SMTL ID : 8ud1.1

High resolution in-situ structure of complex I in respiratory supercomplex (composite)

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

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

PC1.1: 10 residues within 4Å: Chain 4: L.14, E.24 Chain A: N.83, T.86, T.89 Chain J: S.148, Y.149, T.151, W.152, I.155 7 PLIP interactions: 4 interactions with chain J, 1 interactions with chain 4, 2 interactions with chain A Hydrophobic interactions: J:W.152, J:I.155, 4:L.14 Water bridges: J:W.152 pi-Cation interactions: J:Y.149 Hydrogen bonds: A:N.83, A:T.86 PC1.10: 31 residues within 4Å: Chain 1: K.15, E.16, V.18, I.25 Chain D: R.269 Chain H: I.175, W.179, P.180, A.182, M.183, F.186, I.187, T.238, F.242, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 Chain I: T.87, L.88, L.89, W.90, L.93, L.97 Chain Z: I.40, L.43, L.44 Ligands: PC1.14 27 PLIP interactions: 14 interactions with chain H, 6 interactions with chain I, 3 interactions with chain Z, 2 interactions with chain 1, 2 interactions with chain D Hydrophobic interactions: H:I.175, H:W.179, H:P.180, H:F.186, H:F.186, H:F.186, H:F.186, H:I.187, H:T.238, H:F.242, H:I.273, H:Y.277, H:F.293, H:W.303, I:L.88, I:L.89, I:W.90, I:W.90, I:L.93, I:L.97, Z:I.40, Z:L.43, Z:L.44, 1:I.25 Salt bridges: 1:E.16, D:R.269, D:R.269 PC1.11: 26 residues within 4Å: Chain 0: A.39, H.40 Chain A: I.3, M.4, L.7, V.11 Chain H: L.77, N.97, M.98, N.99, L.100, F.104, M.108 Chain J: V.35, G.38, G.42, L.45, N.46, S.50, L.54, F.57 Chain Z: F.140, I.141, W.142, Y.143, T.144 11 PLIP interactions: 3 interactions with chain Z, 2 interactions with chain A, 3 interactions with chain J, 3 interactions with chain H Hydrophobic interactions: Z:I.141, Z:T.144, A:I.3, A:V.11, J:V.35, J:F.57, H:L.77 pi-Cation interactions: Z:F.140 Hydrogen bonds: J:S.50, H:N.99, H:L.100 PC1.14: 21 residues within 4Å: Chain H: I.175, M.183, T.269, W.272 Chain I: D.82, Q.86, L.89, T.91, E.92, V.94, R.95, L.97, G.98 Chain Z: R.27, R.28, L.30, S.31, G.32, M.35 Ligands: PC1.10 Chain h: W.14 12 PLIP interactions: 6 interactions with chain I, 4 interactions with chain H, 1 interactions with chain Z, 1 interactions with chain h Hydrophobic interactions: I:V.94, I:L.97, I:L.97, H:I.175, H:T.269, H:W.272, H:W.272, h:W.14 Hydrogen bonds: I:T.91 Salt bridges: I:D.82, I:R.95, Z:R.28 PC1.22: 10 residues within 4Å: Chain M: N.188, S.189, W.190, I.193 Chain Y: D.86, L.88, F.91, A.123, M.127 Ligands: 3PE.50 7 PLIP interactions: 5 interactions with chain Y, 2 interactions with chain M Hydrophobic interactions: Y:L.88, Y:F.91, Y:F.91, Y:F.91, Y:A.123 pi-Cation interactions: M:W.190, M:W.190 PC1.24: 18 residues within 4Å: Chain 6: V.98, S.103, V.106, A.107, Y.108 Chain L: W.66 Chain M: L.39, P.64, V.67, W.71, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: 3PE.17, CDL.45 13 PLIP interactions: 1 interactions with chain 6, 12 interactions with chain M Hydrophobic interactions: 6:V.98, M:L.39, M:P.64, M:V.67, M:W.71, M:W.71, M:P.443, M:L.447, M:L.449, M:L.449, M:I.454 Water bridges: M:N.450, M:K.452 PC1.30: 9 residues within 4Å: Chain A: W.23, L.24, P.25 Chain P: L.304, F.305, V.307, S.308, F.310, W.313 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: