SMTL ID : 8j9i.1

Cryo-EM structure of Euglena gracilis complex I, turnover state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 12 residues within 4Å: Chain A: H.76, F.77, C.78, Y.79, G.87, N.88, C.89, R.90, M.91, C.92, I.104, C.106 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.78, A:C.89, A:C.92, A:C.106 FES.63: 11 residues within 4Å: Chain w: P.123 Chain x: C.102, T.104, P.106, C.107, C.143, M.144, G.145, A.146, C.147, M.152 4 PLIP interactions: 4 interactions with chain x, Metal complexes: x:C.102, x:C.107, x:C.143, x:C.147

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

SF4.2: 14 residues within 4Å: Chain A: H.138, D.141, C.142, C.145, Q.147, G.148, C.151, L.153, Q.154, R.191, V.251, G.252 Chain n: M.307, I.311 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.138, A:C.142, A:C.145, A:C.151 SF4.3: 15 residues within 4Å: Chain A: M.189, C.192, I.193, H.194, C.195, T.196, K.197, C.198, I.224, I.248, C.249, P.250, V.251, A.253, L.254 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.192, A:C.195, A:C.198, A:C.249 SF4.57: 14 residues within 4Å: Chain n: R.71, H.156 Chain s: A.85, C.86, C.87, G.122, T.123, G.149, S.150, C.151, Y.158, G.180, C.181, P.182 4 PLIP interactions: 4 interactions with chain s, Metal complexes: s:C.86, s:C.87, s:C.151, s:C.181 SF4.58: 15 residues within 4Å: Chain t: H.92, C.114, P.115, A.116, A.118, I.119, L.138, C.143, I.144, Y.145, C.146, G.147, L.148, C.149, E.160 6 PLIP interactions: 6 interactions with chain t, Salt bridges: t:E.160 Metal complexes: t:H.92, t:C.114, t:C.143, t:C.146, t:C.149 SF4.59: 16 residues within 4Å: Chain t: L.94, C.104, I.105, T.106, C.107, Q.108, L.109, C.110, I.121, F.136, A.152, C.153, P.154, V.155, A.157, I.158 4 PLIP interactions: 4 interactions with chain t, Metal complexes: t:C.104, t:C.107, t:C.110, t:C.153 SF4.61: 14 residues within 4Å: Chain w: I.206, P.224, S.379, C.380, N.381, Q.382, C.383, C.386, R.387, S.424, I.425, C.426, L.428, G.429 4 PLIP interactions: 4 interactions with chain w, Metal complexes: w:C.380, w:C.383, w:C.386, w:C.426

1 x K: POTASSIUM ION(Non-covalent)

K.4: 8 residues within 4Å: Chain A: Q.147, I.246, C.249, V.251, G.252, L.254, T.255 Chain p: F.75 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.246, A:V.251, A:L.254

