SMTL ID : 7qsk.1

Bovine complex I in lipid nanodisc, Active-Q10

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

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

3PE.1: 14 residues within 4Å: Chain 1: V.12, E.16, L.19, V.20, S.22, F.23, A.26 Chain A: A.99, L.102, A.103, W.106, T.107 Chain H: K.291, P.295 Ligand excluded by PLIP 3PE.15: 12 residues within 4Å: Chain H: Q.169, E.170, W.173, L.243, G.244, T.245, S.246, N.258, I.261, K.262, L.265 Ligands: PC1.17 Ligand excluded by PLIP 3PE.21: 14 residues within 4Å: Chain J: S.21, K.23, A.92, G.96, M.99 Chain K: M.10, T.13, V.14, M.21, Y.22, R.23 Chain L: K.585, L.592 Ligands: 3PE.44 Ligand excluded by PLIP 3PE.22: 18 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, I.180, G.228, P.530, M.533, H.534, A.537, P.538, N.541 Chain M: V.398, L.405 Chain b: N.115, R.116 Ligand excluded by PLIP 3PE.24: 18 residues within 4Å: Chain 8: I.80, Y.83, Y.84, H.88, K.92 Chain L: N.65, W.66, H.67, W.68, L.76, S.77, N.136, F.138, I.142 Chain M: L.449 Ligands: CDL.23, PC1.50, CDL.51 Ligand excluded by PLIP 3PE.25: 17 residues within 4Å: Chain 9: W.71, W.74, R.75 Chain L: F.44, M.48, M.88, P.91, V.92, F.95, F.334, I.459, G.460, F.463, Y.466, I.467 Chain e: F.77, L.78 Ligand excluded by PLIP 3PE.26: 25 residues within 4Å: Chain D: Y.53 Chain L: L.562, P.563, K.564, S.567, Q.570, M.571 Chain M: N.144, Y.148, F.151, Y.152, A.155, M.201, V.205 Chain N: L.163, W.167, L.170, I.284, T.285, L.287, L.288, Y.291 Ligands: 3PE.27, PC1.45 Chain c: Y.77 Ligand excluded by PLIP 3PE.27: 19 residues within 4Å: Chain M: A.155, G.156, P.159, V.162, A.163, Y.166, S.191, F.194, M.195, A.198 Chain N: N.274, I.276, I.277, F.281, I.284 Chain Y: W.133 Ligands: 3PE.26, 3PE.42, PC1.45 Ligand excluded by PLIP 3PE.28: 19 residues within 4Å: Chain 3: F.36, C.40, L.43, I.44, A.47, V.53, L.54 Chain M: W.16, L.17, T.97, M.98, S.101, F.105 Chain N: I.239, M.335 Chain O: K.326, Y.327 Ligands: 3PE.30, CDL.39 Ligand excluded by PLIP 3PE.30: 24 residues within 4Å: Chain M: W.16, T.90, R.91, L.94, M.98, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, L.243, L.245, A.246, L.249, P.256, L.257, T.301, T.334, M.335, P.338 Chain O: K.326 Ligands: 3PE.28, CDL.39 Ligand excluded by PLIP 3PE.35: 12 residues within 4Å: Chain P: Y.216, N.219, I.220, W.222, F.223, P.227, I.301, F.305, W.313, T.314, R.355 Ligands: PC1.2 Ligand excluded by PLIP 3PE.40: 8 residues within 4Å: Chain L: L.576 Chain Y: V.36, Y.39, S.40, K.44, Y.59 Ligands: 3PE.41, 3PE.43 Ligand excluded by PLIP 3PE.41: 13 residues within 4Å: Chain Y: Y.9, T.25, I.28, R.58, Y.59, T.62, A.63, F.70, L.101, T.105, M.118 Ligands: 3PE.40, 3PE.42 Ligand excluded by PLIP 3PE.42: 12 residues within 4Å: Chain N: I.277 Chain Y: L.6, W.10, T.121, L.124, V.125, G.128, Q.129, W.133, V.135 Ligands: 3PE.27, 3PE.41 Ligand excluded by PLIP 3PE.43: 12 residues within 4Å: Chain L: F.602, F.604 Chain N: N.152, T.156 Chain Y: A.2, K.3, L.6, I.28, A.31, A.32, V.35 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.44: 9 residues within 4Å: Chain Y: V.41, T.45, P.46, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.21 Ligand excluded by PLIP 3PE.47: 16 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, M.261, M.336, L.339, M.342, L.343, V.345 Ligands: PC1.48, CDL.49 Ligand excluded by PLIP 3PE.54: 15 residues within 4Å: Chain M: W.190, V.193, L.197, M.201, L.212, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.29, 3PE.55 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.55: 17 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210, L.264 Chain Y: Y.108, A.112 Ligands: PC1.45, 3PE.54 Chain c: P.82, N.83, T.84, S.87, L.88, G.90, G.94, I.95, L.98 Ligand excluded by PLIP

