SMTL ID : 6zkf.1

Complex I during turnover, open3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.379, A:C.385, A:C.425 SF4.5: 13 residues within 4Å: Chain C: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 Chain D: M.375 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.127 Metal complexes: C:H.124, C:C.128, C:C.131, C:C.137 SF4.6: 13 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.176, C:C.179, C:C.182, C:C.226 SF4.10: 15 residues within 4Å: Chain D: R.118, R.138, H.223 Chain F: A.97, C.98, C.99, G.134, T.135, G.161, S.162, C.163, Y.170, G.192, C.193, P.194 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.98, F:C.163, F:C.193 SF4.13: 12 residues within 4Å: Chain G: H.106, C.128, P.129, I.133, C.157, I.158, Y.159, C.160, G.161, F.162, C.163, E.174 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.174 Metal complexes: G:C.128, G:C.157, G:C.163 SF4.14: 14 residues within 4Å: Chain G: C.118, I.119, A.120, C.121, K.122, L.123, C.124, I.135, Y.150, C.167, P.168, V.169, A.171, I.172 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.118, G:C.121, G:C.124, G:C.167

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.87, R.88, G.89, G.90, K.98, N.116, D.118, E.119, G.120, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 Ligands: NAI.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.208, A:E.208, A:A.426, A:L.427 Hydrogen bonds: A:R.88, A:G.89, A:G.90, A:N.116, A:E.119, A:G.120, A:G.207, A:E.209, A:N.244 Salt bridges: A:K.98

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 17 residues within 4Å: Chain A: G.89, G.90, A.91, F.93, K.98, F.101, E.119, G.120, E.121, Y.204, E.209, F.229, S.323, G.350, T.351, A.426 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.121, A:Y.204, A:T.351 Hydrogen bonds: A:G.89, A:K.98, A:G.120, A:E.121, A:E.209, A:S.323 Salt bridges: A:K.226 pi-Stacking: A:F.93, A:F.229

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

FES.4: 9 residues within 4Å: Chain B: C.132, T.134, P.136, C.137, C.173, L.174, G.175, A.176, C.177 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.137, B:C.173, B:C.177 FES.7: 9 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.64, C:C.75, C:C.78, C:C.92

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain C: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:I.223, C:C.226, C:V.228, C:L.231