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

PC1.5: 20 residues within 4Å: Chain E: R.78, P.79, S.82, P.83, P.86, L.87, V.89, V.90, Y.91, Y.118 Ligands: PC1.6 Chain h: I.362, Y.363, I.365, L.366, L.369 Chain u: X.7, X.8, X.9, X.10 Ligand excluded by PLIP PC1.6: 17 residues within 4Å: Chain 7: F.327, L.329 Chain E: R.78, Q.108, S.109, F.110, G.114, L.115, S.116 Chain L: F.488, P.489 Ligands: PC1.5 Chain h: S.361, I.362, Y.363 Chain u: X.5, X.6 Ligand excluded by PLIP PC1.9: 16 residues within 4Å: Chain L: Y.464, K.466, K.467, L.468, I.469, A.470, F.471, V.474 Chain m: L.34, F.95, N.97, N.98, K.99, Q.102, L.103, I.106 Ligand excluded by PLIP PC1.10: 14 residues within 4Å: Chain L: S.300, N.301, W.302, P.303, I.304, S.306, N.308, H.373, R.375 Chain e: F.22, F.25, R.28, L.29, K.32 Ligand excluded by PLIP PC1.13: 31 residues within 4Å: Chain E: G.4, G.5, G.6, W.7, S.8, V.11, P.12, I.15, L.16, V.19 Chain O: P.69, E.73, R.76, F.77, F.80, L.97, L.100, V.101, L.104, Y.112, E.113, Y.116 Ligands: CDL.15, CDL.16 Chain h: W.404, F.405, L.407 Chain t: F.68, R.69, Q.70, P.71 Ligand excluded by PLIP PC1.20: 27 residues within 4Å: Chain G: A.65, V.66, G.69, Y.70, V.73, A.74, Y.77, E.78, R.84 Chain K: A.202, H.203, G.204, Q.205, F.206, Y.207 Chain P: L.68, L.71, Y.72, R.75, V.76, A.79, F.80, D.83 Chain h: L.668, L.669 Chain j: L.265, Y.269 Ligand excluded by PLIP PC1.21: 30 residues within 4Å: Chain 5: W.194, Y.335 Chain P: G.51, K.52, G.53, V.54, S.55, M.56, A.59, I.63 Ligands: CDL.17, CDL.18, PC1.41 Chain e: Y.426 Chain h: L.549, P.553, L.554, L.556, Y.557, I.560, I.635, I.638, I.639 Chain t: L.52, K.54, M.57, K.58, M.60, W.61, T.64 Ligand excluded by PLIP PC1.22: 28 residues within 4Å: Chain Q: W.6, Q.7, I.9, L.10, V.81, Q.85, V.128, V.162, T.165, A.166, Y.169, H.173, N.175, F.194, L.195, S.196, G.197, I.198, V.199, G.200 Ligands: 3PE.23 Chain i: Y.223, Y.226 Chain l: F.566, Y.570, L.571, N.575, F.579 Ligand excluded by PLIP PC1.26: 25 residues within 4Å: Chain 0: M.62, V.65, W.66, T.69, L.70, I.73 Chain U: T.47, S.51, W.55, R.58 Chain V: L.44 Chain Z: P.34, A.35, F.36, K.37 Ligands: CDL.25, PC1.27, PC1.50, PC1.53 Chain k: I.457, I.461, L.465, L.470 Chain l: I.14, L.18 Ligand excluded by PLIP PC1.27: 31 residues within 4Å: Chain 0: R.46, P.47, T.48, W.50, I.55, W.56, A.58, V.59, L.60, M.62, F.63, W.66 Chain U: V.28, L.31, M.32, R.33, L.35, A.36, X.37, X.38, X.39, W.43, V.46, T.47, A.50 Chain Y: F.141 Ligands: CDL.25, PC1.26, PC1.47 Chain k: F.450, I.454 Ligand excluded by PLIP PC1.29: 12 residues within 4Å: Chain 1: I.90, F.94, W.107 Chain C: X.135 Ligands: CDL.28 Chain f: T.8, R.11, L.12 Chain k: I.18, M.22, K.23, M.24 Ligand excluded by PLIP PC1.31: 40 residues within 4Å: Chain 5: G.78, D.79, G.80, L.81, L.82, R.83, D.149, P.151, P.222, L.223, V.224, S.228, P.229, A.230, L.231, F.234, Y.237, M.238, A.241, I.243, Y.244, P.245, V.247, I.253, V.258, H.289, F.292, I.293, V.296, G.314, I.317, V.318, L.321, L.328, V.329, M.333, V.334, L.336, I.337, I.342 Ligand excluded by PLIP PC1.33: 30 residues within 4Å: Chain 8: F.91, L.92, M.93, K.95, F.96, V.97, K.99, G.100, L.101, R.142, Y.147 Chain