:V.66 Hydrogen bonds: P:Q.137 PLC.51: 7 residues within 4Å: Chain P: E.135, R.303, E.306, I.307, P.309 Ligands: PC1.5, PLC.50 1 PLIP interactions: 1 interactions with chain P Salt bridges: P:R.303 PLC.63: 13 residues within 4Å: Chain Y: I.69, A.96, L.99, I.100, G.102, A.103, R.106, S.107, Y.108, A.112, C.115, A.116 Ligands: 3PE.82 10 PLIP interactions: 10 interactions with chain Y Hydrophobic interactions: Y:I.69, Y:A.96, Y:L.99, Y:L.99, Y:L.99, Y:I.100, Y:Y.108, Y:A.116 Hydrogen bonds: Y:A.103, Y:S.107 PLC.66: 6 residues within 4Å: Chain Z: L.30, S.31, S.34, A.37, V.38, F.45 3 PLIP interactions: 3 interactions with chain Z Hydrophobic interactions: Z:V.38, Z:F.45 Hydrogen bonds: Z:S.34 PLC.74: 12 residues within 4Å: Chain 6: W.85, M.87, R.88, F.92, F.93, L.101 Chain 7: L.70, F.73, Y.74, T.78 Ligands: 3PE.72, PC1.75 5 PLIP interactions: 4 interactions with chain 6, 1 interactions with chain 7 Hydrophobic interactions: 6:F.92, 6:F.93, 6:L.101, 7:T.78 Salt bridges: 6:R.88

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

SF4.7: 14 residues within 4Å: Chain B: A.90, C.91, C.92, G.127, T.128, G.154, S.155, C.156, G.185, 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, G.134, C.137, L.139, 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 SF4.15: 11 residues within 4Å: Chain G: M.173, C.176, I.177, C.179, T.180, R.181, C.182, 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 SF4.22: 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 SF4.23: 14 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, P.163, 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)

U10.8: 34 residues within 4Å: Chain B: W.83, T.86, F.87, G.88, A.93, M.96, M.97, A.100, D.107, V.112, F.113, R.114 Chain D: H.92, Y.141, M.185, T.189, L.192, M.197, F.200, F.201 Chain H: L.14, A.18, E.24, R.25, L.28, R.34, D.51, A.52, L.55, F.220, F.224, M.225, R.274 Ligands: PC1.10 24 PLIP interactions: 6 interactions with chain D, 11 interactions with chain H, 7 interactions with chain B Hydrophobic interactions: D:Y.141, D:L.192, D:L.192, D:M.197, D:F.200, D:F.200, H:L.14, H:A.18, H:E.24, H:L.28, H:D.51, H:L.55, H:F.220, H:F.224, H:F.224, H:F.224, H:F.224, B:W.83, B:T.86, B:A.93, B:A.100, B:D.107, B:V.112, B:F.113

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

FES.11: 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.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: 20 residues within 4Å: Chain F: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, D.127, Y.204, I.205, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.204, F:Y.204, F:I.205, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:G.89, F:N.116, F:E.119, F:G.120, F:D.127, 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 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:I.223, G:V.228, G:L.231

