SMTL ID : 9f5y.1

Structure of the Chlamydomonas reinhardtii respiratory complex I from respiratory supercomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.146, T.148, P.150, C.151, C.187, M.188, G.189, A.190, C.191 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.146, A:C.151, A:C.187, A:C.191 FES.4: 9 residues within 4Å: Chain C: R.81, C.83, Y.84, G.92, N.93, C.94, R.95, C.97, C.111 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.83, C:C.94, C:C.97, C:C.111

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain B: G.108, R.109, G.110, K.119, N.137, D.139, E.140, S.141, Y.225, G.228, E.229, E.230, V.263, T.264, N.265, T.268, A.447, L.448 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.225, B:Y.225, B:E.229, B:A.447, B:L.448 Hydrogen bonds: B:G.110, B:N.137, B:E.140, B:S.141, B:G.228, B:E.230, B:E.230, B:N.265, B:N.265, B:T.268, B:T.268 Water bridges: B:A.112, B:G.113, B:G.228, B:E.230 Salt bridges: B:K.119

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

SF4.3: 13 residues within 4Å: Chain B: I.226, P.244, S.399, C.400, G.401, Q.402, C.403, C.406, T.444, I.445, C.446, L.448, G.449 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.400, B:C.403, B:C.406, B:C.446 SF4.5: 11 residues within 4Å: Chain C: H.143, D.146, C.147, C.150, Q.152, G.153, C.156, Q.159, V.247, G.248 Chain E: M.379 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.143, C:C.147, C:C.150, C:C.156 SF4.6: 13 residues within 4Å: Chain C: M.192, C.195, I.196, Q.197, C.198, T.199, R.200, C.201, I.225, C.245, V.247, A.249, L.250 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.195, C:C.198, C:C.201, C:C.245 SF4.7: 10 residues within 4Å: Chain E: R.142, H.227 Chain F: A.38, C.39, C.40, G.75, S.103, C.104, C.134, P.135 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.39, F:C.40, F:C.104, F:C.134 SF4.8: 10 residues within 4Å: Chain G: H.120, C.142, I.147, C.171, I.172, Y.173, C.174, G.175, C.177, E.188 6 PLIP interactions: 6 interactions with chain G, Salt bridges: G:E.188 Metal complexes: G:H.120, G:C.142, G:C.171, G:C.174, G:C.177 SF4.9: 12 residues within 4Å: Chain G: C.132, I.133, A.134, C.135, K.136, C.138, I.149, Y.164, C.181, V.183, A.185, I.186 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.132, G:C.135, G:C.138, G:C.181