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

PC1.2: 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: PC1.4, CDL.16, 3PE.35 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain H, 1 interactions with chain P Hydrophobic interactions: A:T.15, A:I.19, H:I.72, P:W.222 pi-Cation interactions: A:W.23 Salt bridges: H:R.62 PC1.3: 10 residues within 4Å: Chain 4: L.14 Chain A: N.83, T.86, T.89, M.90 Chain J: S.148, Y.149, T.151, W.152, I.155 8 PLIP interactions: 4 interactions with chain J, 3 interactions with chain A, 1 interactions with chain 4 Hydrophobic interactions: J:T.151, J:W.152, J:I.155, A:T.89, 4:L.14 pi-Cation interactions: J:Y.149 Hydrogen bonds: A:N.83, A:T.86 PC1.4: 13 residues within 4Å: Chain A: 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: PC1.2, PC1.6 7 PLIP interactions: 6 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: P:L.304, P:F.305, P:I.307, P:F.310, P:W.313, A:I.20 pi-Cation interactions: P:F.310 PC1.6: 15 residues within 4Å: Chain A: L.24, Q.26 Chain B: I.74, R.78, L.210, W.213, R.216 Chain H: F.56, I.57 Chain P: D.90, F.310, E.311 Ligands: PC1.4, U10.7, PC1.57 17 PLIP interactions: 8 interactions with chain B, 4 interactions with chain P, 1 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: B:L.210, B:W.213, B:W.213, B:W.213, P:F.310, P:F.310, A:L.24, H:F.56, H:F.56, H:F.56, H:I.57 Water bridges: B:R.216, B:R.216 Salt bridges: B:R.78, B:R.216, P:D.90, P:E.311 PC1.17: 21 residues within 4Å: Chain 1: E.16, V.18, I.25 Chain D: R.266 Chain H: M.183, F.186, I.187, Y.277, L.288, N.292, F.293, L.296, W.303 Chain I: T.60, L.61, W.63, L.66, L.70 Chain Z: I.40, L.43 Ligands: 3PE.15 17 PLIP interactions: 4 interactions with chain I, 2 interactions with chain D, 2 interactions with chain Z, 6 interactions with chain H, 3 interactions with chain 1 Hydrophobic interactions: I:L.61, I:W.63, I:W.63, I:L.70, Z:I.40, Z:L.43, H:F.186, H:F.186, H:I.187, H:Y.277, H:F.293, H:W.303, 1:I.25, 1:I.25 Salt bridges: D:R.266, D:R.266, 1:E.16 PC1.20: 13 residues within 4Å: Chain H: M.183, W.272 Chain I: D.55, Q.59, L.62, T.64, E.65, I.67, R.68 Chain Z: R.28, L.30, M.35 Chain h: W.14 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:Q.59, I:R.68 Salt bridges: I:D.55 Hydrophobic interactions: H:W.272 PC1.29: 6 residues within 4Å: Chain M: N.188, W.190 Chain Y: D.86, L.88, M.127 Ligands: 3PE.54 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:W.190 pi-Cation interactions: M:W.190, M:W.190 PC1.45: 19 residues within 4Å: Chain L: I.561, T.565, I.566, L.568, A.569, Q.570 Chain Y: G.109, I.110, A.112, A.113, A.116, Y.117 Ligands: 3PE.26, 3PE.27, 3PE.55 Chain c: Y.77, P.78, F.80, P.82 10 PLIP interactions: 5 interactions with chain Y, 5 interactions with chain L Hydrophobic interactions: Y:A.113, Y:Y.117, Y:Y.117, Y:Y.117, Y:Y.117, L:I.561, L:T.565, L:I.566, L:L.568, L:A.569 PC1.46: 23 residues within 4Å: Chain 0: A.39, H.40 Chain A: M.1, L.3 Chain H: M.98, N.99, F.104 Chain J: L.9, I.34, V.35, G.38, V.39, C.41, G.42, L.45, N.46, S.50, L.54 Chain Z: F.140, I.141, W.142, Y.143, T.144 10 PLIP