T: L.131, F.134, V.145 Ligands: PC1.34, CDL.51, 3PE.54 Chain k: L.410, I.413, F.414 Chain l: L.219, I.220, M.223, W.230, S.281, L.282, I.284, L.285, I.415, Y.416 Ligand excluded by PLIP PC1.34: 20 residues within 4Å: Chain 8: Y.87, L.90, M.93, D.94, V.97, S.98, L.102, D.103, S.107, Y.109, L.114, Y.115, K.117, A.118, C.121, L.122 Chain T: W.141, A.142 Ligands: PC1.33, CDL.51 Ligand excluded by PLIP PC1.35: 8 residues within 4Å: Chain 8: E.160, S.181, G.182, F.183, V.184, W.205 Ligands: PC1.36, CDL.51 Ligand excluded by PLIP PC1.36: 12 residues within 4Å: Chain 8: Y.115, E.116, L.123, K.148, S.149, W.153, R.158, F.183, W.186 Chain X: N.113 Ligands: PC1.35, CDL.51 Ligand excluded by PLIP PC1.39: 29 residues within 4Å: Chain V: W.23, R.24, T.27, F.28, S.31, C.32, L.35 Chain c: V.82, K.83, K.84, L.85, E.86, R.87, G.88, Q.89, V.90, I.91, A.94, V.95, T.98, L.101, W.102, V.105, A.106 Chain l: Y.30, L.34, I.35, V.37, I.41 Ligand excluded by PLIP PC1.41: 36 residues within 4Å: Chain G: L.51, M.52, R.53, P.54, A.55 Ligands: CDL.7, PC1.21 Chain e: P.420, V.421, F.422 Chain h: Y.557, I.558, I.560, F.561, L.564, P.571, I.639, L.643, F.646, N.650, N.653, L.654, Y.657, Y.658, I.659, F.662 Chain n: N.199, I.200, E.203 Chain t: F.47, Q.50, F.51, L.53, I.56, M.57, M.60 Ligand excluded by PLIP PC1.42: 10 residues within 4Å: Chain h: I.547, L.549, L.556, F.617, Y.620, I.624, I.627, H.628, I.631, I.635 Ligand excluded by PLIP PC1.43: 21 residues within 4Å: Chain C: L.79, I.82, I.83, V.86 Chain Q: F.2, Q.3, P.4, V.5, W.182 Chain X: L.52, V.55 Chain d: H.203, R.204, K.207 Chain i: L.225, I.229, F.230, L.234, F.235 Chain k: I.155, I.158 Ligand excluded by PLIP PC1.44: 28 residues within 4Å: Chain E: L.106 Chain L: A.478, A.479, L.481, Y.482, A.485 Chain P: W.160, N.162 Chain h: I.459, N.460, I.461 Chain j: N.172, V.173, I.174, N.175, I.178 Chain m: L.20, I.21, I.24, I.27, I.28, I.31, I.53, I.57, I.60, N.61, I.65, I.72 Ligand excluded by PLIP PC1.46: 22 residues within 4Å: Chain C: X.133, X.134, X.137, X.138, X.141 Chain U: E.79 Ligands: CDL.45 Chain k: Y.3, I.7, Y.10, I.11, L.14, I.15, I.18, I.53, N.54, I.55, Y.56, I.58, I.66, L.68, I.113 Ligand excluded by PLIP PC1.47: 13 residues within 4Å: Chain 0: T.52, W.56, L.60, F.63 Chain U: T.25, G.26 Ligands: PC1.27 Chain k: K.27, Y.29, R.30, S.33, I.34, I.37 Ligand excluded by PLIP PC1.50: 36 residues within 4Å: Chain V: D.12, F.13 Ligands: CDL.25, PC1.26, PC1.53 Chain k: N.367, S.372, Y.373, Y.375, F.376, L.379, L.380, L.390, F.434, Y.435, T.436, I.464, F.468 Chain l: L.10, I.14, N.17, L.18, K.112, N.113, R.116, I.120, L.123, Y.126, N.127, L.130, M.139, I.142, M.146, L.153, N.159, N.160 Ligand excluded by PLIP PC1.52: 23 residues within 4Å: Chain V: R.57, P.60, Y.64, M.82, F.86 Chain c: W.102, V.103, A.106, G.107, S.110, K.111, N.113, N.114 Chain l: I.41, I.42, W.44, Y.45, L.47, Y.48, I.51, L.484, L.485, I.488 Ligand excluded by PLIP PC1.53: 20 residues within 4Å: Chain 0: Q.77 Chain V: L.44, E.45, H.48 Chain Z: R.32, K.37 Ligands: PC1.26, PC1.50 Chain k: F.468, N.469, L.470 Chain l: I.3, L.64, S.65, Y.66, N.67, L.78, I.80, L.130, M.139 Ligand excluded by PLIP