15 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.10: 20 residues within 4Å: Chain 2: E.14, P.15, V.16, W.19, I.23 Chain G: M.79 Chain Q: P.177, L.180, I.181, L.183, V.184, P.194, A.252, T.256, Y.263, L.271, F.276, L.279 Ligands: 3PH.37 Chain c: M.57 12 PLIP interactions: 10 interactions with chain Q, 2 interactions with chain 2 Hydrophobic interactions: Q:P.177, Q:L.180, Q:I.181, Q:L.183, Q:V.184, Q:P.194, Q:A.252, Q:Y.263, Q:L.271, Q:L.279, 2:W.19, 2:I.23 PTY.16: 8 residues within 4Å: Chain 2: M.17, L.21 Chain R: L.24, R.27 Chain S: V.263, A.267, W.270, G.271 6 PLIP interactions: 4 interactions with chain S, 2 interactions with chain R Hydrophobic interactions: S:V.263, S:A.267, S:W.270, S:W.270 Salt bridges: R:R.27, R:R.27 PTY.18: 20 residues within 4Å: Chain 3: W.53, R.60 Chain R: E.51, V.52, Q.53, A.56, I.59, L.60, L.203, Y.268, G.272, I.273, I.275, I.276, L.279, C.370, F.385, V.386 Ligands: 3PH.15 Chain f: Y.50 10 PLIP interactions: 9 interactions with chain R, 1 interactions with chain 3 Hydrophobic interactions: R:V.52, R:Q.53, R:I.59, R:L.203, R:Y.268, R:I.273, R:I.275, R:L.279, R:F.385 Salt bridges: 3:R.60 PTY.20: 21 residues within 4Å: Chain 4: L.58, L.61, A.62, A.65, A.206 Chain R: L.224, F.225, Q.320, S.323, A.326, A.327, F.330 Ligands: PTY.23, CDL.52 Chain n: L.119, A.122, Y.123, L.130, Y.131, A.134, F.137 16 PLIP interactions: 4 interactions with chain R, 4 interactions with chain 4, 8 interactions with chain n Hydrophobic interactions: R:F.225, R:A.326, R:F.330, 4:A.62, 4:A.65, n:A.122, n:Y.123, n:L.130, n:Y.131, n:A.134, n:F.137, n:F.137 Hydrogen bonds: R:Q.320 Water bridges: 4:R.208, 4:R.208, n:Y.123 PTY.22: 21 residues within 4Å: Chain Q: I.104 Chain S: Y.132, Y.168, Y.170, V.171, T.174, V.175 Chain W: F.2, F.3, E.4, S.6, A.7, I.36, N.37, F.40, L.55 Chain Y: V.15, S.18 Ligands: PC7.14, CDL.35 Chain c: V.142 16 PLIP interactions: 8 interactions with chain W, 6 interactions with chain S, 1 interactions with chain Y, 1 interactions with chain Q Hydrophobic interactions: W:F.2, W:F.3, W:F.3, W:F.40, W:F.40, W:F.40, W:F.40, W:L.55, S:Y.170, S:V.171, S:T.174, S:V.175, Y:V.15, Q:I.104 Hydrogen bonds: S:Y.132, S:Y.132 PTY.23: 21 residues within 4Å: Chain R: F.228, Y.235, F.330, L.333, L.334, V.337, R.341 Chain T: Y.146, K.147, L.150, Y.151, V.205 Chain V: V.541, N.543, L.544 Ligands: PTY.20, PTY.42, CDL.52, CDL.54 Chain g: F.95, Y.96 15 PLIP interactions: 5 interactions with chain T, 1 interactions with chain g, 9 interactions with chain R Hydrophobic interactions: T:K.147, T:L.150, T:Y.151, T:Y.151, T:V.205, R:F.228, R:F.330, R:L.333, R:L.334, R:L.334, R:V.337 Hydrogen bonds: g:Y.96, R:Y.235, R:Y.235, R:R.341 PTY.26: 13 residues within 4Å: Chain 1: G.75, V.78, Y.79, Y.82, H.83, L.87, L.90, Y.94 Chain T: I.432, W.436, K.440, A.443 Ligands: PTY.33 8 PLIP interactions: 3 interactions with chain T, 5 interactions with chain 1 Hydrophobic interactions: T:I.432, T:W.436, 