SMTL ID : 8q47.1

Inward-facing, open1 proteoliposome complex I at 2.9 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

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

PC1.1: 10 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: CDL.23 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:T.15, A:I.19, A:I.19 pi-Cation interactions: A:W.23, A:W.23 Salt bridges: H:R.62 PC1.5: 8 residues within 4Å: Chain A: Q.26 Chain B: I.74, L.210, W.213, R.216 Chain P: D.90, F.310 Ligands: PC1.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain P Hydrophobic interactions: B:I.74, B:I.74, B:L.210, B:W.213, B:W.213, P:F.310 Salt bridges: B:R.216, P:D.90 PC1.7: 19 residues within 4Å: Chain 0: V.11 Chain B: W.76, R.79, K.205 Chain H: F.19, V.39, P.42, L.46, I.49, I.53 Chain I: F.88 Ligands: PC1.5, PLC.6, PC1.74 Chain g: F.28, R.29, N.31, W.75, V.77 9 PLIP interactions: 4 interactions with chain B, 2 interactions with chain H, 2 interactions with chain g, 1 interactions with chain 0 Hydrophobic interactions: B:W.76, B:W.76, H:I.49, H:I.53, g:F.28, g:F.28, 0:V.11 Salt bridges: B:R.79, B:K.205 PC1.16: 23 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, M.108 Chain J: I.34, V.35, C.41, G.42, L.45, S.50, F.57 Chain Z: F.140, I.141, W.142, Y.143, T.144 12 PLIP interactions: 6 interactions with chain J, 3 interactions with chain H, 2 interactions with chain A, 1 interactions with chain Z Hydrophobic interactions: J:I.34, J:L.45, J:F.57, J:F.57, J:F.57, H:F.104, A:L.7, A:F.11 Hydrogen bonds: J:S.50, H:N.99, H:L.100 pi-Cation interactions: Z:F.140 PC1.17: 15 residues within 4Å: Chain H: Q.169, E.170, M.172, W.173, L.243, G.244, T.245, S.246, N.258, I.261, K.262, L.265, S.269 Ligands: PC1.20, 3PE.55 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:W.173, H:L.243, H:I.261, H:K.262, H:L.265 Hydrogen bonds: H:G.244, H:S.246 Salt bridges: H:K.262, H:K.262 PC1.20: 26 residues within 4Å: Chain 1: K.15, E.16, V.18, I.25 Chain D: R.266 Chain H: I.175, W.179, M.183, F.186, I.187, L.266, Y.277, L.288, N.292, F.293, L.296, W.303 Chain I: T.60, L.61, W.63, L.66 Chain Z: L.43, L.44, Y.47 Ligands: PC1.17, 3PE.55 16 PLIP interactions: 7 interactions with chain H, 3 interactions with chain I, 1 interactions with chain Z, 3 interactions with chain 1, 2 interactions with chain D Hydrophobic interactions: H:I.175, H:W.179, H:F.186, H:L.266, H:Y.277, H:F.293, H:L.296, I:W.63, I:W.63, I:L.66, Z:L.44, 1:I.25, 1:I.25 Salt bridges: 1:E.16, D:R.266, D:R.266 PC1.21: 14 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 Chain Z: R.28, L.30, M.35 Ligands: 3PE.55 Chain h: W.14 