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 20 residues within 4Å: Chain H: R.62, S.66, S.67, A.68, S.69, L.73, I.76 Chain J: M.15, G.19, Y.28, I.82, W.83, L.84, F.93 Chain P: W.222, R.286, T.358 Ligands: PC1.4, PC1.18, CDL.52 11 PLIP interactions: 5 interactions with chain H, 2 interactions with chain P, 4 interactions with chain J Hydrophobic interactions: H:I.76, P:W.222, J:W.83, J:W.83, J:W.83, J:F.93 Hydrogen bonds: H:A.68, H:S.69, H:S.69 Salt bridges: H:R.62, P:R.286 CDL.35: 21 residues within 4Å: Chain 6: L.99, T.104 Chain 7: L.68, R.72 Chain L: F.24, L.78, K.116, K.119, Y.120, L.123, I.130, G.146, I.149, M.150, L.153 Chain M: T.357, L.360, L.442, L.445 Ligands: CDL.76, 3PE.78 12 PLIP interactions: 7 interactions with chain L, 3 interactions with chain M, 2 interactions with chain 7 Hydrophobic interactions: L:L.78, L:L.123, L:I.149, L:L.153, M:L.360, M:L.442, M:L.445, 7:R.72 Salt bridges: L:K.116, L:K.119, L:K.119, 7:R.72 CDL.39: 30 residues within 4Å: Chain 3: F.36, C.40, L.43, I.44, A.47, V.53 Chain M: M.12, P.13, W.16, T.90, R.91, L.94, T.97, M.98, L.104, 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.69 24 PLIP interactions: 8 interactions with chain N, 11 interactions with chain M, 5 interactions with chain 3 Hydrophobic interactions: N:L.243, N:A.246, N:P.256, N:T.301, N:T.334, N:M.335, N:P.338, M:P.13, M:W.16, M:W.16, M:R.91, M:L.94, M:L.94, M:L.104, M:V.127, M:I.131, 3:F.36, 3:L.43, 3:I.44, 3:I.44, 3:V.53 Hydrogen bonds: N:I.239, M:T.90 Salt bridges: M:R.91 CDL.43: 29 residues within 4Å: Chain N: P.3, F.6, L.10, I.13, M.14, I.18, K.46, S.125, L.128, I.129, T.132, W.133, I.206, I.209, I.210, S.213, T.217, M.220, K.322, M.323, T.324, F.325, M.329, L.332 Chain O: P.28, H.280 Ligands: PLC.47, CDL.68, PC1.71 18 PLIP interactions: 18 interactions with chain N Hydrophobic interactions: N:I.13, N:I.18, N:L.128, N:W.133, N:W.133, N:W.133, N:I.206, N:I.209, N:I.210, N:K.322, N:F.325, 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 CDL.52: 8 residues within 4Å: Chain J: L.84, K.87, L.90, V.94 Chain P: R.286, P.287, L.289 Ligands: CDL.21 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain J Salt bridges: P:R.286, J:K.87 Hydrophobic interactions: J:L.84, J:V.94 CDL.68: 22 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, V.71, L.75 Chain N: M.323, T.324, F.325, T.328, L.332, M.342 Ligands: CDL.43, PLC.47, 3PE.70 14 PLIP interactions: 11 interactions with chain 3, 2 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:Y.64, 3:Y.64, 3:F.68, 3:F.68, 3:V.71, 3:V.71, 3:L.75, N:L.332 Hydrogen bonds: 3:R.49, 3:R.60, N:F.325 Salt bridges: 3:R.60, 2:K.43 CDL.69: 21 residues within 4Å: Chain 3: T.27, P.29, R.30, F.33, F.36 Chain 5: K.29, N.30, K.33 Chain M: L.2, I.5, I.6, L.55, F.56, F.105, M.108 Chain N: P.256 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.39 18 PLIP interactions: 2 interactions with chain 5, 1 interactions with chain N, 6 interactions with chain M, 7 interactions with chain 3, 2 interactions with chain X Salt bridges: 5:K.29, 5:K.33 Hydrophobic interactions: N:P.256, M:L.2, M:I.5, M:I.6, M:I.6, M:F.56, M:F.105, 3:P.29, 3:R.30, 3:F.33, 3:F.36, 3:F.36, 3:F.36, 3:F.36, X:F.169 Hydrogen bonds: X:T.171 CDL.76: 20 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: F.80 Chain M: L.446 Ligands: PC1.32, CDL.35, 3PE.78 Chain f: V.48, R.49, I.52 17 PLIP interactions: 7 interactions with chain 8, 3 interactions with chain 6, 3 interactions with chain 7, 1 interactions with chain L, 2 interactions with chain f, 1 interactions with chain M Hydrophobic interactions: 8:W.80, 8:Y.84, 8:Y.85, 8:Y.85, 8:Y.85, 6:A.107, 6:Y.108, L:F.80, f:V.48, M:L.446 Hydrogen bonds: 8:Y.84, 6:Y.108, 7:N.90, 7:E.95 Salt bridges: 8:H.89, 7:H.115, f:R.49 CDL.88: 19 residues within 4Å: Chain 0: W.2, F.3, L.6, P.7, A.10 Chain H: Y.43 Ligands: 3PE.85, 3PE.87 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 10 PLIP interactions: 4 interactions with chain 0, 4 interactions with chain g, 2 interactions with chain h Hydrophobic interactions: 0:F.3, 0:L.6, 0:L.6, 0:A.10, g:L.3, g:V.6, g:L.7, h:F.7 Salt bridges: g:R.9 Hydrogen bonds: h:T.5

2 x ZN: ZINC ION(Non-covalent)

ZN.36: 3 residues within 4Å: 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.53: 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.44: 20 residues within 4Å: Chain O: I.54, C.55, S.56, G.57, K.58, S.59, E.76, L.102, Y.106, L.119, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214 Ligands: MG.45 16 PLIP interactions: 16 interactions with chain O Hydrogen bonds: O:C.55, O:S.56, O:G.57, O:K.58, O:S.59, O:E.76, O:Q.120, O:Q.120, O:R.127, O:R.149, O:E.214 Salt bridges: 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.45: 2 residues within 4Å: Chain O: S.59 Ligands: DGT.44 No protein-ligand interaction detected (PLIP)

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

NDP.48: 26 residues within 4Å: Chain B: R.216 Chain P: G.60, 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 18 PLIP interactions: 17 interactions with chain P, 1 interactions with chain B Hydrogen bonds: P:G.60, P:T.62, P:T.62, P:F.64, P:L.65, P:R.85, P:R.85, P:L.129, P:G.131, P:K.184, P:E.205, P:I.206 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.54: 15 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 13 PLIP interactions: 2 interactions with chain T, 11 interactions with chain W Hydrophobic interactions: T:L.113, W:K.29, W:R.33, W:W.39, W:W.39, W:V.63, W:M.66, W:F.67, W:F.67 Hydrogen bonds: T:S.112, W:N.70, W:L.82 Salt bridges: W:K.29 EHZ.55: 18 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, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67 14 PLIP interactions: 13 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:H.26, d:L.27, d:L.44, d:F.48, d:A.60, d:A.67 Hydrogen bonds: d:Q.13, 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.77: 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 16 PLIP interactions: 7 interactions with chain 8, 9 interactions with chain L Hydrophobic interactions: 8:R.66, 8:F.70, 8:F.70, L:T.26, L:K.28, L:L.34, L:Y.35, L:Y.35, L:T.38 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.84: 6 residues within 4Å: Chain L: N.400, Y.485, L.486 Chain b: Y.153, Q.154 Chain e: G.2 4 PLIP interactions: 1 interactions with chain b, 3 interactions with chain L Hydrogen bonds: b:Q.154 Hydrophobic interactions: L:Y.485, L:L.486, L:L.486

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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