1:V.78 Salt bridges: T:K.440, 1:H.83, 1:H.83, 1:H.83 Hydrogen bonds: 1:Y.94 PTY.28: 9 residues within 4Å: Chain 3: C.16, T.19, V.23, A.28, W.29 Chain R: R.288 Chain T: T.15, L.16 Ligands: PC7.17 4 PLIP interactions: 2 interactions with chain 3, 1 interactions with chain R, 1 interactions with chain T Hydrophobic interactions: 3:T.19 Hydrogen bonds: 3:W.29, R:R.288, T:T.15 PTY.32: 16 residues within 4Å: Chain T: V.395 Chain V: K.164, S.165, Q.167, K.168, L.171, L.224, F.225, D.231, V.520, I.523, F.524 Chain X: A.58, A.59, D.60 Chain m: F.78 10 PLIP interactions: 5 interactions with chain V, 2 interactions with chain m, 3 interactions with chain X Hydrophobic interactions: V:F.225, V:V.520, V:I.523, V:F.524, m:F.78, m:F.78 Salt bridges: V:K.164 Hydrogen bonds: X:D.60, X:D.60, X:D.60 PTY.33: 17 residues within 4Å: Chain T: L.365, I.439, K.440 Chain V: F.7, L.11, L.14, D.61, V.62, F.63, G.64, W.76, F.125 Chain Z: M.68, Y.72, N.76 Ligands: PTY.26, PGT.27 17 PLIP interactions: 7 interactions with chain V, 6 interactions with chain Z, 4 interactions with chain T Hydrophobic interactions: V:F.7, V:L.11, V:L.14, V:F.63, V:F.63, V:W.76, V:F.125, Z:Y.72, Z:Y.72, Z:Y.72, T:L.365, T:I.439, T:K.440 Hydrogen bonds: Z:Y.72, Z:N.76, Z:N.76 Salt bridges: T:K.440 PTY.34: 16 residues within 4Å: Chain 0: W.100 Chain V: W.473, G.474, T.477, L.478, F.480, G.481 Chain l: I.21, W.24, W.25, R.28 Chain o: L.80, W.81, A.84, M.85, F.88 11 PLIP interactions: 6 interactions with chain o, 2 interactions with chain V, 1 interactions with chain 0, 2 interactions with chain l Hydrophobic interactions: o:L.80, o:W.81, o:W.81, o:A.84, o:F.88, o:F.88, V:W.473, V:F.480, l:W.25 Hydrogen bonds: 0:W.100 Salt bridges: l:R.28 PTY.38: 9 residues within 4Å: Chain 4: L.49, A.52, V.53, P.57, A.102, T.105, A.109, V.110, F.113 2 PLIP interactions: 2 interactions with chain 4 Hydrophobic interactions: 4:P.57, 4:T.105 PTY.39: 14 residues within 4Å: Chain 4: F.166, L.170, M.171, Y.174 Chain 7: L.127, E.130 Chain R: F.322, A.326 Chain T: V.158, P.161, T.162, V.187, W.190 Ligands: PTY.42 13 PLIP interactions: 6 interactions with chain T, 3 interactions with chain R, 2 interactions with chain 7, 2 interactions with chain 4 Hydrophobic interactions: T:P.161, T:T.162, T:V.187, T:W.190, T:W.190, T:W.190, R:F.322, R:F.322, R:A.326, 7:L.127, 4:F.166, 4:F.166 Hydrogen bonds: 7:E.130 PTY.42: 15 residues within 4Å: Chain 7: L.97, T.101, Y.105, L.127 Chain T: L.193, A.197, P.204, L.254, T.257, L.258, F.265 Chain V: L.539 Ligands: PTY.23, PTY.39, 3PH.41 9 PLIP interactions: 7 interactions with chain T, 1 interactions with chain V, 1 interactions with chain 7 Hydrophobic interactions: T:L.193, T:A.197, T:L.254, T:T.257, T:L.258, T:F.265, T:F.265, V:L.539, 7:L.97 PTY.53: 4 residues within 4Å: Chain W: I.103, P.109 Chain n: W.118, E.121 2 PLIP interactions: 1 interactions with chain W, 1 interactions with chain n Hydrophobic interactions: W:I.103, n:W.118