6 PLIP interactions: 4 interactions with chain I, 1 interactions with chain Z, 1 interactions with chain H Hydrophobic interactions: I:I.67, H:W.272 Hydrogen bonds: I:T.64 Salt bridges: I:D.55, I:R.68, Z:R.28 PC1.24: 10 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 4 PLIP interactions: 2 interactions with chain 4, 1 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: 4:V.12, 4:L.14, A:F.93 pi-Cation interactions: J:Y.149 PC1.33: 18 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, I.180, G.228, M.533, H.534, A.537, P.538, N.541, L.542 Chain M: L.405 Ligands: 3PE.30 Chain b: N.115, R.116 13 PLIP interactions: 11 interactions with chain L, 2 interactions with chain M Hydrophobic interactions: L:L.173, L:I.177, L:I.177, L:I.180, L:A.537, L:N.541, L:L.542, M:L.405, M:L.405 Hydrogen bonds: L:Q.170 Salt bridges: L:D.163, L:H.534, L:H.534 PC1.36: 16 residues within 4Å: Chain 6: V.98, S.103, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, W.71, I.317, P.443, L.446, L.449, N.450, I.454 Ligands: 3PE.29, CDL.64 11 PLIP interactions: 10 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: M:P.64, M:I.67, M:W.71, M:W.71, M:I.317, M:P.443, M:L.449, M:N.450, M:I.454, 6:V.98 Hydrogen bonds: M:N.450 PC1.38: 6 residues within 4Å: Chain M: N.188, W.190 Chain Y: D.86, L.88, M.127 Ligands: 3PE.37 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:W.190 PC1.60: 15 residues within 4Å: Chain 3: T.3, T.10, F.11, Q.12, F.13, R.78 Chain 4: F.3, F.4 Chain N: L.136, Y.143, I.206, V.345, L.346 Ligands: CDL.39, 3PE.59 12 PLIP interactions: 3 interactions with chain N, 5 interactions with chain 3, 4 interactions with chain 4 Hydrophobic interactions: N:L.136, N:I.206, N:L.346, 3:F.11, 4:F.3, 4:F.4, 4:F.4 Hydrogen bonds: 3:F.11, 3:Q.12 Salt bridges: 3:R.78, 3:R.78 pi-Cation interactions: 4:F.3 PC1.65: 7 residues within 4Å: Chain 7: I.89, W.110, I.117, R.119, W.120, R.123 Chain f: Y.61 7 PLIP interactions: 7 interactions with chain 7 Hydrophobic interactions: 7:I.89, 7:I.117, 7:W.120, 7:W.120 Salt bridges: 7:R.119, 7:R.123, 7:R.123 PC1.70: 14 residues within 4Å: Chain L: I.561, T.565, I.566, L.568, A.569 Chain Y: G.109, A.113, A.116, Y.117 Ligands: 3PE.32, 3PE.40 Chain c: Y.77, F.80, P.82 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain Y Hydrophobic interactions: L:I.561, L:I.561, L:T.565, L:I.566, Y:A.116 PC1.74: 6 residues within 4Å: Ligands: PC1.7 Chain g: R.21, L.24, R.25, F.28, F.74 7 PLIP interactions: 7 interactions with chain g Hydrophobic interactions: g:L.24, g:F.28, g:F.28 Salt bridges: g:R.21, g:R.21, g:R.25 pi-Cation interactions: g:F.74