P:V.307, P:V.307 pi-Cation interactions: P:F.310 Water bridges: A:Q.26 PC1.31: 15 residues within 4Å: Chain A: L.24, Q.26 Chain B: L.112, V.116, R.120, R.251, L.252, W.255, R.258 Chain H: L.53, V.56, T.57 Chain P: D.90, F.310, E.311 16 PLIP interactions: 9 interactions with chain B, 3 interactions with chain H, 1 interactions with chain A, 3 interactions with chain P Hydrophobic interactions: B:L.112, B:L.112, B:V.116, B:L.252, B:W.255, B:W.255, H:L.53, H:V.56, H:T.57, A:L.24, P:F.310, P:F.310 Water bridges: B:R.120 Salt bridges: B:R.120, B:R.258, P:D.90 PC1.43: 21 residues within 4Å: Chain 3: R.10, V.11, P.12, L.13, Q.14, F.15, R.80 Chain 4: F.3, F.4, D.5 Chain N: I.202, L.203, M.261, V.336, M.339, T.340, A.342, L.343, S.345, L.346 Ligands: CDL.42 17 PLIP interactions: 4 interactions with chain N, 3 interactions with chain 4, 10 interactions with chain 3 Hydrophobic interactions: N:L.203, N:V.336, N:A.342, N:L.346, 4:D.5, 3:R.10, 3:P.12, 3:F.15 Hydrogen bonds: 4:F.3, 3:R.10, 3:R.10, 3:L.13, 3:Q.14 pi-Cation interactions: 4:F.3 Water bridges: 3:R.80 Salt bridges: 3:R.10, 3:R.80 PC1.44: 16 residues within 4Å: Chain 5: F.21, C.25, R.29 Chain 6: L.101, T.104, F.105 Chain 7: I.86, R.123, T.124, F.125, Y.126, D.127 Chain M: K.3, I.37, S.40 Ligands: PC1.46 17 PLIP interactions: 3 interactions with chain M, 5 interactions with chain 6, 5 interactions with chain 7, 4 interactions with chain 5 Hydrophobic interactions: M:I.37, 6:L.101, 6:T.104, 6:F.105, 6:F.105, 6:F.105, 7:I.86, 7:F.125, 7:F.125, 7:F.125, 5:F.21, 5:F.21 Hydrogen bonds: M:S.40 Salt bridges: M:K.3, 7:D.127, 5:R.29 Water bridges: 5:R.29 PC1.46: 11 residues within 4Å: Chain 6: L.101 Chain 7: T.78, P.81, I.93, W.110, P.116, R.119, W.120, R.123 Ligands: PC1.44 Chain f: Y.61 10 PLIP interactions: 1 interactions with chain 6, 9 interactions with chain 7 Hydrophobic interactions: 6:L.101, 7:T.78, 7:P.81, 7:I.93, 7:W.120, 7:W.120, 7:W.120 Salt bridges: 7:R.119, 7:R.123, 7:R.123 PC1.49: 17 residues within 4Å: Chain L: T.560, I.561, F.568, I.569 Chain Y: G.109, I.110, A.113, A.114, A.116, Y.117, T.121 Ligands: 3PE.37 Chain c: Y.77, P.78, N.79, F.80, P.82 12 PLIP interactions: 6 interactions with chain L, 5 interactions with chain Y, 1 interactions with chain c Hydrophobic interactions: L:T.560, L:I.561, L:I.561, L:F.568, L:F.568, L:I.569, Y:A.113, Y:A.114, Y:Y.117, Y:Y.117, Y:Y.117 pi-Cation interactions: c:Y.77 PC1.53: 14 residues within 4Å: Chain B: L.115, W.118, R.121, K.247 Chain H: V.39, P.42, L.45, L.46, I.49 Ligands: PC1.54 Chain g: F.28, R.29, N.31, W.75 16 PLIP interactions: 4 interactions with chain H, 9 interactions with chain B, 3 interactions with chain g Hydrophobic interactions: H:P.42, H:L.45, H:L.46, H:I.49, B:L.115, B:W.118, B:W.118, B:W.118, B:W.118, g:F.28, g:F.28, g:W.75 Water bridges: B:R.121, B:R.121 Salt bridges: B:R.121, B:K.247 PC1.54: 12 residues within 4Å: Chain B: K.111, D.114, L.115, R.121, K.247 Chain H: L.15, L.46, I.49 Ligands: PC1.53 Chain g: D.72, W.75, D.76 9 PLIP interactions: 2 interactions with chain g, 6 interactions with chain B, 1 interactions with chain H Salt bridges: g:D.72, g:D.76, B:R.121, B:K.247, B:K.247 Hydrophobic interactions: B:D.114, B:L.115, B:L.115, H:L.15