interactions: 6 interactions with chain J, 2 interactions with chain H, 2 interactions with chain Z Hydrophobic interactions: J:L.9, J:I.34, J:V.35, J:V.39, H:F.104, Z:T.144 Hydrogen bonds: J:S.50, J:S.50, H:N.99 pi-Cation interactions: Z:F.140 PC1.48: 16 residues within 4Å: Chain 3: T.3, T.10, F.11, Q.12, F.13, R.78 Chain 4: F.3, R.9 Chain N: M.21, W.133, L.136, Y.143, I.206, V.345, L.346 Ligands: 3PE.47 15 PLIP interactions: 5 interactions with chain N, 3 interactions with chain 4, 7 interactions with chain 3 Hydrophobic interactions: N:W.133, N:L.136, N:L.136, N:I.206, N:L.346, 4:F.3, 4:F.3, 3:F.11, 3:F.13 pi-Cation interactions: 4:F.3 Hydrogen bonds: 3:T.10, 3:F.11, 3:Q.12 Salt bridges: 3:R.78, 3:R.78 PC1.50: 18 residues within 4Å: Chain 6: V.98, L.99, S.103, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, W.71, P.443, L.446, L.447, L.449, N.450, I.453, I.454 Ligands: 3PE.24, CDL.51 12 PLIP interactions: 10 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: M:W.71, M:W.71, M:P.443, M:L.446, M:L.447, M:L.449, M:I.453, M:I.454, 6:V.98, 6:L.99 Water bridges: M:N.450, M:N.450 PC1.52: 13 residues within 4Å: Chain 6: T.104 Chain 7: P.81, V.82, G.85, I.86, I.89, I.93, W.110, P.116, R.119, W.120, R.123 Chain f: Y.61 12 PLIP interactions: 11 interactions with chain 7, 1 interactions with chain 6 Hydrophobic interactions: 7:V.82, 7:I.86, 7:I.89, 7:I.93, 7:P.116, 7:W.120, 7:W.120, 7:W.120, 6:T.104 Hydrogen bonds: 7:R.123 Salt bridges: 7:R.119, 7:R.123 PC1.57: 18 residues within 4Å: Chain B: K.69, D.72, L.73, W.76, R.79, K.205 Chain H: V.39, L.46, I.49, I.53 Ligands: PC1.6, U10.7, PC1.58 Chain g: F.28, R.29, N.31, W.75, V.77 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:L.73, B:W.76, B:W.76, H:I.53 Salt bridges: B:R.79, B:K.205, B:K.205 Water bridges: H:G.41 PC1.58: 9 residues within 4Å: Chain H: L.15, F.19, P.42, L.45, L.46 Ligands: PC1.57 Chain g: F.28, F.74, W.75 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain g Hydrophobic interactions: H:L.15, H:F.19, H:P.42, H:L.45, H:L.46, g:F.28 pi-Cation interactions: g:F.74

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

SF4.5: 13 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 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 G: H.124, P.125, 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: 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 SF4.18: 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: 11 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, 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)

U10.7: 30 residues within 4Å: Chain B: W.83, T.86, F.87, G.88, A.93, M.96, M.97, V.112, F.113, R.114 Chain D: P.89, H.92, Y.141, L.192, M.197, F.200 Chain H: L.14, L.15, V.17, A.18, R.25, L.28, R.34, D.51, L.55, F.224, M.225, R.274 Ligands: PC1.6, PC1.57 18 PLIP interactions: 6 interactions with chain B, 9 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: B:W.83, B:T.86, B:V.112, B:F.113, B:F.113, B:F.113, H:L.14, H:L.15, H:V.17, H:A.18, H:L.28, H:D.51, H:L.55, H:F.224, H:F.224, D:L.192, D:F.200 Hydrogen bonds: D:H.92

