SMTL ID : 8q0f.1

Inward-facing, open2 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

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

3PE.1: 11 residues within 4Å: Chain 1: E.16, L.19, F.23, A.26, G.27 Chain A: A.99, A.103, W.106 Chain H: K.291, P.295 Ligands: 3PE.19 Ligand excluded by PLIP 3PE.7: 29 residues within 4Å: Chain D: W.43, Q.46, Y.47, M.52, Y.53 Chain L: P.563, I.566, S.567, Q.570, M.571 Chain M: N.144, L.147, F.151, Y.152, A.155, G.156, M.201, V.205, L.212 Chain N: L.163, W.167, I.284, T.285, L.287, L.288, Y.291 Ligands: 3PE.25, 3PE.32, PC1.64 Ligand excluded by PLIP 3PE.19: 7 residues within 4Å: Chain 1: A.6, L.9, K.10, W.13 Chain I: D.49, M.50 Ligands: 3PE.1 Ligand excluded by PLIP 3PE.22: 9 residues within 4Å: Chain J: S.21, K.23, A.92 Chain K: T.13, V.17, M.21, Y.22, R.23 Ligands: 3PE.45 Ligand excluded by PLIP 3PE.24: 16 residues within 4Å: Chain 8: I.81, Y.84, Y.85, H.89 Chain L: W.66, H.67, W.68, S.77, L.78, N.136, F.138, Q.139, I.142 Ligands: CDL.23, PC1.33, CDL.61 Ligand excluded by PLIP 3PE.25: 14 residues within 4Å: Chain L: K.572, L.576 Chain N: L.163, W.167, F.281 Chain Y: Y.117, T.121, L.124 Ligands: 3PE.7, 3PE.26, 3PE.32, 3PE.46, 3PE.47, PC1.64 Ligand excluded by PLIP 3PE.26: 13 residues within 4Å: Chain L: L.576, F.602 Chain N: N.152, T.156, L.160, W.167 Chain Y: A.2, K.3, L.6, F.136 Ligands: 3PE.25, 3PE.47, 3PE.48 Ligand excluded by PLIP 3PE.31: 14 residues within 4Å: Chain L: I.561 Chain M: N.188, W.190, L.197, M.201, F.256, P.260, F.261, L.264 Ligands: PC1.34, PC1.64 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.32: 17 residues within 4Å: Chain M: P.159, V.162, A.163, Y.166, S.191, F.194, M.195, A.198, M.201 Chain N: N.274, I.276, I.277, T.280 Chain Y: W.133 Ligands: 3PE.7, 3PE.25, PC1.64 Ligand excluded by PLIP 3PE.37: 12 residues within 4Å: Chain A: V.100, Y.104, T.107, Q.108 Chain J: I.155, W.159 Chain N: N.2, I.4, I.5 Chain O: Y.31, R.277 Ligands: PC1.2 Ligand excluded by PLIP 3PE.45: 10 residues within 4Å: Chain L: K.585, L.589 Chain Y: V.41, T.45, P.46, F.49, G.52, V.53, T.56 Ligands: 3PE.22 Ligand excluded by PLIP 3PE.46: 17 residues within 4Å: Chain Y: Y.9, W.10, I.28, G.29, A.32, Y.59, A.63, I.66, G.67, F.70, L.101, T.105, A.122, V.125 Ligands: 3PE.25, 3PE.47, 3PE.48 Ligand excluded by PLIP 3PE.47: 18 residues within 4Å: Chain L: L.576, T.594, S.598, L.601, F.602 Chain N: L.160 Chain Y: A.2, A.32, V.35, V.36, Y.39, S.40, L.43, K.44, Y.59 Ligands: 3PE.25, 3PE.26, 3PE.46 Ligand excluded by PLIP 3PE.48: 13 residues within 4Å: Chain N: I.277, F.281 Chain Y: L.6, R.7, W.10, L.124, V.125, G.128, Q.129, W.133, V.135 Ligands: 3PE.26, 3PE.46 Ligand excluded by PLIP 3PE.49: 6 residues within 4Å: Chain Y: S.27, V.53, G.57, R.58, T.60, F.61 Ligand excluded by PLIP 3PE.51: 12 residues within 4Å: Chain H: L.176, W.179 Chain I: L.62 Chain Z: R.27, R.28, G.29, L.30, M.35, G.39 Ligands: PC1.16, PC1.21 Chain h: W.14 Ligand excluded by PLIP 3PE.53: 13 residues within 4Å: Chain 1: L.32, L.35, S.36, Y.38 Chain H: W.303, L.307 Chain Z: L.44, Y.47, W.48, M.51, K.52, R.55 Ligands: PC1.20 Ligand excluded by PLIP 3PE.55: 15 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, L.75 Chain 4: R.9 Chain N: I.210, M.261, M.336, L.339, L.343, V.345, L.346 Ligands: CDL.54, PC1.56 Ligand excluded by PLIP 3PE.57: 14 residues within 4Å: Chain 5: H.13, P.17 Chain 6: D.79, V.82, W.85, V.89, F.93 Chain M: K.19, N.21, M.22, V.25, H.30, L.33 Ligands: PLC.58 Ligand excluded by PLIP 3PE.62: 15 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: Y.108, A.112 Ligands: PLC.50 Chain c: P.82, N.83, T.84, S.87, G.90, A.91, G.94, I.95, L.98 Ligand excluded by PLIP 3PE.63: 10 residues within 4Å: Chain L: F.227, F.529, L.536, M.540 Chain b: W.126, N.127, F.134 Chain c: S.9, R.10, L.11 Ligand excluded by PLIP