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

3PE.2: 12 residues within 4Å: Chain A: V.100, A.103, Y.104, T.107, Q.108 Chain J: L.162 Chain N: N.2, I.5 Chain O: K.36, N.275, R.277 Ligands: 3PE.3 Ligand excluded by PLIP 3PE.3: 8 residues within 4Å: Chain 1: F.23 Chain A: I.96, V.100, A.103, T.107 Ligands: 3PE.2, 3PE.56, PLC.57 Ligand excluded by PLIP 3PE.22: 7 residues within 4Å: Chain 1: L.9, K.10, W.13 Chain I: D.49, M.50 Chain Z: Y.33, F.36 Ligand excluded by PLIP 3PE.25: 7 residues within 4Å: Chain J: N.86, K.87, G.91, T.95 Chain Y: F.49 Ligands: 3PE.26, 3PE.51 Ligand excluded by PLIP 3PE.26: 18 residues within 4Å: Chain J: S.21, S.22, K.23, A.88, A.92, T.95, M.99, V.115 Chain K: M.10, V.14, V.17, M.21, Y.22, R.23 Chain L: K.585 Ligands: 3PE.25, 3PE.28, 3PE.51 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, T.13, L.16 Chain L: M.599, I.600, H.605, E.606 Chain N: M.93 Ligands: 3PE.26 Ligand excluded by PLIP 3PE.29: 14 residues within 4Å: Chain 8: Y.84, Y.85, H.89, K.93 Chain L: W.66, H.67, W.68, S.77, L.78, F.138, I.142 Ligands: CDL.27, PC1.36, CDL.64 Ligand excluded by PLIP 3PE.30: 12 residues within 4Å: Chain L: I.180, L.184, M.211, N.541 Chain M: N.390, I.391, I.393, I.394, V.398 Ligands: PC1.33 Chain c: W.101, R.111 Ligand excluded by PLIP 3PE.32: 13 residues within 4Å: Chain L: A.569, K.572, A.573, L.576 Chain N: W.167 Chain Y: T.105, I.110, Y.117, T.121 Ligands: 3PE.40, 3PE.52, 3PE.53, PC1.70 Ligand excluded by PLIP 3PE.37: 15 residues within 4Å: Chain M: W.190, V.193, L.197, M.201, G.211, L.212, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.38, 3PE.68 Chain c: Y.102, K.106 Ligand excluded by PLIP 3PE.40: 25 residues within 4Å: Chain D: Q.46, Y.47, M.52, Y.53 Chain L: S.567, Q.570, M.571 Chain M: N.144, L.147, Y.148, F.151, Y.152, A.155, G.156, M.201, V.205 Chain N: L.163, W.167, T.285, L.287, Y.291, R.295 Ligands: 3PE.32, 3PE.50, PC1.70 Ligand excluded by PLIP 3PE.41: 11 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, L.160, W.167 Chain Y: A.2, K.3, L.6, F.136 Ligands: 3PE.53, 3PE.54 Ligand excluded by PLIP 3PE.50: 17 residues within 4Å: Chain M: A.155, V.162, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: N.274, I.276, I.277 Chain Y: L.120, L.124, W.133 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.51: 11 residues within 4Å: Chain L: L.589 Chain Y: A.38, V.41, P.46, T.47, S.48, F.49, G.52, T.56 Ligands: 3PE.25, 3PE.26 Ligand excluded by PLIP 3PE.52: 17 residues within 4Å: Chain Y: Y.9, I.28, G.29, Y.59, T.62, A.63, I.66, G.67, F.70, L.101, T.105, M.118, T.121, V.125 Ligands: 3PE.32, 3PE.53, 3PE.54 Ligand excluded by PLIP 3PE.53: 21 residues within 4Å: Chain L: L.576, T.594, S.598, L.601, F.602, F.604 Chain N: L.153, L.157, L.160 Chain Y: A.2, A.31, A.32, V.35, V.36, Y.39, S.40, Y.59 Ligands: 3PE.32, 3PE.41, 3PE.52, 3PE.54 Ligand excluded by PLIP 3PE.54: 13 residues within 4Å: Chain N: I.277 Chain Y: W.10, I.28, L.124, V.125, G.128, Q.129, W.133, V.135, F.136 Ligands: 3PE.41, 3PE.52, 3PE.53 Ligand excluded by PLIP 3PE.55: 14 residues within 4Å: Chain H: I.175, L.176, W.179 Chain I: I.67 Chain Z: R.27, R.28, G.29, L.30, M.35, V.38 Ligands: PC1.17, PC1.20, PC1.21 Chain h: W.14 Ligand excluded by PLIP 3PE.56: 12 residues within 4Å: Chain 1: E.16, L.19, V.20, F.23, A.26 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295 Ligands: 3PE.3 Ligand excluded by PLIP 3PE.59: 16 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, M.336, L.339, L.343, V.345 Ligands: CDL.58, PC1.60 Ligand excluded by PLIP 3PE.61: 16 residues within 4Å: Chain 5: D.9, H.10, H.13 Chain 6: A.81, V.82, W.85, V.89, F.93 Chain M: K.19, M.22, V.25, A.29, H.30, L.33 Ligands: 3PE.62, PLC.63 Ligand excluded by PLIP 3PE.62: 9 residues within 4Å: Chain 5: V.7, H.10, W.11, H.13, V.14, P.17, V.21, Y.25 Ligands: 3PE.61 Ligand excluded by PLIP 3PE.67: 17 residues within 4Å: Chain 9: W.71, W.74, R.75, H.78 Chain L: F.44, M.48, M.88, P.91, V.92, F.334, I.459, F.463, Y.466, I.467, I.468 Ligands: 3PE.72 Chain e: L.78 Ligand excluded by PLIP 3PE.68: 10 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: Y.108 Ligands: 3PE.37 Chain c: P.82, N.83, T.84, S.87, G.94 Ligand excluded by PLIP 3PE.69: 10 residues within 4Å: Chain L: L.536, Y.539 Chain b: W.126, N.127, C.130, L.133, F.134, V.137 Chain c: S.9, R.10 Ligand excluded by PLIP 3PE.72: 12 residues within 4Å: Chain L: M.52, I.55, M.88, N.471 Ligands: 3PE.67 Chain e: P.75, N.76, F.77, L.78 Chain f: T.24, S.25, L.26 Ligand excluded by PLIP