2 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Non-covalent)

8Q1.11: 14 residues within 4Å: Chain J: D.84, S.85 Chain K: R.18, A.24, F.27, I.31, F.61, Y.64, K.65, V.67, V.73, I.77, I.84, Y.87 13 PLIP interactions: 4 interactions with chain J, 9 interactions with chain K Hydrogen bonds: J:S.85, J:S.85, J:S.85, J:L.86, K:R.18, K:Y.64, K:K.65 Hydrophobic interactions: K:F.27, K:I.31, K:F.61, K:F.61, K:V.67, K:V.73 8Q1.45: 16 residues within 4Å: Chain a: H.11, K.12, V.15, M.18, F.47, S.50, K.51, I.59, K.62, L.63, G.66, L.69, L.70 Chain h: D.84, S.85 Chain o: I.50 15 PLIP interactions: 10 interactions with chain a, 3 interactions with chain h, 2 interactions with chain o Hydrophobic interactions: a:V.15, a:F.47, a:I.59, a:L.69, a:L.69, a:L.70, a:L.70, o:I.50, o:I.50 Hydrogen bonds: a:H.11, a:S.50, a:S.50, h:S.85, h:S.85, h:S.85

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

NDP.12: 22 residues within 4Å: Chain F: K.164 Chain P: G.60, N.62, G.63, F.64, L.65, R.85, S.86, I.111, C.130, V.131, G.132, R.134, W.140, S.170, D.171, K.186, P.205, G.206, D.207, I.208, H.214 29 PLIP interactions: 28 interactions with chain P, 1 interactions with chain F Hydrophobic interactions: P:P.205, P:I.208 Hydrogen bonds: P:G.60, P:N.62, P:F.64, P:L.65, P:R.85, P:S.86, P:S.86, P:C.130, P:G.132, P:R.134, P:W.140, P:K.186, P:G.206, P:I.208 Water bridges: P:G.66, P:R.85, P:R.85, P:I.111, P:H.214 Salt bridges: P:R.85, P:R.134, P:R.134, P:H.214, P:H.214, F:K.164 pi-Cation interactions: P:R.85, P:R.85

1 x UQ5: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE(Non-covalent)

UQ5.13: 12 residues within 4Å: Chain F: W.31, I.60, R.62 Chain Q: T.21, R.25, F.49, D.51, G.52, F.219, I.220, Y.223, R.257 8 PLIP interactions: 4 interactions with chain Q, 4 interactions with chain F Hydrophobic interactions: Q:F.49, Q:D.51, Q:I.220, Q:I.220, F:W.31, F:W.31, F:I.60 Hydrogen bonds: F:R.62

4 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.14: 8 residues within 4Å: Chain Q: M.1, I.2, V.3, L.7 Chain S: Y.168, I.172, I.176 Ligands: PTY.22 2 PLIP interactions: 2 interactions with chain Q Hydrophobic interactions: Q:L.7, Q:L.7 PC7.17: 14 residues within 4Å: Chain R: R.288, L.289, A.291, L.292, W.347, A.349, V.351 Chain T: L.12, A.95, M.98, T.99, L.102, L.132 Ligands: PTY.28 12 PLIP interactions: 5 interactions with chain T, 1 interactions with chain a, 6 interactions with chain R Hydrophobic interactions: T:M.98, T:T.99, T:L.102, T:L.132, R:L.289, R:A.291, R:L.292, R:W.347 Water bridges: T:A.95, a:L.117 pi-Cation interactions: R:W.347, R:W.347 PC7.25: 30 residues within 4Å: Chain 1: Y.82, L.90, I.92 Chain 4: F.3, S.4, G.5 Chain T: W.44, F.47, A.49, G.51, H.52, G.53, G.71, V.72, L.74, S.75, L.78, V.82, Y.304, S.307, F.308, I.311, L.315, P.429, I.432, G.433, L.437, P.441 Chain e: R.32, Y.63 15 PLIP interactions: 13 interactions with chain T, 1 interactions with chain 4, 1 interactions with chain e Hydrophobic interactions: T:W.44, T:V.72, T:L.78, T:V.82, T:Y.304, T:F.308, T:F.308, T:I.311, T:L.315, T:I.432, T:L.437, T:L.437 Water bridges: T:G.71, 4:G.5 Hydrogen bonds: e:Y.63 PC7.48: 16 residues within 4Å: Ligands: CDL.49 Chain b: V.59, Y.62, Y.63, A.66 Chain i: H.18, L.24, E.26, T.28, L.29, F.36 Chain k: V.28, R.31, L.32, Q.33, G.34 11 PLIP interactions: 5 interactions with chain i, 3 interactions with chain b, 3 interactions with chain k Hydrophobic interactions: i:L.24, i:T.28, i:L.29, i:L.29, b:V.59, b:Y.62, b:Y.62, k:V.28, k:L.32 Salt bridges: i:E.26 Water bridges: k:Y.36