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

SF4.2: 14 residues within 4Å: Chain B: A.132, C.133, C.134, G.169, T.170, G.196, S.197, C.198, Y.205, G.227, C.228, P.229 Chain D: R.141, H.226 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.133, B:C.134, B:C.198, B:C.228 SF4.5: 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 SF4.6: 11 residues within 4Å: Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, V.228, G.229 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.127 Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.7: 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 SF4.12: 12 residues within 4Å: Chain I: H.128, C.150, P.151, I.155, C.179, I.180, Y.181, C.182, G.183, F.184, C.185, E.196 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.196 Metal complexes: I:C.150, I:C.179, I:C.182, I:C.185 SF4.13: 13 residues within 4Å: Chain I: C.140, I.141, A.142, C.143, K.144, L.145, C.146, I.157, Y.172, C.189, V.191, A.193, I.194 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.140, I:C.143, I:C.146, I:C.189

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

FES.3: 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.8: 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.4: 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 21 PLIP interactions: 21 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:G.207, F:E.209, F:E.209, F:N.244, F:N.244, F:T.247 Water bridges: F:G.92, F:T.95, F:K.98, F:K.98 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.9: 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

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

3PE.15: 18 residues within 4Å: Chain J: S.21, S.22, K.23, N.86, T.88, A.92, S.95, M.99 Chain K: M.10, A.13, I.14, A.17, M.21, Y.22, R.23 Chain L: K.585, L.592 Ligands: 3PE.39 Ligand excluded by PLIP 3PE.16: 19 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, G.228, L.229, Y.529, M.533, H.534, T.538, N.541, L.542 Chain M: M.401, L.405 Ligands: 3PE.18 Chain b: N.115, R.116 Ligand excluded by PLIP 3PE.17: 19 residues within 4Å: Chain 8: I.81, Y.85, H.89 Chain L: W.66, H.67, W.68, L.76, S.77, L.78, N.136, F.138, Q.139, I.142 Chain M: P.371, T.448, L.449 Ligands: CDL.20, PC1.24, CDL.45 Ligand excluded by PLIP 3PE.18: 9 residues within 4Å: Chain L: L.184, W.188, H.192, P.209, N.210, M.211, I.214, L.218 Ligands: 3PE.16 Ligand excluded by PLIP 3PE.19: 19 residues within 4Å: Chain L: L.290, I.293, T.294, L.413, I.414, S.417, A.421, R.425, F.429, V.493, M.496, G.497, L.500, L.504, T.508, Y.520 