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

3PE.9: 20 residues within 4Å: Chain D: W.43, Q.46, Y.47, M.52, Y.53 Chain L: L.562, P.563, S.567, Q.570, M.571 Chain M: N.144, Y.148, F.151, Y.152 Chain N: I.284, L.287, L.288, Y.291 Ligands: PC1.26, CDL.33 16 PLIP interactions: 2 interactions with chain D, 4 interactions with chain L, 5 interactions with chain M, 5 interactions with chain N Hydrogen bonds: D:Q.46, D:Y.53, M:N.144 Hydrophobic interactions: L:L.562, L:L.562, L:P.563, M:Y.148, M:F.151, M:Y.152, M:Y.152, N:L.287, N:L.288, N:Y.291, N:Y.291, N:Y.291 Salt bridges: L:K.564 3PE.16: 16 residues within 4Å: Chain 5: V.12, E.16, L.19, V.20, S.22, F.23, A.24, A.26, G.27 Chain H: F.96, A.99, L.102, A.103, W.106 Chain I: P.295, M.302 12 PLIP interactions: 4 interactions with chain H, 7 interactions with chain 5, 1 interactions with chain I Hydrophobic interactions: H:F.96, H:A.99, H:L.102, H:A.103, 5:V.12, 5:F.23, 5:F.23, 5:F.23, 5:F.23, 5:F.23, 5:A.26, I:P.295 3PE.18: 25 residues within 4Å: Chain 9: F.140, I.141, W.142, T.144 Chain H: L.3, M.4, L.7, F.11 Chain I: L.77, L.81, M.98, N.99, F.104, M.108 Chain J: L.31, I.34, V.35, G.38, G.42, L.45, N.46, S.50, L.54, F.57 Chain i: H.40 18 PLIP interactions: 3 interactions with chain H, 8 interactions with chain J, 6 interactions with chain I, 1 interactions with chain i Hydrophobic interactions: H:L.7, H:L.7, H:F.11, J:L.31, J:I.34, J:V.35, J:L.54, J:F.57, J:F.57, I:L.77, I:L.81, I:F.104, I:F.104 Hydrogen bonds: J:S.50, J:S.50, I:N.99, I:L.100, i:H.40 3PE.19: 15 residues within 4Å: Chain J: S.21, K.23, V.88, T.92, T.95, G.96 Chain K: V.14, T.17, M.21, Y.22, R.23 Chain L: K.585, L.592, L.596 Ligands: 3PE.30 11 PLIP interactions: 3 interactions with chain L, 4 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: L:L.592, L:L.596, J:T.92, J:T.92, J:T.95, K:V.14, K:V.14, K:M.21 Salt bridges: L:K.585, J:K.23 Hydrogen bonds: K:R.23 3PE.20: 23 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, I.217, L.218, T.221, F.227, G.228, L.229, L.280, Y.529, M.533, H.534, T.537, P.538, N.541 Chain M: L.405 Chain e: N.115, R.116, V.117 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain e Hydrophobic interactions: L:L.173, L:Y.174, L:I.177, L:I.217, L:T.221, L:L.229, L:L.280, L:T.537, L:P.538, L:N.541, e:R.116 Salt bridges: L:H.534, L:H.534 3PE.23: 6 residues within 4Å: Chain 6: V.64 Chain L: M.383, T.494, I.495, F.498, I.499 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:T.494, L:I.495, L:I.495, L:F.498, L:F.498, L:F.498 3PE.24: 16 residues within 4Å: Chain L: L.558, I.561, L.562 Chain M: N.188, W.190, F.194, Y.210, G.211, F.256, M.257, P.260, F.261, L.264 Chain O: L.88, M.127 Ligands: CDL.33 13 PLIP interactions: 8 interactions with chain M, 3 interactions with chain L, 2 interactions with chain O Hydrophobic interactions: M:W.190, M:F.194, M:F.194, M:P.260, M:F.261, M:F.261, M:L.264, L:L.558, L:I.561, L:L.562, O:L.88, O:L.88 Hydrogen bonds: M:N.188 3PE.28: 18 residues within 4Å: Chain 4: P.2 Chain N: K.46, S.125, L.128, I.129, T.132, W.133, L.136, I.206, I.209, I.210, S.213, T.217, M.220, R.322, T.324, L.325, M.329 12 PLIP interactions: 11 interactions with chain N, 1 interactions with chain 4 Hydrophobic interactions: N:L.128, N:I.129, N:W.133, N:I.206, N:I.209, N:I.210, N:T.217, N:L.325, 4:P.2 Hydrogen bonds: N:S.125, N:S.125 Salt bridges: N:K.46 3PE.29: 11 residues within 4Å: Chain 4: P.2 Chain 7: Q.8, P.12, L.13, F.15, R.80 Chain N: Y.143, I.206, I.345, L.346 Ligands: CDL.44 8 PLIP interactions: 2 interactions with chain N, 5 interactions with chain 7, 1 interactions with chain 4 Hydrophobic interactions: N:I.206, N:L.346, 7:F.15 Hydrogen bonds: 7:L.13, 7:F.15, 7:R.80, 4:F.3 Salt bridges: 7:R.80 3PE.30: 12 residues within 4Å: Chain L: L.589, I.593 Chain O: L.34, A.38, V.41, P.46, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.19 9 PLIP interactions: 7 interactions with chain O, 2 interactions with chain L Hydrophobic interactions: O:L.34, O:A.38, O:V.41, O:F.49, O:V.53, O:T.56, L:L.589, L:I.593 Hydrogen bonds: O:F.49 3PE.31: 11 residues within 4Å: Chain N: I.277 Chain O: L.6, W.10, L.124, V.125, G.128, Q.129, W.133, K.134 Ligands: PC1.26, CDL.32 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: O:L.6, O:L.124, N:I.277 Salt bridges: O:K.134, O:K.134 3PE.34: 13 residues within 4Å: Chain 8: P.83, N.84, T.85, S.88, L.89, G.91, A.92 Chain L: W.557, L.558 Chain O: Y.108, G.109, A.112 Ligands: CDL.33 7 PLIP interactions: 4 interactions with chain L, 2 interactions with chain 8, 1 interactions with chain O Hydrophobic interactions: L:W.557, L:W.557, L:W.557, L:L.558, O:A.112 Hydrogen bonds: 8:T.85, 8:T.85 3PE.41: 15 residues within 4Å: Chain 1: R.29, W.75, V.77 Chain F: Y.72, V.73, D.79, L.80, W.83, R.86, K.212 Chain I: L.46, I.49, I.53 Ligands: PC1.11, 3PE.42 14 PLIP interactions: 10 interactions with chain F, 1 interactions with chain 1, 3 interactions with chain I Hydrophobic interactions: F:Y.72, F:V.73, F:D.79, F:W.83, F:W.83, F:W.83, I:L.46, I:I.49, I:I.53 Salt bridges: F:R.86, F:R.86, F:K.212, F:K.212 Hydrogen bonds: 1:R.29 3PE.42: 7 residues within 4Å: Chain 1: F.28, F.74, W.75 Chain I: F.19, P.42, L.46 Ligands: 3PE.41 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain 1 Hydrophobic interactions: I:F.19, I:P.42, I:L.46 Hydrogen bonds: 1:W.75