8 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.15: 8 residues within 4Å: Chain 3: F.47, A.50 Chain R: L.50, V.52, F.55, A.56 Ligands: PTY.18, CDL.19 2 PLIP interactions: 2 interactions with chain 3 Hydrophobic interactions: 3:F.47, 3:A.50 3PH.21: 10 residues within 4Å: Chain 2: Y.24, A.32, F.33 Chain R: F.13 Chain S: W.253, N.256, L.257, A.260 Ligands: PGT.44 Chain b: I.35 4 PLIP interactions: 1 interactions with chain S, 2 interactions with chain 2, 1 interactions with chain R Hydrophobic interactions: S:A.260, 2:A.32, 2:F.33, R:F.13 3PH.29: 9 residues within 4Å: Chain 6: K.25, R.26 Chain V: S.369, I.373, T.418, F.421 Ligands: 3PH.40 Chain o: F.66, Y.74 5 PLIP interactions: 1 interactions with chain o, 2 interactions with chain 6, 2 interactions with chain V Hydrophobic interactions: o:F.66, V:I.373, V:F.421 Salt bridges: 6:K.25, 6:R.26 3PH.30: 10 residues within 4Å: Chain V: I.223, L.224, M.265, F.266, I.269, L.273 Chain X: G.83, A.87, F.90, A.94 7 PLIP interactions: 5 interactions with chain V, 2 interactions with chain X Hydrophobic interactions: V:I.223, V:L.224, V:F.266, V:F.266, V:I.269, X:F.90, X:A.94 3PH.37: 3 residues within 4Å: Chain 2: V.26 Ligands: PTY.10 Chain c: H.65 2 PLIP interactions: 1 interactions with chain c, 1 interactions with chain 2 Salt bridges: c:H.65 Hydrophobic interactions: 2:V.26 3PH.40: 14 residues within 4Å: Chain 0: K.78, A.84, L.89 Chain 6: K.25, R.26, F.29, P.30, G.31, V.32, G.33, I.34, F.36 Chain V: W.375 Ligands: 3PH.29 10 PLIP interactions: 7 interactions with chain 6, 3 interactions with chain 0 Hydrophobic interactions: 6:F.29, 6:F.36, 0:A.84, 0:L.89 Hydrogen bonds: 6:F.29, 6:G.31, 6:G.31, 6:G.33, 6:I.34 Salt bridges: 0:K.78 3PH.41: 20 residues within 4Å: Chain 7: G.98, F.100, T.101, A.102, A.103, A.104, Y.105, A.106, V.109, F.110, R.113 Chain T: L.260, V.261, L.264 Chain V: L.538 Ligands: PTY.42, 3PH.51 Chain m: F.79, V.82, I.86 13 PLIP interactions: 4 interactions with chain m, 6 interactions with chain 7, 2 interactions with chain T, 1 interactions with chain V Hydrophobic interactions: m:F.79, m:F.79, m:V.82, m:I.86, 7:F.100, 7:A.102, 7:A.104, 7:Y.105, 7:A.106, T:V.261, T:L.264, V:L.538 Hydrogen bonds: 7:R.113 3PH.51: 7 residues within 4Å: Chain 7: A.102, A.103 Ligands: 3PH.41 Chain m: M.72, Y.90, T.93, D.97 3 PLIP interactions: 3 interactions with chain m Hydrophobic interactions: m:Y.90 Hydrogen bonds: m:D.97 Water bridges: m:D.89