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

PC1.2: 12 residues within 4Å: Chain 4: V.12 Chain A: N.83, T.86, T.89, M.90, F.93 Chain J: S.148, Y.149, T.151, W.152, I.155 Ligands: 3PE.37 7 PLIP interactions: 3 interactions with chain A, 2 interactions with chain 4, 2 interactions with chain J Hydrophobic interactions: A:T.89, A:F.93, A:F.93, 4:V.12, J:T.151, J:W.152 Salt bridges: 4:E.24 PC1.3: 13 residues within 4Å: Chain A: L.27, N.28, V.29 Chain B: L.70, R.78, R.209, L.210, W.213, R.216 Chain H: I.53 Chain P: D.90, F.310 Ligands: PC1.67 12 PLIP interactions: 5 interactions with chain B, 2 interactions with chain P, 4 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: B:L.70, B:L.210, B:W.213, P:F.310, A:L.27, A:L.27, A:L.27, H:I.53 Salt bridges: B:R.78, B:R.216, P:D.90 Hydrogen bonds: A:N.28 PC1.15: 22 residues within 4Å: Chain 0: A.39, H.40 Chain A: L.3, M.4, L.7, F.11 Chain H: M.98, N.99, L.100, F.104 Chain J: I.34, G.38, G.42, L.45, N.46, S.50, L.54, F.57 Chain Z: F.140, I.141, W.142, T.144 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain Z, 2 interactions with chain H Hydrophobic interactions: J:I.34, J:F.57, Z:I.141 Hydrogen bonds: J:S.50, H:N.99, H:L.100 PC1.16: 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, S.269 Chain I: L.70 Ligands: PC1.20, 3PE.51 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:W.173, H:I.261, H:K.262, H:L.265, I:L.70 Hydrogen bonds: H:G.244, H:S.246, H:N.258 Salt bridges: H:K.262, H:K.262, H:K.262 PC1.20: 29 residues within 4Å: Chain 1: K.15, E.16, I.25 Chain D: R.266 Chain H: W.179, P.180, A.182, M.183, F.186, I.187, T.238, I.273, 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: I.40, L.43, L.44 Ligands: PC1.16, PC1.21, 3PE.53 21 PLIP interactions: 11 interactions with chain H, 3 interactions with chain Z, 2 interactions with chain 1, 3 interactions with chain I, 2 interactions with chain D Hydrophobic interactions: H:W.179, H:P.180, H:F.186, H:F.186, H:I.187, H:T.238, H:I.273, H:Y.277, H:F.280, H:F.293, H:L.296, Z:I.40, Z:L.43, Z:L.44, 1:I.25, I:W.63, I:W.63, I:W.63 Salt bridges: 1:E.16, D:R.266, D:R.266 PC1.21: 15 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, L.30, M.35 Ligands: PC1.20, 3PE.51 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain Z Hydrophobic interactions: I:I.67, I:I.67, I:L.74 Hydrogen bonds: I:T.64, Z:R.28 Salt bridges: I:D.55, I:R.68, Z:R.28 PC1.27: 16 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, G.228, L.229, H.534, A.537, P.538, N.541, L.542 Chain M: L.405 Chain b: N.115, R.116 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:L.173, L:L.173, L:Y.174, L:I.177, L:L.229, L:A.537, L:P.538, L:L.542, L:L.542, M:L.405 Salt bridges: L:D.163, L:H.534, L:H.534 PC1.33: 20 residues within 4Å: Chain 6: V.98, S.103, V.106, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, L.68, W.71, L.321, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: CDL.23, 3PE.24, CDL.61 10 PLIP interactions: 8 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: M:L.68, M:W.71, M:W.71, M:L.321, M:L.446, M:L.447, M:I.454, 6:V.98, 6:V.106 Hydrogen bonds: M:N.450 PC1.34: 8 residues within 4Å: Chain M: N.188, W.190 Chain Y: L.88, L.91, L.120, M.127 Ligands: 3PE.31, PC1.64 4 PLIP interactions: 2 interactions with chain Y, 2 interactions with chain M Hydrophobic interactions: Y:L.91, Y:L.120, M:W.190 pi-Cation interactions: M:W.190 PC1.56: 19 residues within 4Å: Chain 3: T.3, R.8, T.10, F.11, Q.12, F.13, R.78 Chain 4: F.3, F.4 Chain N: W.133, L.136, Y.143, L.202, I.206, V.345, L.346, E.347 Ligands: CDL.36, 3PE.55 13 PLIP interactions: 4 interactions with chain 4, 4 interactions with chain N, 5 interactions with chain 3 Hydrophobic interactions: 4:F.4, 4:F.4, 4:F.4, N:W.133, N:L.136, N:I.206, N:L.346, 3:F.11 pi-Cation interactions: 4:F.3 Hydrogen bonds: 3:R.8, 3:F.11, 3:Q.12 Salt bridges: 3:R.78 PC1.59: 8 residues within 4Å: Chain 7: I.89, I.93, W.110, I.117, R.119, W.120, R.123 Chain f: Y.61 9 PLIP interactions: 9 interactions with chain 7 Hydrophobic interactions: 7:I.89, 7:I.93, 7:I.117, 7:W.120, 7:W.120, 7:W.120 Salt bridges: 7:R.119, 7:R.123, 7:R.123 PC1.64: 20 residues within 4Å: Chain L: I.561, T.565, L.568, A.569 Chain M: A.155 Chain N: I.284 Chain Y: G.109, I.110, A.113, A.116, Y.117 Ligands: 3PE.7, 3PE.25, 3PE.31, 3PE.32, PC1.34 Chain c: Y.77, P.78, F.80, P.82 7 PLIP interactions: 4 interactions with chain Y, 1 interactions with chain L, 2 interactions with chain N Hydrophobic interactions: Y:A.113, Y:A.116, Y:Y.117, Y:Y.117, L:A.569, N:I.284, N:I.284 PC1.67: 15 residues within 4Å: Chain B: L.73, W.76, R.79, K.205 Chain H: F.19, V.39, P.42, L.45, L.46 Ligands: PC1.3, PLC.6, PC1.68 Chain g: F.28, R.29, W.75 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain g, 2 interactions with chain H Hydrophobic interactions: B:W.76, g:F.28, g:F.28, H:F.19, H:L.46 Salt bridges: B:R.79, B:K.205 PC1.68: 7 residues within 4Å: Chain H: P.42 Ligands: PC1.67 Chain g: R.21, L.24, R.25, L.27, F.74 5 PLIP interactions: 4 interactions with chain g, 1 interactions with chain H Hydrophobic interactions: g:L.27, H:P.42 Salt bridges: g:R.21, g:R.25 pi-Cation interactions: g:F.74