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

PC1.11: 14 residues within 4Å: Chain F: L.77, I.81, L.217, W.220, R.223 Chain H: L.24, L.27, N.28, V.29, Y.30 Chain I: I.53, F.56 Chain W: D.90 Ligands: 3PE.41 11 PLIP interactions: 6 interactions with chain F, 3 interactions with chain I, 1 interactions with chain W, 1 interactions with chain H Hydrophobic interactions: F:L.77, F:I.81, F:I.81, F:W.220, F:W.220, I:I.53, I:F.56, I:F.56, H:L.24 Salt bridges: F:R.223, W:D.90 PC1.12: 26 residues within 4Å: Chain 5: K.15, E.16, I.25, L.28 Chain 9: F.36, I.40 Chain D: R.266 Chain G: T.65, L.66, W.68, L.71, L.75 Chain I: W.179, P.180, M.183, M.184, F.186, I.187, P.197, Y.277, F.280, H.287, L.288, N.292, F.293, L.296 21 PLIP interactions: 11 interactions with chain I, 3 interactions with chain 5, 3 interactions with chain G, 2 interactions with chain 9, 2 interactions with chain D Hydrophobic interactions: I:W.179, I:P.180, I:P.180, I:M.183, I:F.186, I:F.186, I:P.197, I:F.280, I:L.288, I:F.293, I:L.296, 5:I.25, 5:L.28, G:W.68, G:L.71, G:L.75, 9:F.36, 9:I.40 Salt bridges: 5:E.16, D:R.266, D:R.266 PC1.15: 7 residues within 4Å: Chain 4: L.14 Chain H: N.83, T.86 Chain J: Y.149, T.151, W.152, I.155 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain J, 1 interactions with chain 4 Hydrogen bonds: H:N.83, H:T.86 Hydrophobic interactions: J:W.152, J:I.155, 4:L.14 PC1.21: 19 residues within 4Å: Chain L: W.66, H.67, W.68, L.76, S.77, L.78, F.138, I.142 Chain M: P.371, L.449 Ligands: CDL.22, PC1.25, CDL.35 Chain a: I.81, Y.84, Y.85, H.89, K.93 Chain f: E.116 25 PLIP interactions: 13 interactions with chain L, 9 interactions with chain a, 2 interactions with chain M, 1 interactions with chain f Hydrophobic interactions: L:W.66, L:W.66, L:W.66, L:W.68, L:W.68, L:W.68, L:W.68, L:L.76, L:L.78, L:F.138, L:F.138, L:I.142, a:I.81, a:Y.84, a:Y.84, a:Y.85, a:Y.85, a:H.89, M:P.371, M:P.371 Hydrogen bonds: L:H.67 Salt bridges: a:H.89, a:K.93, a:K.93, f:E.116 PC1.25: 22 residues within 4Å: Chain L: T.16, W.66, L.123 Chain M: P.64, I.67, L.68, W.71, L.446, L.447, L.449, N.450, I.454 Ligands: PC1.21, CDL.22, CDL.35 Chain f: V.98, L.99, G.102, S.103, V.106, A.107, Y.108 12 PLIP interactions: 9 interactions with chain M, 2 interactions with chain L, 1 interactions with chain f Hydrophobic interactions: M:P.64, M:L.68, M:W.71, M:W.71, M:L.446, M:L.447, M:L.447, M:L.449, M:I.454, L:T.16, L:L.123, f:V.98 PC1.26: 25 residues within 4Å: Chain L: I.566 Chain M: Y.152, A.155, G.156, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Chain N: D.274, I.276, I.277, T.280, L.281, I.284 Chain O: L.124, E.131, W.133 Ligands: 3PE.9, 3PE.31, CDL.33 20 PLIP interactions: 5 interactions with chain N, 9 interactions with chain M, 5 interactions with chain O, 1 interactions with chain L Hydrophobic interactions: N:I.276, N:I.277, N:T.280, N:L.281, N:I.284, M:P.159, M:P.159, M:F.194, M:L.197, M:L.197, M:A.198, M:M.201, M:V.205, O:L.124, O:L.124, O:W.133, O:W.133, O:W.133, L:I.566 Hydrogen bonds: M:Y.166