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 17 residues within 4Å: Chain 3: L.46 Chain R: F.38, Q.41, C.42, V.45, M.46, I.59, Q.363, L.366, T.367 Ligands: 3PH.15, CDL.49 Chain b: L.56, A.60, Y.63, F.64, K.67 13 PLIP interactions: 7 interactions with chain R, 1 interactions with chain 3, 5 interactions with chain b Hydrophobic interactions: R:F.38, R:Q.41, R:V.45, R:V.45, R:I.59, R:L.366, 3:L.46, b:L.56, b:A.60 Water bridges: R:L.366 Hydrogen bonds: b:Y.63, b:Y.63 Salt bridges: b:K.67 CDL.31: 15 residues within 4Å: Chain V: F.276, T.284, M.411, L.412, G.495, S.496, E.497, R.498, C.505 Chain X: F.82 Chain l: Y.7, N.8, L.11, L.12 Chain o: L.86 12 PLIP interactions: 6 interactions with chain V, 4 interactions with chain l, 1 interactions with chain o, 1 interactions with chain X Hydrophobic interactions: V:F.276, V:T.284, V:L.412, l:Y.7, l:L.11, l:L.12, o:L.86, X:F.82 Hydrogen bonds: V:E.497, l:N.8 Salt bridges: V:R.498, V:R.498 CDL.35: 33 residues within 4Å: Chain Q: G.69, A.70, A.73, M.76, I.77, V.80, L.107, Y.110 Chain S: T.174, T.178 Chain W: L.10, L.13, I.16, Y.20, T.21, S.23, M.26, M.29, Y.30, V.32, M.33, I.36, V.59 Chain Y: L.3, N.6, I.7, T.9, F.10, A.11, A.13, V.14, V.15 Ligands: PTY.22 31 PLIP interactions: 11 interactions with chain W, 10 interactions with chain Y, 9 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: W:L.10, W:L.13, W:I.16, W:Y.20, W:V.32, W:M.33, W:I.36, W:V.59, Y:F.10, Y:F.10, Y:F.10, Y:F.10, Y:A.11, Y:A.13, Y:V.14, Y:V.15, Q:A.73, Q:M.76, Q:I.77, Q:I.77, Q:L.107, Q:Y.110, Q:Y.110, S:T.174 Hydrogen bonds: W:T.21, W:S.23, W:S.23, Y:N.6, Q:G.69, Q:A.70 Water bridges: Y:T.9 CDL.43: 14 residues within 4Å: Chain 4: A.135, F.139, M.147, P.148, P.150, V.151, P.154, L.155 Chain 7: W.85, N.86, Y.87, T.90, L.94 Ligands: CDL.54 15 PLIP interactions: 7 interactions with chain 4, 8 interactions with chain 7 Hydrophobic interactions: 4:A.135, 4:F.139, 4:F.139, 4:V.151, 4:P.154, 4:L.155, 4:L.155, 7:W.85, 7:W.85, 7:Y.87, 7:T.90, 7:L.94, 7:L.94 Hydrogen bonds: 7:Y.87, 7:T.90 CDL.49: 18 residues within 4Å: Chain 3: F.17, Y.34, G.37, A.38, G.39, A.42 Chain R: L.366, A.373 Ligands: CDL.19, PC7.48 Chain i: L.43 Chain k: M.18, S.21, A.24, L.25, R.27, V.28, R.31 13 PLIP interactions: 4 interactions with chain k, 6 interactions with chain 3, 1 interactions with chain i, 2 interactions with chain R Hydrophobic interactions: k:A.24, 3:F.17, 3:F.17, 3:Y.34, 3:Y.34, 3:Y.34, 3:A.42, i:L.43, R:L.366, R:A.373 Salt bridges: k:R.27, k:R.31, k:R.31 CDL.50: 23 residues within 4Å: Chain 3: F.15, W.29, F.30, P.33, H.36, M.40 Chain T: C.13, L.16, P.18, H.21, M.24 Chain j: R.228 Chain k: N.2, P.3, N.5, G.6, T.9, I.10, R.13, V.14, A.17, R.52, H.53 18 PLIP interactions: 10 interactions with chain k, 4 interactions with chain 3, 3 interactions with chain T, 1 interactions with chain j Hydrophobic interactions: k:I.10, k:I.10, k:R.13, k:V.14, k:A.17, 3:F.15, 3:W.29, 3:F.30, 3:H.36, T:L.16, T:L.16 Hydrogen bonds: k:T.9 Salt bridges: k:R.13, k:R.52, k:R.52, k:H.53, T:H.21, j:R.228 CDL.52: 35 residues within 4Å: Chain 4: L.61, A.65, A.68, Q.69, W.153 Chain R: P.177, H.179, M.180, L.224, F.225, F.228, I.229, I.232, G.233, Y.246 Chain V: L.544 Ligands: PTY.20, PTY.23, CDL.54 Chain n: T.104, Y.107, L.108, A.111, F.115, A.116, A.134, F.137, F.138, Y.141, R.143, K.144, A.145 Chain o: L.6, I.10, W.12 34 PLIP interactions: 17 interactions with chain n, 3 interactions with chain o, 11 interactions with chain R, 3 interactions with chain 4 Hydrophobic interactions: n:T.104, n:Y.107, n:L.108, n:A.111, n:F.115, n:F.115, n:F.137, n:F.137, n:F.138, n:F.138, n:F.138, n:Y.141, o:L.6, o:I.10, o:W.12, R:P.177, R:L.224, R:L.224, R:F.225, R:F.228, R:I.229, R:I.232, 4:L.61, 4:A.68, 4:W.153 Hydrogen bonds: n:K.144, n:A.145, R:Y.246, R:Y.246 Water bridges: n:R.143 Salt bridges: n:R.143, n:R.143, R:H.179, R:H.179 CDL.54: 18 residues within 4Å: Chain 4: P.148, A.152, L.155, A.156 Chain 7: W.85 Chain V: L.538, L.539, V.541, G.542, N.543, L.544 Ligands: PTY.23, CDL.43, CDL.52 Chain o: I.10, R.11, W.12, R.13 8 PLIP interactions: 1 interactions with chain 7, 2 interactions with chain V, 5 interactions with chain o Hydrophobic interactions: 7:W.85, V:L.538 Hydrogen bonds: V:G.542, o:R.11, o:R.13 Water bridges: o:R.13 Salt bridges: o:R.13, o:R.13