18 x CDL: CARDIOLIPIN(Non-covalent)

CDL.7: 25 residues within 4Å: Chain 9: G.31, K.32, W.33, G.34, W.36, M.73 Chain G: T.44, F.46, R.47, M.50, L.51, A.55, F.57, H.58, L.61 Ligands: CDL.38, PC1.41 Chain i: L.26 Chain t: G.40, L.41, M.43, G.44, F.47, M.48, F.51 Ligand excluded by PLIP CDL.14: 14 residues within 4Å: Chain E: W.7, V.11 Chain J: H.17, I.20, Q.21, W.24 Chain O: P.68, G.72, E.73, F.74, W.75, R.78 Chain t: F.68, R.69 Ligand excluded by PLIP CDL.15: 15 residues within 4Å: Chain O: R.98, V.101, R.102, R.105, T.106, G.150, S.151, F.153, T.154 Ligands: PC1.13, CDL.16 Chain h: W.404 Chain s: W.9, P.11, Y.12 Ligand excluded by PLIP CDL.16: 27 residues within 4Å: Chain E: L.16, V.20, L.24 Chain O: R.105, R.108, F.153 Ligands: PC1.13, CDL.15 Chain h: S.377, L.381, Y.401, N.402, G.403, W.404, L.407, V.408, I.410, V.411, Q.412, I.415 Chain s: T.8, W.9, T.64, Q.67, V.68, W.71, K.200 Ligand excluded by PLIP CDL.17: 23 residues within 4Å: Chain 5: F.18, W.194, V.312, D.315, S.316, A.319, L.320, R.331, Y.335, R.338 Chain P: G.53, V.54, S.55, R.57, T.58, A.61, I.62, S.65, L.66, F.69 Ligands: CDL.18, PC1.21 Chain e: S.432 Ligand excluded by PLIP CDL.18: 21 residues within 4Å: Chain 5: R.196, A.319, L.320, Q.322, W.323, R.331, Y.335 Chain J: R.19, Q.22, W.23 Chain P: K.52, G.53, V.54, A.59, I.62, I.63, L.66 Ligands: CDL.17, PC1.21 Chain h: P.553 Chain t: W.61 Ligand excluded by PLIP CDL.19: 23 residues within 4Å: Chain G: F.62 Chain P: M.56, R.57, W.60, I.63, G.64, T.67, L.68, L.71 Chain e: Y.426, P.429, T.430, S.432, R.433 Chain h: L.554, F.662, L.669 Chain t: L.41, G.42, L.45, A.46, M.48, N.49 Ligand excluded by PLIP CDL.24: 23 residues within 4Å: Chain S: R.23, H.24, A.25, F.26, F.31, S.33, R.34, X.38, X.39, X.40, X.41, X.42, X.43, X.45, X.46, X.47, X.49 Chain c: W.43, M.47, G.52, R.53 Chain l: I.515, Y.518 Ligand excluded by PLIP CDL.25: 28 residues within 4Å: Chain 0: T.40, Y.42, Q.43, R.46, M.62 Chain U: X.38, X.40, X.41, W.43, A.44, P.45, A.48 Chain V: F.13 Ligands: PC1.26, PC1.27, PC1.50 Chain k: Y.373, F.376, I.377, F.450, I.453, I.454, I.457, L.460 Chain l: I.15, L.18, N.21, I.22 Ligand excluded by PLIP CDL.28: 51 residues within 4Å: Chain 1: Y.85, L.86, G.89, I.90, F.91, G.93, F.94, M.97, A.98, N.100, Y.101, T.105, V.106, W.107, W.108, P.111, W.112, F.114, P.115, M.118, A.119, A.122 Chain C: M.32, Y.33, I.36, I.40, L.45, X.123, X.124, X.127, X.130, X.131, X.134 Ligands: PC1.29, CDL.30, CDL.45, U10.49 Chain f: L.12, A.15, C.19 Chain k: M.17, L.21, M.22, K.23, Y.25, Y.102, I.106, F.129, I.132, P.133, L.136 