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: 8 residues within 4Å: Chain G: 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: 18 residues within 4Å: Chain F: G.87, R.88, G.89, 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 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:Y.204, F:Y.204, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:G.89, F:N.116, F:E.119, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247 Water bridges: F:G.87, F:G.92, F:G.92, F:E.119, F:D.127 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.16: 13 residues within 4Å: Chain H: R.62, A.68, S.69, I.72 Chain J: Y.28, L.31, I.82, W.83, L.84 Chain P: W.222, R.286, T.358 Ligands: PC1.2 18 PLIP interactions: 7 interactions with chain H, 8 interactions with chain J, 3 interactions with chain P Hydrophobic interactions: H:I.72, J:Y.28, J:L.31, J:W.83, J:W.83, J:L.84, P:W.222, P:W.222 Hydrogen bonds: H:A.68, H:S.69, J:W.83, J:L.84 Water bridges: H:R.62, H:S.67, J:Y.28 Salt bridges: H:R.62, H:R.62, P:R.286 CDL.23: 26 residues within 4Å: Chain 7: L.68, L.71, R.72, I.75, L.76, G.79 Chain L: M.22, S.23, F.24, L.78, K.116, K.119, Y.120, L.123, T.127, I.130, I.142, M.150, L.153 Chain M: L.354, T.357, W.358, P.371, L.442 Ligands: 3PE.24, CDL.51 20 PLIP interactions: 3 interactions with chain 7, 13 interactions with chain L, 4 interactions with chain M Hydrophobic interactions: 7:I.75, 7:L.76, L:F.24, L:L.78, L:L.78, L:L.123, L:I.130, L:I.142, L:L.153, M:W.358, M:W.358, M:L.442 Salt bridges: 7:R.72, L:K.116, L:K.119, L:K.119, L:K.119, L:K.119 Hydrogen bonds: L:Y.120, M:T.357 CDL.31: 17 residues within 4Å: Chain N: F.6, I.7, L.10, S.125, I.129, T.132, W.133, L.136, I.209, T.217, M.220, K.322, T.324, F.325, M.329 Chain O: P.28, H.280 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.7, N:L.10, N:I.129, N:W.133, N:L.136, N:I.209, N:F.325 Hydrogen bonds: N:S.125, N:T.324 Salt bridges: O:H.280 CDL.39: 28 residues within 4Å: Chain 3: T.27, P.29, R.30, A.32, F.33 Chain 5: L.26, K.29, K.33 Chain M: L.2, I.5, I.6, I.9, M.12, L.55, L.104, F.105, M.108, I.120, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: 3PE.28, 3PE.30 22 PLIP interactions: 3 interactions with chain X, 8 interactions with chain M, 7 interactions with chain 5, 1 interactions with chain 3, 3 interactions with chain N Hydrophobic interactions: X:F.169, M:L.2, M:I.5, M:I.6, M:I.9, M:L.104, M:F.105, M:I.120, M:L.121, 5:L.26, 3:F.33, N:P.256, N:L.337, N:P.338 Hydrogen bonds: X:T.171, X:T.171, 5:K.33, 5:K.33 Water bridges: 5:N.30 Salt bridges: 5:K.29, 5:K.33, 5:K.33 CDL.49: 21 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, G.72, L.75 Chain N: M.323, T.324, F.325, M.336, M.342 Ligands: 3PE.47 13 PLIP interactions: 10 interactions with chain 3, 1 interactions with chain N, 2 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:L.63, 3:Y.64, 3:F.68, 3:F.68, 3:F.70, 3:V.71, 3:L.75 Hydrogen bonds: 3:R.60, 3:Y.64, N:F.325 Salt bridges: 2:K.43, 2:K.43 CDL.51: 23 residues within 4Å: Chain 6: T.104, A.107, Y.108 Chain 7: A.83, T.87, N.90, V.91, E.95, H.115 Chain 8: W.79, Y.83, Y.84, H.88 Chain M: L.449 Ligands: CDL.23, 3PE.24, PC1.50 Chain f: P.44, V.45, V.48, R.49, I.52, H.56 16 PLIP interactions: 6 interactions with chain 8, 1 interactions with chain 6, 4 interactions with chain 7, 4 interactions with chain f, 1 interactions with chain M Hydrophobic interactions: 8:W.79, 8:W.79, 8:Y.83, 8:Y.84, 7:A.83, f:P.44, f:V.45, f:V.48, M:L.449 Water bridges: 8:H.88 Salt bridges: 8:H.88, 7:H.115, f:R.49 Hydrogen bonds: 6:Y.108, 7:N.90, 7:E.95 CDL.59: 18 residues within 4Å: Chain 0: M.1, 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, Y.23 Chain h: S.3, A.4, T.5, F.7, I.8 11 PLIP interactions: 6 interactions with chain 0, 3 interactions with chain h, 2 interactions with chain g Hydrophobic interactions: 0:F.3, 0:F.3, 0:F.3, 0:L.6, 0:L.6, 0:P.7, h:F.7, h:I.8 Hydrogen bonds: h:T.5, g:R.9 Salt bridges: g:R.9