4 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.24: 17 residues within 4Å: Chain T: M.1, S.4, I.8, A.11, A.32, P.36, V.39, W.42, M.43, M.56, L.57, V.58, F.67, I.69, E.104, L.108 Chain f: E.24 13 PLIP interactions: 11 interactions with chain T, 2 interactions with chain f Hydrophobic interactions: T:I.8, T:A.11, T:P.36, T:V.58, T:F.67, T:F.67, T:F.67, T:E.104, T:L.108 Hydrogen bonds: T:M.1, T:M.1, f:E.24, f:E.24 PGT.27: 23 residues within 4Å: Chain T: G.343, A.344, P.347, S.350, T.351, F.354, P.364, F.405 Chain V: T.17, H.111, L.114, Y.118, Y.121, F.125, E.143, G.144, V.147, L.151, Y.155, S.157 Chain Z: Y.39, H.41 Ligands: PTY.33 11 PLIP interactions: 2 interactions with chain Z, 9 interactions with chain V Salt bridges: Z:H.41, Z:H.41, V:H.111 Hydrophobic interactions: V:L.114, V:Y.121, V:Y.121, V:F.125, V:V.147 Water bridges: V:H.111, V:G.154, V:H.158 PGT.36: 10 residues within 4Å: Chain 1: G.32, S.33, F.34, W.35 Chain V: I.31, I.34, G.35, M.100, V.440, L.441 6 PLIP interactions: 2 interactions with chain 1, 4 interactions with chain V Hydrophobic interactions: 1:F.34, V:I.31, V:I.34, V:V.440, V:L.441 Hydrogen bonds: 1:G.32 PGT.44: 18 residues within 4Å: Chain R: M.6, E.8, L.9, C.12, F.13, L.17 Chain S: W.253, T.254, L.257 Chain W: D.135, I.138 Ligands: 3PH.21 Chain b: F.17, D.32, P.33, N.34, I.35, K.84 14 PLIP interactions: 4 interactions with chain R, 4 interactions with chain W, 6 interactions with chain b Hydrophobic interactions: R:E.8, R:L.9, R:F.13, R:L.17, W:D.135, W:I.138, W:I.138, W:I.138, b:F.17, b:F.17, b:I.35, b:I.35, b:K.84 Hydrogen bonds: b:D.32