1 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.17: 11 residues within 4Å: Chain F: W.90 Chain I: T.21, R.25, D.51, A.52, L.55, F.56, F.220, A.221, F.224, M.225 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:T.21, I:A.52, I:L.55, I:F.56, I:F.56, I:A.221, I:F.224 Hydrogen bonds: I:D.51 pi-Stacking: I:F.224

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.22: 38 residues within 4Å: Chain L: I.22, N.23, F.24, L.78, Q.116, K.119, Y.120, L.123, T.127, I.130, Q.139, I.142, M.150, L.153 Chain M: P.353, L.354, A.357, W.358, L.360, L.361, L.364, L.369, P.370, P.371, S.372, L.442, L.445, L.446, S.448, L.449 Chain P: L.68, R.72, I.75 Ligands: PC1.21, PC1.25, CDL.35 Chain f: L.99, S.103 21 PLIP interactions: 2 interactions with chain P, 11 interactions with chain L, 6 interactions with chain M, 2 interactions with chain f Hydrophobic interactions: P:R.72, P:I.75, L:F.24, L:L.78, L:T.127, L:I.130, L:Q.139, L:I.142, L:I.142, M:W.358, M:L.361, M:L.361, M:L.442, M:L.442, M:L.446, f:L.99, f:L.99 Hydrogen bonds: L:Q.116, L:Y.120 Salt bridges: L:K.119, L:K.119 CDL.27: 33 residues within 4Å: Chain 3: F.328, Q.329, K.338, Y.339 Chain 7: A.34, G.37, F.38, Y.41, L.45, I.46, A.49, V.55, L.56 Chain M: W.16, L.17, N.88, A.90, R.91, L.94, M.98, L.101, V.127, I.131, R.135 Chain N: P.238, I.239, T.241, I.242, L.245, I.246, L.249, L.257, M.335 28 PLIP interactions: 8 interactions with chain 7, 5 interactions with chain 3, 10 interactions with chain M, 5 interactions with chain N Hydrophobic interactions: 7:Y.41, 7:Y.41, 7:Y.41, 7:L.45, 7:L.45, 7:I.46, 7:L.56, M:W.16, M:L.17, M:L.94, M:L.101, M:V.127, M:I.131, M:I.131, M:R.135, N:I.242, N:I.242, N:I.246, N:L.249, N:L.257 Hydrogen bonds: 7:V.55, 3:Q.329, 3:K.338, 3:K.338, 3:Y.339 Salt bridges: 3:K.338, M:R.91, M:R.135 CDL.32: 39 residues within 4Å: Chain L: M.573, T.576, I.577, S.579, Q.580, T.594, S.598, L.601, L.602, F.604 Chain N: M.100, P.110, F.113, T.156, L.157, L.160, I.164 Chain O: L.6, Y.9, W.10, A.25, I.28, G.29, S.32, V.35, V.36, Y.39, S.40, L.43, K.44, Y.59, T.62, A.63, I.66, G.67, F.70, V.125 Ligands: 3PE.31, CDL.33 33 PLIP interactions: 7 interactions with chain L, 20 interactions with chain O, 6 interactions with chain N Hydrophobic interactions: L:I.577, L:T.594, L:L.601, L:L.602, L:F.604, O:L.6, O:Y.9, O:W.10, O:A.25, O:I.28, O:V.35, O:V.36, O:V.36, O:Y.39, O:Y.39, O:Y.39, O:A.63, O:I.66, O:F.70, O:F.70, O:F.70, O:V.125, N:P.110, N:F.113, N:T.156, N:L.157, N:L.160, N:I.164 Hydrogen bonds: L:S.579, L:Q.580, O:Y.59 Salt bridges: O:K.44, O:K.44 CDL.33: 20 residues within 4Å: Chain L: T.560, I.561, L.562, T.565, I.566, L.568, A.569, K.572 Chain O: G.109, I.110, A.113, A.114, A.116, Y.117, T.121 Ligands: 3PE.9, 