Ligand excluded by PLIP CDL.30: 25 residues within 4Å: Chain 1: H.99, V.110, W.112, R.113, M.116, W.117, A.120, G.123, V.124 Chain 9: L.12, W.57, F.61 Chain C: N.113, F.114, X.121 Ligands: CDL.28, CDL.37 Chain e: T.330, H.331 Chain f: C.19, A.22, L.23, R.25, W.26 Chain g: L.18 Ligand excluded by PLIP CDL.32: 22 residues within 4Å: Chain 7: K.295, A.296, F.299, S.300, R.302, W.303 Chain L: H.154, P.155, V.156, N.210, Q.211, S.212, P.389, G.390 Chain h: I.418 Chain j: I.194, I.197, I.198 Chain s: S.59, V.61, V.65, F.69 Ligand excluded by PLIP CDL.37: 21 residues within 4Å: Chain 9: Q.4, N.5, H.6, R.11, A.53, V.54, K.56, W.57, P.58, F.61 Chain C: F.114, X.117, X.118 Ligands: CDL.30 Chain f: W.26, L.30 Chain g: I.11 Chain i: F.39, L.41, I.66, I.67 Ligand excluded by PLIP CDL.38: 17 residues within 4Å: Chain 9: K.32, W.36, R.40, L.62, L.64, N.65, G.66, T.69, A.70, F.71, W.72, M.73, F.76, A.80 Ligands: CDL.7 Chain i: Q.23, N.28 Ligand excluded by PLIP CDL.45: 54 residues within 4Å: Chain 1: I.79, L.128, F.129, F.131, R.132, V.135, N.139, R.143 Chain C: I.46, N.48, I.51, A.52, T.54, S.55, L.58, X.125, X.129, X.130 Chain U: W.93, R.94, G.97, Q.100, Q.101 Ligands: CDL.28, PC1.46 Chain i: I.56, Y.265, N.266, Y.269, Y.270, Y.273, I.276, S.277, I.280 Chain k: L.60, I.61, I.62, G.63, Y.64, I.66, I.110, I.113, I.120, I.121, T.122, S.124, L.125, I.126, F.129, Y.172, M.175, Y.176, Y.179, S.185 Ligand excluded by PLIP CDL.51: 39 residues within 4Å: Chain 8: A.80, G.83, A.84, Y.87, F.88, H.89, F.91, L.92, T.113, Y.115 Chain X: K.100, Y.101, L.103, G.104, A.105, C.108, F.109, F.112, N.113, I.116 Ligands: PC1.33, PC1.34, PC1.35, PC1.36, 3PE.54, CDL.55 Chain l: W.230, L.236, G.237, I.284, L.285, I.288, L.289, I.292, L.296, Y.416, L.537, Y.538, I.539 Ligand excluded by PLIP CDL.55: 52 residues within 4Å: Chain 8: M.24, R.74, G.77, R.78, M.81 Chain X: K.100, L.103, G.104, L.107, C.108, I.111, F.112, L.115 Chain Y: W.102 Ligands: CDL.51, CDL.64 Chain l: L.287, I.288, G.291, I.292, L.295, L.296, F.299, S.300, I.302, N.303, M.324, S.414, Y.416, I.420, L.422, L.423, F.424, I.426, T.526, L.527, I.529, F.530, N.531, I.532, H.533, N.534, N.535, L.537, Y.538 Chain y: G.203, T.204, A.206, V.207, S.208, F.213, F.217 Ligand excluded by PLIP CDL.64: 28 residues within 4Å: Chain 8: F.14, P.15, W.16, T.17, N.19, S.20, Y.23, M.24 Ligands: CDL.55 Chain l: F.299, I.302, L.430, L.512, L.516, Y.519, Y.521, Y.523, H.525, T.526, L.527 Chain y: L.4, I.7, S.8, K.10, Y.11, F.15, F.213, M.216 Ligand excluded by PLIP