Chain b: F.139, M.140 Chain d: V.32 Ligand excluded by PLIP 3PE.21: 21 residues within 4Å: Chain M: A.155, P.159, V.162, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: E.274, I.276, I.277, T.280, L.281, M.284 Chain Y: L.124, W.133 Ligands: 3PE.25, 3PE.38 Ligand excluded by PLIP 3PE.23: 24 residues within 4Å: Chain 3: Y.35 Chain M: T.90, R.91, L.94, M.98, L.101, F.105, V.127, I.131, R.135, W.136 Chain N: P.238, V.239, S.242, L.243, M.245, V.246, P.256, L.335, P.338 Chain O: T.334, K.340 Ligands: CDL.35, 3PE.41 Ligand excluded by PLIP 3PE.25: 22 residues within 4Å: Chain D: Q.49, M.55, Y.56 Chain L: L.562, P.563, S.567, Q.570, M.571 Chain M: N.144, L.147, F.151, Y.152, G.156 Chain N: L.163, W.167, L.170, M.284, T.285, L.287, Y.291, R.295 Ligands: 3PE.21 Ligand excluded by PLIP 3PE.27: 9 residues within 4Å: Chain L: F.602, Y.604 Chain N: N.152, T.156 Chain Y: K.3, V.135, F.136, E.138 Ligands: 3PE.38 Ligand excluded by PLIP 3PE.36: 9 residues within 4Å: Chain D: E.60 Chain L: M.576, Q.580 Chain Y: Y.39, S.40, L.43, K.44, Y.59 Ligands: 3PE.37 Ligand excluded by PLIP 3PE.37: 15 residues within 4Å: Chain Y: Y.9, S.25, I.28, G.29, T.32, R.55, R.58, Y.59, T.62, S.63, I.66, G.67, F.70 Ligands: 3PE.36, PC1.49 Ligand excluded by PLIP 3PE.38: 11 residues within 4Å: Chain N: I.277, L.281 Chain Y: L.124, V.125, G.128, Q.129, W.133, Q.134, V.135 Ligands: 3PE.21, 3PE.27 Ligand excluded by PLIP 3PE.39: 8 residues within 4Å: Chain Y: P.46, A.47, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.15 Ligand excluded by PLIP 3PE.40: 17 residues within 4Å: Chain 1: L.9, E.16, L.19, V.20, S.22, F.23, G.27, I.30 Chain A: I.96, A.99, A.103, W.106, T.107 Chain H: K.291, P.295, A.299, M.302 Ligand excluded by PLIP 3PE.41: 16 residues within 4Å: Chain 3: F.38, Y.41, C.42, L.45, I.46, A.49, P.54, V.55, V.56 Chain M: W.16, T.90, L.101 Chain O: K.340, Y.341 Ligands: 3PE.23, CDL.35 Ligand excluded by PLIP 3PE.47: 16 residues within 4Å: Chain 9: W.68, W.71, R.72 Chain L: F.44, L.48, M.88, P.91, V.92, F.95, F.334, I.459, F.463, F.466, I.468 Chain e: F.77, L.78 Ligand excluded by PLIP 3PE.50: 15 residues within 4Å: Chain L: L.562 Chain M: L.197, M.201, G.211, L.212, Y.256, M.257, P.260, F.261, L.264 Ligands: PC1.22 Chain c: L.98, Y.102, K.106, D.110 Ligand excluded by PLIP 3PE.51: 18 residues within 4Å: Chain L: W.557, L.558 Chain M: Y.210 Chain Y: R.106, S.107, Y.108, G.109, A.112 Chain c: P.82, T.83, P.84, S.87, L.88, G.90, A.91, G.94, I.95, L.98 Ligand excluded by PLIP