1 x COO: CROTONYL COENZYME A(Non-covalent)

COO.46: 23 residues within 4Å: Chain g: T.45 Chain i: Q.150, H.179, L.193, G.195, M.196, A.213, A.214, V.229, L.238, R.239, S.252, Y.256 Chain j: H.118, R.146, C.163, E.164, V.179, P.181, P.182, R.184, S.195, P.196 9 PLIP interactions: 7 interactions with chain i, 2 interactions with chain j Hydrophobic interactions: i:A.213, i:V.229 Hydrogen bonds: i:A.214, i:A.214, i:R.239, i:S.252 Salt bridges: i:R.239, j:R.184, j:R.184

1 x ZN: ZINC ION(Non-covalent)

ZN.47: 3 residues within 4Å: Chain i: H.156, H.184 Chain k: H.129 3 PLIP interactions: 2 interactions with chain i, 1 Ligand-Water interactions Metal complexes: i:H.156, i:H.184, H2O.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waltz, F. et al., In-cell architecture of the mitochondrial respiratory chain. Science (2025)

Release Date

2025-03-12

Peptides

NADH:ubiquinone oxidoreductase 24 kD subunit: A
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: B
NADH:ubiquinone oxidoreductase 78 kDa subunit: C
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein: D
NADH:ubiquinone oxidoreductase 49 kD subunit: E
NADH:ubiquinone oxidoreductase subunit 10: F
NADH:ubiquinone oxidoreductase subunit 8: G
B14.5a: H
Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit: I
Acyl carrier protein: Jh
NADH:ubiquinone oxidoreductase B14 subunit: K
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: L
NADH:ubiquinone oxidoreductase 13 kD-like subunit: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: N
NADH:ubiquinone oxidoreductase B8 subunit: O
Putative NADH:ubiquinone oxidoreductase 39 kDa subunit: P
NADH-ubiquinone oxidoreductase chain 1: Q
NADH-ubiquinone oxidoreductase chain 2: R
NADH-ubiquinone oxidoreductase chain 3: S
NADH-ubiquinone oxidoreductase chain 4: T
NADH dehydrogenase subunit 4L: U
NADH-ubiquinone oxidoreductase chain 5: V
NADH-ubiquinone oxidoreductase chain 6: W
ASHI: X
P9: Y
KFYI: Z
AGGG: 0
ESSS: 1
B9: 2
Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit: 3
Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit: 4
Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit: 5
Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit: 6
Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit: 7
NADH:ubiquinone oxidoreductase 15 kDa subunit-like: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: a
NADH:ubiquinone oxidoreductase 20,9 kD-like subunit: b
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: c
Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit: d
Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit: e
Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit: f
Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit: g
Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit: i
CAG2 - CA-like: j
CAG1: k
P10: l
Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit: m
NUOP8: n
NUOP7: o

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

h
r

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

i
s

j
t

k
u

l
v

m
w

n
x

o
y

Membrane

We predict this structure to be a membrane protein.
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NADH:ubiquinone oxidoreductase 24 kD subunit

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH:ubiquinone oxidoreductase 78 kDa subunit

NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein

NADH:ubiquinone oxidoreductase 49 kD subunit

NADH:ubiquinone oxidoreductase subunit 10

NADH:ubiquinone oxidoreductase subunit 8

B14.5a

Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit

Acyl carrier protein

NADH:ubiquinone oxidoreductase B14 subunit

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

NADH:ubiquinone oxidoreductase 13 kD-like subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH:ubiquinone oxidoreductase B8 subunit

Putative NADH:ubiquinone oxidoreductase 39 kDa subunit

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4

NADH dehydrogenase subunit 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

ASHI

P9

KFYI

AGGG

ESSS

B9

Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit

Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit

NADH:ubiquinone oxidoreductase 15 kDa subunit-like

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH:ubiquinone oxidoreductase 20,9 kD-like subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit

Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit

Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit

CAG2 - CA-like

CAG1

P10

Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit

NUOP8

NUOP7