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

PLC.4: 11 residues within 4Å: Chain 1: V.30, T.34, L.35, S.36, T.39 Chain A: N.85, L.88, T.89, L.92, F.93, I.96 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain 1 Hydrophobic interactions: A:L.88, A:F.93, A:I.96, 1:V.30 PLC.6: 8 residues within 4Å: Chain B: K.69, L.70, D.72, L.73, K.205, R.211 Ligands: PC1.67 Chain g: W.75 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain g Hydrophobic interactions: B:L.70, B:L.73 Salt bridges: B:D.72, B:K.205 Hydrogen bonds: g:W.75 PLC.28: 11 residues within 4Å: Chain L: M.290, L.293, T.294, F.418, R.425, I.504, T.508, A.519, F.520, S.523 Chain d: W.30 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.293, L:F.418 Hydrogen bonds: L:S.523 Salt bridges: L:R.425 PLC.35: 9 residues within 4Å: Chain 3: L.54, L.58, L.62 Chain 5: W.11 Chain M: W.16, L.17, S.18, N.20 Ligands: CDL.44 2 PLIP interactions: 2 interactions with chain 3 Hydrophobic interactions: 3:L.58, 3:L.62 PLC.50: 9 residues within 4Å: Chain Y: L.99, G.102, A.103, R.106, S.107, Y.108, A.112, A.116 Ligands: 3PE.62 5 PLIP interactions: 5 interactions with chain Y Hydrophobic interactions: Y:L.99, Y:L.99, Y:Y.108, Y:A.116 Hydrogen bonds: Y:S.107 PLC.52: 6 residues within 4Å: Chain Z: L.30, S.31, S.34, A.37, V.38, F.45 5 PLIP interactions: 5 interactions with chain Z Hydrophobic interactions: Z:L.30, Z:A.37, Z:V.38, Z:F.45 Hydrogen bonds: Z:S.34 PLC.58: 6 residues within 4Å: Chain 6: W.85, R.88 Chain 7: L.70, F.73, Y.74 Ligands: 3PE.57 1 PLIP interactions: 1 interactions with chain 6 Hydrophobic interactions: 6:W.85

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

SF4.5: 13 residues within 4Å: Chain B: A.90, C.91, C.92, G.127, 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 SF4.10: 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 SF4.11: 11 residues within 4Å: Chain G: H.124, D.127, C.128, C.131, Q.133, 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 SF4.12: 14 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, P.227, 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 SF4.17: 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 6 PLIP interactions: 6 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:H.101, I:C.123, I:C.152, I:C.155, I:C.158 SF4.18: 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.8: 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.13: 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.9: 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 16 PLIP interactions: 16 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:D.127, F:D.127, F:G.207, F:E.209, F:N.244 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.14: 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