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

NDP.8: 29 residues within 4Å: Chain L: G.123, N.125, G.126, F.127, L.128, R.148, N.151, R.161, Y.180, P.182, C.201, I.202, G.203, G.204, F.215, L.220, F.221, L.224, T.243, S.244, H.245, I.246, K.260, P.279, A.280, D.281, I.282, D.287, N.288 18 PLIP interactions: 18 interactions with chain L Hydrophobic interactions: L:P.279, L:I.282 Hydrogen bonds: L:N.125, L:G.126, L:F.127, L:L.128, L:R.148, L:N.151, L:I.202, L:G.203, L:K.260, L:I.282, L:D.287, L:N.288 Salt bridges: L:R.148, L:R.161 pi-Stacking: L:F.215 pi-Cation interactions: L:R.148

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

ZMP.11: 27 residues within 4Å: Chain I: S.58, I.61, R.62, L.68, V.88, I.92, R.95, F.96, E.97, Q.98, G.99, P.100, K.101, L.102, R.111, V.115, D.118, L.119, Y.122, F.127, V.132, Y.136, N.137 Chain M: D.90, S.91, L.92 Chain p: Q.50 20 PLIP interactions: 17 interactions with chain I, 1 interactions with chain p, 2 interactions with chain M Hydrophobic interactions: I:I.92, I:R.95, I:F.96, I:F.96, I:V.115, I:D.118, I:L.119, I:Y.122, I:Y.122, I:F.127, I:Y.136, I:Y.136, M:L.92 Hydrogen bonds: I:F.96, I:L.102, I:R.111, I:R.111, p:Q.50, M:S.91 Salt bridges: I:R.62 ZMP.12: 25 residues within 4Å: Chain 8: I.36, F.37 Chain N: S.91, L.92 Chain Y: S.37, V.39, Q.40, A.46, V.49, I.50, V.71, E.74, I.75, Q.76, N.78, A.79, N.80, A.81, K.86, L.89, L.90, F.93, H.96, I.97, R.100 14 PLIP interactions: 12 interactions with chain Y, 2 interactions with chain N Hydrophobic interactions: Y:A.46, Y:V.49, Y:I.50, Y:E.74, Y:I.75, Y:K.86, Y:L.89, Y:F.93, Y:I.97, N:L.92 Hydrogen bonds: Y:S.37, Y:N.78, Y:A.81, N:S.91