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

SF4.4: 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 SF4.10: 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: 12 residues within 4Å: Chain D: M.375 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 SF4.12: 12 residues within 4Å: Chain G: M.173, C.176, I.177, 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 SF4.18: 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 SF4.19: 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

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

PLC.6: 8 residues within 4Å: Chain B: K.69, L.70, D.72, W.76, K.205 Ligands: PC1.7 Chain g: W.75, D.76 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain g Hydrophobic interactions: B:L.70, B:W.76 Salt bridges: B:D.72, B:K.205 Hydrogen bonds: g:D.76 PLC.31: 10 residues within 4Å: Chain L: M.290, L.293, T.294, R.425, L.500, I.504, A.519, F.520, S.523 Chain d: W.30 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:T.294, L:L.500 Hydrogen bonds: L:R.425 PLC.44: 9 residues within 4Å: Chain N: I.7, K.322 Chain O: L.24, G.27, P.28, L.29, I.32 Ligands: CDL.39, CDL.58 4 PLIP interactions: 2 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: O:I.32 Hydrogen bonds: O:L.29 Salt bridges: N:K.322, N:K.322 PLC.57: 9 residues within 4Å: Chain 1: V.30, T.34, L.35, S.36 Chain A: N.85, L.88, T.89, L.92 Ligands: 3PE.3 2 PLIP interactions: 1 interactions with chain 1, 1 interactions with chain A Hydrophobic interactions: 1:V.30, A:L.92 PLC.63: 8 residues within 4Å: Chain 6: M.87, R.88, F.93 Chain 7: L.70, F.73, Y.74, L.77 Ligands: 3PE.61 1 PLIP interactions: 1 interactions with chain 6 Hydrophobic interactions: 6:F.93

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

FES.8: 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.13: 11 residues within 4Å: Chain G: R.62, F.63, C.64, Y.65, G.73, N.74, C.75, R.76, M.77, 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 13 PLIP interactions: 13 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:G.120, F:E.209, F:N.244, F:N.244 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.14: 6 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 Chain Q: M.87 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:I.223, G:C.226, G:V.228, G:L.231

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

U10.15: 13 residues within 4Å: Chain B: W.83, V.112, A.115, S.116, Q.119 Chain H: A.18, R.25, P.48, D.51, A.52, F.220, F.224, M.225 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:A.18, H:D.51, H:A.52, H:F.224, H:F.224, H:F.224, B:V.112