3PE.24, PC1.26, CDL.32, 3PE.34 14 PLIP interactions: 8 interactions with chain L, 6 interactions with chain O Hydrophobic interactions: L:T.560, L:I.561, L:I.561, L:L.562, L:T.565, L:I.566, L:A.569, O:I.110, O:I.110, O:A.113, O:A.113, O:A.116, O:Y.117 Salt bridges: L:K.572 CDL.35: 31 residues within 4Å: Chain L: L.9, L.12, I.13, T.16, N.65, L.78, F.80, I.130 Chain P: L.76, G.79, V.83, I.86, T.87, N.90, E.95, H.115 Chain S: P.43, V.47, R.48, I.51, H.55 Ligands: PC1.21, CDL.22, PC1.25 Chain a: W.80, Y.84, Y.85, H.89 Chain f: T.104, A.107, Y.108 31 PLIP interactions: 2 interactions with chain f, 9 interactions with chain L, 8 interactions with chain P, 7 interactions with chain a, 5 interactions with chain S Hydrophobic interactions: f:Y.108, L:L.9, L:L.12, L:I.13, L:I.13, L:T.16, L:L.78, L:F.80, L:F.80, L:I.130, P:V.83, P:V.83, P:V.83, P:I.86, P:I.86, a:W.80, a:W.80, a:W.80, a:W.80, a:Y.85, S:V.47, S:V.47, S:I.51 Hydrogen bonds: f:Y.108, P:N.90, P:N.90, a:H.89, S:R.48, S:H.55 Salt bridges: P:H.115, a:H.89 CDL.37: 32 residues within 4Å: Chain 7: T.29, P.31, R.32, A.34, Y.35, F.38 Chain M: L.2, I.5, I.6, M.9, M.10, M.12, S.53, T.55, F.56, L.101, L.104, F.105, F.117, I.120, M.121 Chain N: P.256, L.337, P.338 Chain R: F.169, W.170, T.171, M.172 Chain h: F.23, K.30, N.31, K.34 34 PLIP interactions: 15 interactions with chain M, 3 interactions with chain h, 4 interactions with chain R, 9 interactions with chain 7, 3 interactions with chain N Hydrophobic interactions: M:I.5, M:I.6, M:I.6, M:I.6, M:M.9, M:M.12, M:F.56, M:L.101, M:L.104, M:F.105, M:F.117, M:I.120, R:F.169, R:F.169, 7:P.31, 7:R.32, 7:A.34, 7:Y.35, 7:Y.35, 7:F.38, 7:F.38, 7:F.38, 7:F.38, N:P.256, N:L.337, N:P.338 Hydrogen bonds: M:S.53, M:T.55, M:T.55, h:N.31, h:N.31, h:K.34, R:T.171, R:T.171 CDL.44: 22 residues within 4Å: Chain 7: I.36, D.47, R.62, L.65, Y.66, S.69, F.70, F.72, V.73, L.77 Chain N: M.323, T.324, L.325, T.328, L.332, L.336, L.339 Ligands: 3PE.29 Chain g: K.43, L.46, T.47, T.50 18 PLIP interactions: 11 interactions with chain 7, 1 interactions with chain g, 6 interactions with chain N Hydrophobic interactions: 7:I.36, 7:R.62, 7:L.65, 7:L.65, 7:Y.66, 7:Y.66, 7:F.72, 7:F.72, 7:V.73, 7:V.73, N:L.325, N:L.332, N:L.336, N:L.339 Salt bridges: 7:R.62, g:K.43 Hydrogen bonds: N:M.323, N:L.325 CDL.46: 18 residues within 4Å: Chain 0: S.4, A.5, T.6, L.8, I.9 Chain 1: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 Chain I: Y.43 Chain i: M.1, W.2, F.3, L.6, P.7 13 PLIP interactions: 6 interactions with chain 1, 4 interactions with chain i, 3 interactions with chain 0 Hydrophobic interactions: 1:L.3, 1:L.3, 1:V.6, 1:L.7, i:F.3, i:F.3, i:L.6, i:L.6, 0:L.8, 0:I.9 Hydrogen bonds: 1:Q.13, 0:T.6 Salt bridges: 1:R.9