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

3PE.23: 27 residues within 4Å: Chain Q: P.155, Q.156, V.159, L.160, I.198, A.201, A.202, V.205, R.209 Ligands: PC1.22, 3PE.48 Chain k: I.166, L.170, I.212, F.223, Y.268, F.272 Chain l: Y.570, L.571, I.573, N.575, I.576, I.577, F.579, L.580, L.583, I.584 10 PLIP interactions: 7 interactions with chain l, 2 interactions with chain Q, 1 interactions with chain k Hydrophobic interactions: l:I.576, l:I.577, l:F.579, l:F.579, l:L.580, l:L.580, l:L.583, Q:I.198, Q:A.201, k:I.212 3PE.40: 35 residues within 4Å: Chain 0: G.1, R.5 Chain T: K.83, Y.85 Chain e: L.210, V.237, G.239, A.240, I.254, I.255, G.256, S.257, V.272, V.273, G.274, A.275, S.277, V.290, V.292, G.293, L.299, R.300, E.313 Chain f: R.108, I.111, I.130, S.132, M.149, E.150, V.165, T.167, E.168, V.181, P.182, K.184 10 PLIP interactions: 5 interactions with chain f, 4 interactions with chain e, 1 interactions with chain T Hydrophobic interactions: f:I.111, f:V.165, f:T.167, f:V.181, e:L.210, e:V.237, e:V.290, e:V.292 Salt bridges: f:K.184, T:K.83 3PE.48: 24 residues within 4Å: Chain C: F.57, I.61, F.64, F.70, I.73 Chain Q: V.216, S.217, Y.220 Ligands: 3PE.23 Chain k: I.166, L.169, L.170, N.173, I.201, L.202, N.204, Y.205, I.208, N.209, Y.265, Y.268 Chain l: I.577, L.580, I.584 18 PLIP interactions: 3 interactions with chain l, 4 interactions with chain Q, 7 interactions with chain k, 4 interactions with chain C Hydrophobic interactions: l:L.580, l:I.584, l:I.584, Q:V.216, Q:Y.220, k:I.166, k:L.169, k:N.173, C:F.57, C:F.64, C:F.64, C:F.70 Hydrogen bonds: Q:Y.220, Q:Y.220, k:N.204, k:Y.265, k:Y.265, k:Y.268 3PE.54: 37 residues within 4Å: Chain X: A.82, M.83, D.84 Chain Y: I.23 Ligands: PC1.33, CDL.51 Chain k: I.281, I.285, F.288, Y.289, F.414, I.417, L.418, S.421, Y.428 Chain l: E.163, K.166, A.167, L.169, K.170, V.173, Y.174, I.177, I.227, W.230, L.236, G.237, F.238, D.244, E.247, D.540, L.543, S.544, M.547, F.550, S.551, I.554 20 PLIP interactions: 13 interactions with chain l, 6 interactions with chain k, 1 interactions with chain X Hydrophobic interactions: l:L.169, l:W.230, l:F.238, l:F.238, l:F.550, l:F.550, l:I.554, k:I.285, k:F.288, k:F.288, k:Y.289, k:L.418, k:Y.428 Hydrogen bonds: l:D.244, l:D.244, l:E.247, l:S.544, X:D.84 Salt bridges: l:K.166, l:K.170

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

U10.49: 29 residues within 4Å: Chain 0: R.45, E.49, W.50, S.51, V.54 Chain C: N.27 Chain U: P.10, P.11, S.12, K.13, H.15, P.16, K.20, Y.22, R.24 Ligands: CDL.28 Chain e: S.319 Chain f: K.6 Chain k: Q.20, Y.25, N.26, R.93, Y.94, Y.95, N.99, T.101, Y.102, I.356, F.448 13 PLIP interactions: 7 interactions with chain k, 6 interactions with chain U Hydrophobic interactions: k:Y.25, k:Y.25, k:Y.94, k:Y.95, U:P.10, U:P.11, U:K.13, U:P.16, U:Y.22, U:Y.22 Hydrogen bonds: k:N.99, k:T.101 pi-Stacking: k:Y.25

2 x ZN: ZINC ION(Non-covalent)

ZN.56: 7 residues within 4Å: Chain r: C.88, G.90, H.100, C.115, Y.117, C.118, N.120 4 PLIP interactions: 4 interactions with chain r Metal complexes: r:C.88, r:H.100, r:C.115, r:C.118 ZN.65: 5 residues within 4Å: Chain y: A.59, C.61, H.62, H.66, C.164 4 PLIP interactions: 4 interactions with chain y Metal complexes: y:C.61, y:H.62, y:H.66, y:C.164

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.60: 23 residues within 4Å: Ligands: NAI.62 Chain w: G.86, R.87, G.88, A.90, K.97, N.117, D.119, E.120, S.121, D.128, Y.205, I.206, G.208, E.209, E.210, V.243, T.244, N.245, T.248, C.426, A.427, L.428 15 PLIP interactions: 15 interactions with chain w Hydrophobic interactions: w:Y.205, w:I.206, w:E.209, w:E.209, w:A.427, w:L.428 Hydrogen bonds: w:R.87, w:G.88, w:N.117, w:N.117, w:S.121, w:E.210, w:N.245, w:T.248 Salt bridges: w:K.97