6 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.20: 36 residues within 4Å: Chain 7: L.68 Chain L: I.19, S.22, N.23, Y.27, K.28, L.78, F.80, R.116, K.119, Y.120, L.123, I.130, Q.139, I.142, G.146, I.149, M.150, L.153 Chain M: P.353, L.354, T.357, W.358, L.360, M.361, L.364, L.369, P.370, P.371, S.372, L.442, L.445, L.446, T.448 Ligands: 3PE.17, CDL.45 27 PLIP interactions: 17 interactions with chain L, 9 interactions with chain M, 1 interactions with chain 7 Hydrophobic interactions: L:I.19, L:L.78, L:F.80, L:L.123, L:I.130, L:I.130, L:I.130, L:Q.139, L:I.142, L:I.149, L:L.153, M:W.358, M:L.364, M:L.369, M:L.442, M:L.445, M:L.445, M:L.446, M:T.448, 7:L.68 Hydrogen bonds: L:S.22, L:R.116, L:Y.120, M:T.357 Salt bridges: L:K.28, L:K.119, L:K.119 CDL.26: 19 residues within 4Å: Chain N: P.3, Y.6, T.7, I.10, Q.125, L.128, T.132, W.133, L.136, I.209, L.213, M.217, K.321, M.323, K.324, L.325, M.329 Chain O: P.42, R.295 13 PLIP interactions: 12 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.10, N:W.133, N:L.136, N:I.209, N:L.213, N:L.325 Hydrogen bonds: N:Y.6, N:Y.6, N:Q.125, N:K.324 Salt bridges: N:K.46, N:K.321, O:R.295 CDL.35: 27 residues within 4Å: Chain 3: T.29, P.31, R.32, V.34, Y.35, F.38 Chain 5: L.27, R.30, K.34 Chain M: I.5, I.6, T.9, F.56, L.101, L.104, F.105, M.108, I.120 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: 3PE.23, 3PE.41 26 PLIP interactions: 11 interactions with chain 3, 6 interactions with chain M, 3 interactions with chain N, 3 interactions with chain 5, 3 interactions with chain X Hydrophobic interactions: 3:P.31, 3:V.34, 3:Y.35, 3:Y.35, 3:Y.35, 3:F.38, 3:F.38, 3:F.38, M:I.5, M:I.6, M:F.56, M:L.101, M:F.105, M:I.120, N:P.256, N:L.337, N:P.338, X:F.169 Water bridges: 3:K.27, 3:K.27 Salt bridges: 3:K.27, 5:R.30, 5:K.34, 5:K.34 Hydrogen bonds: X:T.171, X:M.172 CDL.42: 20 residues within 4Å: Chain 2: K.43, T.47, T.50, L.54 Chain 3: M.36, D.47, R.51, R.62, L.65, Y.66, S.69, F.70, F.72, F.73, L.77 Chain N: K.324, L.325, L.332, V.336 Ligands: PC1.43 23 PLIP interactions: 16 interactions with chain 3, 4 interactions with chain 2, 3 interactions with chain N Hydrophobic interactions: 3:L.65, 3:Y.66, 3:Y.66, 3:F.70, 3:F.70, 3:F.72, 3:F.73, 3:F.73, 3:F.73, 3:L.77, 2:T.50, 2:L.54, N:L.332, N:V.336 Hydrogen bonds: 3:R.51, 3:R.62, N:L.325 Water bridges: 3:R.62, 3:R.62, 3:Y.66, 2:K.43 Salt bridges: 3:R.62, 2:K.43 CDL.45: 25 residues within 4Å: Chain 6: A.107, Y.108 Chain 7: A.83, I.86, T.87, N.90, V.91, H.115 Chain 8: W.80, Y.84, Y.85, H.89 Chain L: I.13, N.65, F.80 Chain M: L.446, L.449 Ligands: 3PE.17, CDL.20, PC1.24 Chain f: P.44, V.45, R.49, I.52, H.56 24 PLIP interactions: 5 interactions with chain 7, 3 interactions with chain f, 9 interactions with chain 8, 2 interactions with chain M, 3 interactions with chain 6, 2 interactions with chain L Hydrophobic interactions: 7:A.83, 7:I.86, f:V.45, f:I.52, 8:W.80, 8:W.80, 8:W.80, 8:Y.84, 8:Y.84, 8:Y.84, 8:Y.85, 8:Y.85, M:L.446, M:L.449, 6:A.107, 6:Y.108, L:I.13, L:F.80 Hydrogen bonds: 7:N.90, 7:N.90, 6:Y.108 Salt bridges: 7:H.115, f:R.49, 8:H.89 CDL.55: 18 residues within 4Å: Chain 0: W.2, F.3, L.6, P.7 Chain H: Y.43 Chain I: F.105 Chain g: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 Chain h: S.3, A.4, T.5, V.7, I.8 14 PLIP interactions: 4 interactions with chain g, 4 interactions with chain h, 4 interactions with chain 0, 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: g:R.9, g:R.9, h:T.5, h:T.5 Water bridges: g:Q.13 Salt bridges: g:R.9 Hydrophobic interactions: h:V.7, h:I.8, 0:F.3, 0:L.6, 0:L.6, 0:P.7, H:Y.43, I:F.105

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

GTP.28: 21 residues within 4Å: Chain O: N.67, I.68, C.69, S.70, G.71, K.72, G.73, E.90, L.116, F.119, Y.120, L.133, Q.134, L.137, R.141, R.163, D.168, F.171, E.228, Y.235 Ligands: MG.29 17 PLIP interactions: 17 interactions with chain O Hydrogen bonds: O:C.69, O:S.70, O:K.72, O:G.73, O:Y.120, O:Q.134, O:R.141, O:R.163, O:E.228, O:Y.235 Water bridges: O:E.90 Salt bridges: O:K.72, O:K.72, O:K.72, O:R.163 pi-Stacking: O:F.171, O:F.171