2 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)(Non-covalent)

ZMP.36: 16 residues within 4Å: Chain Q: D.112, S.113, L.114 Chain c: H.12, Q.13, V.16, L.44, R.47, F.48, H.51, K.52, A.60, L.63, A.67, E.70, F.71 8 PLIP interactions: 6 interactions with chain c, 2 interactions with chain Q Hydrophobic interactions: c:V.16, c:L.44, c:K.52, c:A.67, c:E.70, Q:L.114 Hydrogen bonds: c:Q.13, Q:S.113 ZMP.40: 14 residues within 4Å: Chain 2: S.113, L.114 Chain Z: K.41, V.44, W.51, V.75, M.78, F.79, N.82, A.83, V.85, V.91, L.94, F.118 16 PLIP interactions: 14 interactions with chain Z, 2 interactions with chain 2 Hydrophobic interactions: Z:K.41, Z:V.44, Z:W.51, Z:W.51, Z:W.51, Z:V.75, Z:F.79, Z:F.79, Z:F.118, Z:F.118, 2:L.114 Hydrogen bonds: Z:K.41, Z:N.82, Z:V.85, 2:S.113 Salt bridges: Z:K.41

1 x ZN: ZINC ION(Non-covalent)

ZN.38: 5 residues within 4Å: Chain U: C.87, G.89, H.96, C.112, C.115 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.87, U:H.96, U:C.112, U:C.115

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

NDP.39: 25 residues within 4Å: Chain F: R.223 Chain W: 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.148, I.167, S.168, H.169, Y.180, K.184, P.203, I.206, R.212 25 PLIP interactions: 24 interactions with chain W, 1 interactions with chain F Hydrophobic interactions: W:P.203, W:I.206, W:I.206 Hydrogen bonds: W:G.60, W:T.62, W:T.62, W:T.62, W:F.64, W:L.65, W:R.85, W:R.85, W:V.130, W:G.131, W:K.184, W:I.206, W:I.206 Salt bridges: W:R.85, W:R.132, W:R.132, W:R.212, W:R.212, F:R.223 pi-Stacking: W:F.139 pi-Cation interactions: W:R.85, W:R.85

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.43: 13 residues within 4Å: Chain 3: I.66, S.71, E.88, L.114, F.117, Y.118, Q.132, L.135, R.139, R.161, F.169, M.173, Y.233 6 PLIP interactions: 6 interactions with chain 3 Hydrogen bonds: 3:Y.118, 3:Q.132, 3:Y.233 Salt bridges: 3:R.161 pi-Stacking: 3:F.169, 3:F.169