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

NAI.62: 20 residues within 4Å: Ligands: FMN.60 Chain w: G.88, G.89, A.90, F.92, K.97, F.100, E.120, S.121, E.122, T.125, Y.205, E.210, K.227, F.230, P.231, G.351, T.352, A.427, W.434 11 PLIP interactions: 11 interactions with chain w Hydrophobic interactions: w:E.122, w:Y.205, w:T.352 Hydrogen bonds: w:G.88, w:K.97, w:S.121, w:E.122, w:E.210, w:K.227 pi-Stacking: w:F.92, w:F.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Z. et al., Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun (2024)

Release Date

2024-02-28

Peptides

NDUFS1A: A
NDUFS1B: B
ND2B: C
ND4L: D
NDUFA1: E
NDUFA2: F
NDUFA3: G
NDUFA5: H
NDUFA6: I
NDUFA7: J
NDUFA8: K
NDUFA9: L
NDUFAB1-alpha: M
NDUFAB1-beta: N
NDUFA12: O
NDUFA13: P
NDUFA11: Q
NDUFB2: R
NDUFB3: S
NDUFB4: T
NDUFB5: U
NDUFB6: V
NDUFB7: W
NDUFB8: X
NDUFB9: Y
NDUFB10: Z
NDUFB11: 0
NDUFC2: 1
NDUEG1: 2
NDUEG2: 3
NDUEG3: 4
NDUEG4: 5
NDUEG5: 6
NDUEG6: 7
NDUEG8: 8
NDUEG10: 9
NDUEG11: a
NDUEG12: b
NDUEG13: c
NDUFX: d
NDUCA1: e
NDUCA2: f
NDUCA3: g
ND1: h
ND2A: i
ND3: jm
NADH-ubiquinone oxidoreductase chain 4: k
ND5: l
NDUFS2: n
NDUFS3: o
NDUFS4: p
NDUFS5: q
NDUFS6: r
NDUFS7: s
NDUFS8: t
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK: uv
NDUFV1: w
NDUFV2: x
NDUEG7: y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1A

B
1B

C
2B

D
4L

E
A1

F
A2

G
A3

H
A5

I
A6

J
A7

K
A8

L
A9

M
AB

N
AC

O
AL

P
AM

Q
AN

R
B2

S
B3

T
B4

U
B5

V
B6

W
B7

X
B8

Y
B9

Z
BL

0
BM

1
C4

2
E1

3
E2

4
E3

5
E4

6
E5

7
E6

8
E8

9
EA

a
EB

b
EC

c
ED

d
FX

e
G1

f
G2

g
G3

h
N1

i
N2

j
N3

m
N6

k
N4

l
N5

n
S2

o
S3

p
S4

q
S5

r
S6

s
S7

t
S8

u
U1

v
U2

w
V1

x
V2

y
E7

Membrane

We predict this structure to be a membrane protein.
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NDUFS1A

NDUFS1B

ND2B

ND4L

NDUFA1

NDUFA2

NDUFA3

NDUFA5

NDUFA6

NDUFA7

NDUFA8

NDUFA9

NDUFAB1-alpha

NDUFAB1-beta

NDUFA12

NDUFA13

NDUFA11

NDUFB2

NDUFB3

NDUFB4

NDUFB5

NDUFB6

NDUFB7

NDUFB8

NDUFB9

NDUFB10

NDUFB11

NDUFC2

NDUEG1

NDUEG2

NDUEG3

NDUEG4

NDUEG5

NDUEG6

NDUEG8

NDUEG10

NDUEG11

NDUEG12

NDUEG13

NDUFX

NDUCA1

NDUCA2

NDUCA3

ND1

ND2A

ND3

NADH-ubiquinone oxidoreductase chain 4

ND5

NDUFS2

NDUFS3

NDUFS4

NDUFS5

NDUFS6

NDUFS7

NDUFS8

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK

NDUFV1

NDUFV2

NDUEG7

Related Entries With Identical Sequence