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.23: 13 residues within 4Å: Chain H: R.62, A.64, S.66, S.67, A.68, S.69 Chain J: Y.28, I.82, W.83 Chain P: W.222, R.286, T.358 Ligands: PC1.1 7 PLIP interactions: 4 interactions with chain H, 1 interactions with chain J, 2 interactions with chain P Hydrogen bonds: H:R.62, H:A.64, H:A.68, H:S.69, P:R.286 Hydrophobic interactions: J:I.82, P:W.222 CDL.27: 29 residues within 4Å: Chain 6: L.99, V.100 Chain 7: L.68, L.71, R.72, G.79, V.82 Chain L: S.23, N.25, L.78, K.116, K.119, Y.120, L.123, I.130, I.149, M.150, L.153 Chain M: T.357, L.360, L.364, L.369, P.370, P.371, L.442, L.445, L.446 Ligands: 3PE.29, CDL.64 15 PLIP interactions: 5 interactions with chain L, 6 interactions with chain M, 1 interactions with chain 6, 3 interactions with chain 7 Hydrophobic interactions: L:L.78, L:L.123, L:I.149, M:L.360, M:L.364, M:L.369, M:L.445, M:L.446, 6:V.100, 7:L.71, 7:R.72, 7:V.82 Salt bridges: L:K.119, L:K.119 Hydrogen bonds: M:T.357 CDL.35: 28 residues within 4Å: Chain 3: F.33, F.36, C.40, A.47, V.53 Chain M: W.16, N.88, T.90, R.91, L.94, T.97, M.98, S.101, L.104, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, A.246, P.256, L.257, T.301, T.334, M.335, P.338 Ligands: CDL.49 21 PLIP interactions: 1 interactions with chain O, 13 interactions with chain M, 5 interactions with chain N, 2 interactions with chain 3 Hydrogen bonds: O:Q.317, M:N.88, M:T.90, M:R.135 Hydrophobic interactions: M:W.16, M:W.16, M:L.94, M:L.94, M:T.97, M:L.104, M:V.127, M:I.131, M:R.135, N:V.242, N:A.246, N:P.256, N:L.257, N:P.338, 3:F.33, 3:F.36 Salt bridges: M:R.91 CDL.39: 19 residues within 4Å: Chain N: F.6, L.10, L.11, M.14, K.46, S.125, I.129, T.132, W.133, I.209, T.217, M.220, T.324, M.329 Chain O: P.28, H.280, M.284 Ligands: PLC.44, PC1.60 12 PLIP interactions: 11 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:L.10, N:L.11, N:I.129, N:W.133, N:I.209 Hydrogen bonds: N:K.46, N:S.125, N:M.323, N:T.324 Salt bridges: N:K.46, N:K.322, O:H.280 CDL.49: 29 residues within 4Å: Chain 3: T.27, D.28, P.29, R.30, A.32, F.33, F.36 Chain 5: F.22, L.26, N.30, K.33 Chain M: L.2, I.5, I.6, I.9, L.55, F.56, F.105, M.108, L.117, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.35 20 PLIP interactions: 9 interactions with chain M, 4 interactions with chain 3, 2 interactions with chain 5, 3 interactions with chain X, 2 interactions with chain N Hydrophobic interactions: M:L.2, M:I.5, M:I.6, M:I.9, M:L.55, M:F.56, M:F.105, M:L.117, M:L.121, 3:R.30, 3:F.33, 3:F.36, 3:F.36, X:F.169, X:F.169, N:P.256, N:L.337 Hydrogen bonds: 5:N.30, X:T.171 Salt bridges: 5:K.33 CDL.58: 18 residues within 4Å: Chain 2: K.43, L.46, 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 Ligands: PLC.44, 3PE.59 11 PLIP interactions: 8 interactions with chain 3, 2 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: 3:Y.64, 3:F.68, 3:L.75, N:F.325, 2:L.46 Hydrogen bonds: 3:R.49, 3:R.49, 3:R.51, 3:Y.64, N:F.325 Salt bridges: 3:R.60 CDL.64: 24 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, I.81, I.82, Y.84, Y.85, H.89 Chain L: L.12, N.65 Chain M: L.449 Ligands: CDL.27, 3PE.29, PC1.36 Chain f: P.44, V.48, R.49, I.52 24 PLIP interactions: 5 interactions with chain 7, 2 interactions with chain 6, 10 interactions with chain 8, 1 interactions with chain M, 1 interactions with chain L, 5 interactions with chain f Hydrophobic interactions: 7:I.86, 6:A.107, 6:Y.108, 8:W.80, 8:W.80, 8:I.81, 8:I.82, 8:Y.84, 8:Y.84, 8:Y.85, 8:Y.85, M:L.449, L:L.12, f:P.44, f:V.48, f:V.48, f:I.52 Hydrogen bonds: 7:N.90, 7:N.90, 7:E.95, 8:Y.84 Salt bridges: 7:H.115, 8:H.89, f:R.49 CDL.73: 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 10 PLIP interactions: 5 interactions with chain 0, 2 interactions with chain h, 3 interactions with chain g Hydrophobic interactions: 0:W.2, 0:W.2, 0:F.3, 0:F.3, 0:L.6, h:F.7 Hydrogen bonds: h:T.5, g:R.9, g:Q.13 Salt bridges: g:R.9