1 x MYR: MYRISTIC ACID(Covalent)

MYR.45: 7 residues within 4Å: Chain L: L.413, L.486, T.489 Chain b: G.2, A.3, L.5 Chain e: T.152 4 PLIP interactions: 1 interactions with chain b, 3 interactions with chain L Hydrophobic interactions: b:L.5, L:L.413, L:L.486, L:T.489

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kampjut, D. et al., The coupling mechanism of mammalian respiratory complex I. Science (2020)

Release Date

2020-10-14

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
Mitochondrial complex I, 24 kDa subunit: B
NADH:ubiquinone oxidoreductase core subunit S1: C
Mitochondrial complex I, 49 kDa subunit: D
NADH:ubiquinone oxidoreductase core subunit S3: E
Mitochondrial complex I, PSST subunit: F
Mitochondrial complex I, TYKY subunit: G
NADH-ubiquinone oxidoreductase chain 3: H
NADH-ubiquinone oxidoreductase chain 1: 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
Mitochondrial complex I, B14.7 subunit: O
NADH:ubiquinone oxidoreductase subunit B5: P
Acyl carrier protein: Q2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: R
Mitochondrial complex I, PDSW subunit: S
Mitochondrial complex I, 10 kDa subunit: T
Mitochondrial complex I, 13 kDa subunit: U
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: V
NADH:ubiquinone oxidoreductase subunit A9: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: X
Mitochondrial complex I, B13 subunit: Y
NADH:ubiquinone oxidoreductase subunit A6: Z
Mitochondrial complex I, B14.5a subunit: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 3
NADH:ubiquinone oxidoreductase subunit S5: 4
NADH:ubiquinone oxidoreductase subunit A3: 5
NADH:ubiquinone oxidoreductase subunit B3: 6
NADH dehydrogenase [ubiquinone] 1 subunit C2: 7
NADH:ubiquinone oxidoreductase subunit B4: 8
Mitochondrial complex I, B16.6 subunit: 9
Mitochondrial complex I, B17 subunit: a
NADH:ubiquinone oxidoreductase subunit B7: b
NADH:ubiquinone oxidoreductase subunit B9: c
NADH:ubiquinone oxidoreductase subunit B2: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: e
Mitochondrial complex I, ESSS subunit: f
Mitochondrial complex I, KFYI subunit: g
Mitochondrial complex I, MNLL subunit: h
Mitochondrial complex I, MWFE subunit: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
A

I
H

J
J

K
K

L
L

M
M

N
N

O
V

P
W

Q
X

2
j

R
Y

S
Z

T
a

U
b

V
c

W
d

X
e

Y
f

Z
g

0
h

1
i

3
k

4
l

5
m

6
n

7
o

8
p

9
q

a
r

b
s

c
t

d
u

e
v

f
w

g
x

h
y

i
z

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

Mitochondrial complex I, 24 kDa subunit

NADH:ubiquinone oxidoreductase core subunit S1

Mitochondrial complex I, 49 kDa subunit

NADH:ubiquinone oxidoreductase core subunit S3

Mitochondrial complex I, PSST subunit

Mitochondrial complex I, TYKY subunit

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

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

Mitochondrial complex I, B14.7 subunit

NADH:ubiquinone oxidoreductase subunit B5

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

Mitochondrial complex I, PDSW subunit

Mitochondrial complex I, 10 kDa subunit

Mitochondrial complex I, 13 kDa subunit

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

NADH:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Mitochondrial complex I, B13 subunit

NADH:ubiquinone oxidoreductase subunit A6

Mitochondrial complex I, B14.5a subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH:ubiquinone oxidoreductase subunit S5

NADH:ubiquinone oxidoreductase subunit A3

NADH:ubiquinone oxidoreductase subunit B3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

Mitochondrial complex I, B16.6 subunit

Mitochondrial complex I, B17 subunit

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

NADH:ubiquinone oxidoreductase subunit B2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

Mitochondrial complex I, ESSS subunit

Mitochondrial complex I, KFYI subunit

Mitochondrial complex I, MNLL subunit

Mitochondrial complex I, MWFE subunit

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