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.23: 33 residues within 4Å: Chain 6: V.100, T.104 Chain 7: L.68, L.71, R.72, I.75, G.79, V.82 Chain L: T.16, M.20, M.22, S.23, F.24, L.78, K.116, K.119, Y.120, L.123, I.130, I.142, M.150, L.153 Chain M: P.353, L.354, T.357, L.360, L.361, P.371, L.442, L.445 Ligands: 3PE.24, PC1.33, CDL.61 22 PLIP interactions: 11 interactions with chain L, 4 interactions with chain 7, 5 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: L:T.16, L:F.24, L:L.78, L:L.78, L:L.123, L:I.142, L:L.153, 7:L.71, 7:I.75, 7:V.82, M:L.360, M:L.361, M:P.371, M:L.442, 6:V.100, 6:V.100 Salt bridges: L:K.116, L:K.119, L:K.119, L:K.119, 7:R.72 Hydrogen bonds: M:T.357 CDL.30: 25 residues within 4Å: Chain 3: C.40, A.47, V.53 Chain M: I.9, M.12, P.13, W.16, T.90, 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, P.256, T.301, T.334, M.335 Ligands: CDL.44 20 PLIP interactions: 4 interactions with chain N, 15 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: N:I.239, N:V.242, N:P.256, N:T.301, M:I.9, M:P.13, M:W.16, M:W.16, M:L.94, M:L.94, M:T.97, M:L.104, M:F.105, M:F.105, M:V.127, M:I.131, M:I.131 Hydrogen bonds: M:N.88, M:T.90 Salt bridges: O:K.326 CDL.36: 20 residues within 4Å: Chain N: P.3, F.6, I.7, L.10, M.14, K.46, S.125, L.128, I.129, T.132, W.133, I.209, S.213, T.217, M.220, T.324, M.329 Chain O: P.28, H.280 Ligands: PC1.56 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:L.10, N:L.128, N:W.133, N:I.209 Hydrogen bonds: N:S.125, N:M.323, N:T.324 Salt bridges: O:H.280 CDL.44: 28 residues within 4Å: Chain 3: L.26, T.27, P.29, R.30, A.32, F.33, G.35, F.36, I.65 Chain 5: L.26, N.30, K.33 Chain M: L.2, I.6, L.55, F.56, F.105, M.108, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.30, PLC.35 20 PLIP interactions: 7 interactions with chain 3, 6 interactions with chain M, 1 interactions with chain X, 3 interactions with chain 5, 3 interactions with chain N Hydrophobic interactions: 3:R.30, 3:A.32, 3:F.33, 3:F.33, 3:F.36, 3:F.36, 3:I.65, M:L.2, M:I.6, M:I.6, M:F.56, M:F.105, M:L.121, N:P.256, N:L.337, N:P.338 Hydrogen bonds: X:T.171, 5:N.30 Salt bridges: 5:K.33, 5:K.33 CDL.54: 20 residues within 4Å: Chain 2: K.43, T.47, T.50 Chain 3: D.45, R.49, R.60, L.63, Y.64, S.67, F.68, V.71, L.75 Chain N: T.324, F.325, T.328, L.332, M.336, L.339, M.342 Ligands: 3PE.55 11 PLIP interactions: 6 interactions with chain 3, 3 interactions with chain N, 2 interactions with chain 2 Hydrophobic interactions: 3:Y.64, 3:F.68, 3:V.71, 3:L.75, N:L.332, N:L.339, 2:T.50 Hydrogen bonds: 3:R.49, N:F.325 Salt bridges: 3:R.60, 2:K.43 CDL.61: 21 residues within 4Å: Chain 6: A.107, Y.108 Chain 7: A.83, I.86, T.87, N.90, E.95, H.115 Chain 8: W.80, I.81, Y.84, Y.85, H.89 Chain L: L.12, F.80 Ligands: CDL.23, 3PE.24, PC1.33 Chain f: V.48, R.49, I.52 17 PLIP interactions: 7 interactions with chain 8, 2 interactions with chain f, 2 interactions with chain 6, 2 interactions with chain L, 4 interactions with chain 7 Hydrophobic interactions: 8:W.80, 8:W.80, 8:I.81, 8:Y.84, 8:Y.85, f:I.52, 6:A.107, L:L.12, L:F.80 Hydrogen bonds: 8:Y.84, 6:Y.108, 7:N.90, 7:N.90, 7:E.95 Salt bridges: 8:H.89, f:R.49, 7:H.115 CDL.66: 16 residues within 4Å: Chain 0: W.2, F.3, L.6, P.7 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 9 PLIP interactions: 3 interactions with chain 0, 3 interactions with chain g, 3 interactions with chain h Hydrophobic interactions: 0:L.6, 0:L.6, 0:P.7, g:L.3, g:L.7, h:F.7 Salt bridges: g:R.9 Hydrogen bonds: h:S.3, h:T.5