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.32: 21 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, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214 Ligands: MG.33 17 PLIP interactions: 17 interactions with chain O Hydrogen bonds: O:C.55, O:S.56, O:S.56, O:G.57, O:K.58, O:S.59, O:Y.106, O:R.127, O:E.214, 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.33: 5 residues within 4Å: Chain O: K.58, S.59, E.76, E.148 Ligands: GTP.32 2 PLIP interactions: 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:S.59, H2O.28

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

NDP.34: 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, V.144, F.145, I.167, S.168, H.169, Y.180, K.184, P.203, A.204, E.205, I.206, R.212 29 PLIP interactions: 28 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:P.203, 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:L.129, P:R.132, P:Y.180, P:K.184, P:I.206, P:I.206, P:R.212 Water bridges: P:G.60, P:G.63, P:G.66, P:R.85, P:R.85, P:Y.180 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

1 x ZN: ZINC ION(Non-covalent)

ZN.36: 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

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.37: 14 residues within 4Å: Chain T: S.112 Chain W: K.29, W.39, V.43, T.46, V.63, M.66, F.67, N.70, A.71, H.72, I.73, V.79, L.82 11 PLIP interactions: 10 interactions with chain W, 1 interactions with chain T Hydrophobic interactions: W:W.39, W:V.43, W:T.46, W:V.63, W:M.66, W:F.67, W:I.73 Hydrogen bonds: W:N.70, W:A.71, W:A.71, T:S.112 EHZ.38: 20 residues within 4Å: Chain L: Y.513 Chain U: S.112 Chain d: H.12, Q.13, V.16, L.17, L.19, L.27, F.40, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, L.64, A.67, E.70 12 PLIP interactions: 1 interactions with chain L, 10 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: L:Y.513, d:Q.13, d:V.16, d:L.17, d:L.27, d:F.40, d:L.44, d:A.60 Hydrogen bonds: d:Q.13, d:H.51, d:K.52, U:S.112

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.53: 9 residues within 4Å: Chain 8: K.62, R.65, H.66, F.69, H.73 Chain L: N.31, L.34, Y.35, T.38 11 PLIP interactions: 6 interactions with chain L, 5 interactions with chain 8 Hydrophobic interactions: L:N.31, L:L.34, L:Y.35, L:Y.35, L:T.38, 8:F.69 Salt bridges: L:K.37, 8:K.62, 8:R.65, 8:H.66 Hydrogen bonds: 8:R.65

1 x MYR: MYRISTIC ACID(Covalent)

MYR.56: 8 residues within 4Å: Chain L: N.400, L.409, L.413, Y.485, L.486, T.489 Chain b: Q.154 Chain e: G.2 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain b Hydrophobic interactions: L:L.409, L:L.413, L:L.486, L:T.489 Hydrogen bonds: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, I. et al., Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Nat Commun (2022)

Release Date

2022-05-25

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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