2 x ZN: ZINC ION(Non-covalent)

ZN.34: 4 residues within 4Å: Chain 6: D.63 Chain M: H.82, E.335, H.338 3 PLIP interactions: 1 interactions with chain 6, 2 interactions with chain M Metal complexes: 6:D.63, M:E.335, M:H.338 ZN.46: 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.42: 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.43 21 PLIP interactions: 21 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:S.59, O:S.59, O:S.59, O:Q.120, O:Q.120, O:Q.120, O:R.127, 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.43: 2 residues within 4Å: Chain O: S.59 Ligands: DGT.42 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.59

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

NDP.45: 25 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, I.206 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:C.86, P:V.130, P:G.131, P:Y.180, P:K.184, P:I.206 Salt bridges: P:R.85, P:R.132, P:R.132, B:R.216 pi-Cation interactions: P:R.85, 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.47: 16 residues within 4Å: Chain T: S.112, L.113 Chain W: K.29, V.32, W.39, T.46, G.59, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.107 15 PLIP interactions: 13 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:V.32, W:W.39, W:W.39, W:W.39, W:T.46, W:V.63, W:F.67, W:F.67, W:I.73, W:F.107, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 EHZ.48: 20 residues within 4Å: Chain L: H.514 Chain U: D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, H.26, L.27, W.30, R.47, F.48, H.51, K.52, E.54, A.67, F.71, G.74, Q.75 12 PLIP interactions: 10 interactions with chain d, 2 interactions with chain U Hydrophobic interactions: d:Q.13, d:H.26, d:L.27, d:F.48, d:K.52, d:A.67, d:F.71, U:L.113 Hydrogen bonds: d:Q.13, d:R.47, d:K.52, U:S.112

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.66: 8 residues within 4Å: Chain 8: K.63, R.66, H.67, F.70, H.74 Chain L: L.34, Y.35, T.38 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain 8 Hydrophobic interactions: L:L.34, L:Y.35, L:Y.35 Hydrogen bonds: 8:R.66 Salt bridges: 8:K.63, 8:H.67

1 x MYR: MYRISTIC ACID(Covalent)

MYR.71: 8 residues within 4Å: Chain L: L.409, Y.485, L.486 Chain b: A.152, Q.154 Chain e: G.2, A.3, L.5 6 PLIP interactions: 2 interactions with chain b, 2 interactions with chain L, 2 interactions with chain e Hydrophobic interactions: b:A.152, 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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