2 x ZN: ZINC ION(Non-covalent)

ZN.29: 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.41: 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.38: 20 residues within 4Å: Chain O: 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.39 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:R.127, O:R.149, O:E.214, O:Y.221 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.39: 3 residues within 4Å: Chain O: S.59, E.76 Ligands: DGT.38 No protein-ligand interaction detected (PLIP)

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

NDP.40: 26 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, E.133, F.139, F.145, I.148, I.167, S.168, Y.180, K.184, P.203, A.204, 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:R.85, P:L.129, P:G.131, P:K.184, P:I.206, P:R.212 Salt bridges: P:R.85, P:R.132, P:R.132, P:R.212, 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.42: 17 residues within 4Å: Chain T: S.112, L.113 Chain W: K.29, V.32, L.35, W.39, T.46, G.59, K.62, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.106 13 PLIP interactions: 11 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:V.32, W:L.35, W:W.39, W:T.46, W:K.62, W:M.66, W:F.67, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 EHZ.43: 22 residues within 4Å: Chain L: Y.513, H.514 Chain U: M.105, D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, W.30, R.47, F.48, H.51, K.52, N.53, E.54, L.63, A.67, E.70, F.71, G.74 10 PLIP interactions: 2 interactions with chain U, 8 interactions with chain d Hydrogen bonds: U:S.112, U:L.113, d:R.47, d:H.51, d:K.52, d:E.54 Hydrophobic interactions: d:A.23, d:F.48, d:F.48, d:F.71

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.60: 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 14 PLIP interactions: 7 interactions with chain L, 7 interactions with chain 8 Hydrophobic interactions: L:Y.27, L:N.31, L:L.34, L:Y.35, L:Y.35, 8:R.66, 8:F.70, 8:F.70 Hydrogen bonds: L:K.28, L:K.28, 8:R.66 Salt bridges: 8:K.63, 8:R.66, 8:H.67

1 x MYR: MYRISTIC ACID(Covalent)

MYR.65: 7 residues within 4Å: Chain L: L.409, L.486 Chain b: Y.153, Q.154 Chain e: G.2, A.3, L.5 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain b, 2 interactions with chain e Hydrophobic interactions: L:L.409, L:L.486, e:A.3, e:L.5 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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