1 x MG: MAGNESIUM ION(Non-covalent)

MG.29: 5 residues within 4Å: Chain O: K.72, E.90, E.162, R.163 Ligands: GTP.28 3 PLIP interactions: 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.90, H2O.71, H2O.71

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

NDP.32: 29 residues within 4Å: Chain B: R.258 Chain P: G.60, A.61, T.62, G.63, F.64, L.65, G.66, R.85, C.86, W.108, L.129, V.130, G.131, R.132, F.139, V.144, F.145, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, S.204, D.205, I.206, R.212 45 PLIP interactions: 4 interactions with chain B, 41 interactions with chain P Water bridges: B:R.258, B:R.258, B:R.258, P:G.63, P:R.85, P:R.85, P:R.85, P:R.85, P:R.85, P:R.85, P:C.86, P:R.132, P:R.132, P:R.132, P:R.132, P:Y.180, P:Y.180, P:D.205, P:E.210, P:D.211, P:R.212, P:R.212, P:R.212 Salt bridges: B:R.258, P:R.85, P:R.132, P:R.132, P:R.212 Hydrophobic interactions: P:I.206, P:I.206 Hydrogen bonds: P:G.60, P:T.62, P:T.62, P:T.62, P:F.64, P:L.65, P:G.66, P:R.85, P:L.129, P:G.131, P:K.184, P:I.206 pi-Stacking: P:F.139 pi-Cation interactions: P:R.85, P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.33: 5 residues within 4Å: Chain R: C.86, G.88, H.95, C.111, C.114 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.86, R:H.95, R:C.111, R:C.114

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)(Non-covalent)

EHZ.34: 18 residues within 4Å: Chain T: S.112 Chain W: K.29, V.32, L.35, W.39, G.59, K.62, V.63, M.66, F.67, N.70, A.71, V.73, V.79, L.82, G.86, F.106, F.107 19 PLIP interactions: 17 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:V.32, W:W.39, W:W.39, W:K.62, W:F.67, W:A.71, W:V.79, W:F.106, W:F.106, W:F.106, W:F.106, W:F.107 Hydrogen bonds: W:K.29, W:N.70, W:A.71, T:S.112 Water bridges: W:R.33, T:S.112 Salt bridges: W:K.29 EHZ.52: 21 residues within 4Å: Chain L: Y.515 Chain U: S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, H.26, M.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, L.64, A.67, E.70, F.71, G.74 13 PLIP interactions: 12 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:A.23, d:H.26, d:R.47, d:F.48, d:E.54, d:A.60, d:A.67, d:F.71 Hydrogen bonds: d:Q.13, d:K.52, U:S.112 Salt bridges: d:K.52

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.48: 11 residues within 4Å: Chain L: N.400, L.413, M.486, T.489, I.492 Chain b: S.152, Y.153, Q.154 Chain e: G.2, H.4, L.5 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain e, 1 interactions with chain b Hydrophobic interactions: L:L.413, L:I.492, L:I.492 Hydrogen bonds: e:G.2 Water bridges: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, W. et al., High-resolution in situ structures of mammalian respiratory supercomplexes. Nature (2024)

Release Date

2024-06-19

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:ubiquinone oxidoreductase subunit A9: 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
NADH:ubiquinone oxidoreductase subunit AB1: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1: 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:ubiquinone oxidoreductase subunit A13: 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:ubiquinone oxidoreductase subunit B2: 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
1A

B
1B

C
1C

D
1D

E
1E

F
1F

G
1G

H
1H

I
1I

J
1J

K
1K

L
1L

M
1M

N
1N

O
1O

P
1P

Q
1Q

R
1R

S
1S

T
1T

U
1U

V
1V

W
1W

X
1X

Y
1Y

Z
1Z

0
1a

1
1b

2
1c

3
1d

4
1e

5
1f

6
1g

7
1h

8
1i

9
1j

a
1k

b
1l

c
1m

d
1n

e
1o

f
1p

g
1q

h
1r

i
1s

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:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH:ubiquinone oxidoreductase subunit AB1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1

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:ubiquinone oxidoreductase subunit A13

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:ubiquinone oxidoreductase subunit B2

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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