SMTL ID : 6y79.1

Cryo-EM structure of a respiratory complex I F89A mutant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.96 Å

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-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.129, P.130, D.132, C.133, C.136, Q.138, C.142, L.144, Q.145, R.182, V.235, G.236 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.132 Metal complexes: A:H.129, A:C.133, A:C.136, A:C.142 SF4.2: 12 residues within 4Å: Chain A: M.180, C.183, I.184, H.185, C.186, T.187, C.189, I.213, C.233, V.235, A.237, L.238 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.183, A:C.186, A:C.189, A:C.233 SF4.4: 12 residues within 4Å: Chain B: P.225, S.380, C.381, G.382, Q.383, C.384, C.387, T.425, I.426, C.427, L.429, G.430 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.381, B:C.384, B:C.387, B:C.427 SF4.9: 12 residues within 4Å: Chain I: H.118, C.140, P.141, I.145, C.169, I.170, Y.171, C.172, G.173, Y.174, C.175, E.186 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.186 Metal complexes: I:C.140, I:C.169, I:C.172, I:C.175 SF4.10: 11 residues within 4Å: Chain I: C.130, I.131, A.132, C.133, K.134, L.135, C.136, I.147, C.179, A.183, I.184 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.130, I:C.133, I:C.136, I:C.179 SF4.15: 9 residues within 4Å: Chain C: R.141, H.226 Chain K: A.84, C.85, C.86, G.121, S.149, C.150, C.180 5 PLIP interactions: 5 interactions with chain K, Metal complexes: K:C.85, K:C.86, K:C.150, K:C.180, K:C.180

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

FES.3: 8 residues within 4Å: Chain A: R.67, C.69, Y.70, G.78, C.80, R.81, C.83, C.97 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.69, A:C.80, A:C.83, A:C.97 FES.7: 9 residues within 4Å: Chain H: C.127, P.131, C.132, C.168, L.169, G.170, A.171, C.172, M.177 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.127, H:C.132, H:C.168, H:C.172

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 17 residues within 4Å: Chain B: G.86, R.87, G.88, K.97, N.118, D.120, E.121, Y.206, G.209, E.210, E.211, V.244, T.245, N.246, T.249, A.428, L.429 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.210, B:E.210, B:A.428, B:L.429 Hydrogen bonds: B:R.87, B:G.88, B:N.118, B:D.120, B:G.209, B:E.211, B:E.211, B:N.246 Salt bridges: B:K.97

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

NDP.6: 19 residues within 4Å: Chain E: G.60, N.62, G.63, F.64, L.65, R.85, L.109, L.128, I.129, G.130, R.131, F.138, V.143, F.169, F.179, A.203, M.205, K.211, F.213 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.169 Hydrogen bonds: E:G.60, E:N.62, E:F.64, E:L.65, E:R.85, E:L.128, E:R.131 Salt bridges: E:R.85, E:R.131, E:R.131, E:K.211, E:K.211 pi-Cation interactions: E:R.85, E:R.85

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

3PE.8: 27 residues within 4Å: Chain 3: F.28, I.32 Chain 8: P.184, L.187, I.188, F.190, I.191, F.202, S.292, W.295, V.296, F.303, F.311, I.315, L.319 Chain C: R.269, I.270, L.273 Chain I: A.74, T.75, Y.77, F.78, L.80, M.83, F.84, L.87 Chain T: L.34 22 PLIP interactions: 5 interactions with chain I, 10 interactions with chain 8, 2 interactions with chain C, 1 interactions with chain T, 4 interactions with chain 3 Hydrophobic interactions: I:F.78, I:F.78, I:F.84, I:L.87, 8:P.184, 8:L.187, 8:I.188, 8:F.202, 8:W.295, 8:V.296, 8:F.311, 8:F.311, 8:L.319, 8:L.319, C:I.270, T:L.34, 3:F.28, 3:F.28, 3:F.28, 3:I.32 Hydrogen bonds: I:Y.77 Salt bridges: C:R.269 3PE.11: 12 residues within 4Å: Chain 9: V.401 Chain J: R.89, D.93, G.94, W.95, A.127, A.128, G.130, L.131, W.134 Ligands: LMN.27, T7X.41 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain 9 Hydrogen bonds: J:R.89, J:G.94 Hydrophobic interactions: 9:V.401 3PE.13: 23 residues within 4Å: Chain 9: I.262, I.265, L.266 Chain J: V.35, G.38, A.39, A.43, A.46, R.47 Chain c: L.606, L.620, I.623, S.627, L.628, L.630, L.631, L.633, V.634, V.645, L.646, I.649, L.650, I.652 16 PLIP interactions: 12 interactions with chain c, 2 interactions with chain J, 2 interactions with chain 9 Hydrophobic interactions: c:I.623, c:L.628, c:L.630, c:L.631, c:L.631, c:L.633, c:V.634, c:V.645, c:I.649, c:I.649, c:L.650, c:L.650, J:A.39, 9:I.265, 9:L.266 Salt bridges: J:R.47 3PE.19: 18 residues within 4Å: Chain R: N.113 Chain Y: F.4, L.7, S.11, G.12, F.15, A.16, F.19, P.28, A.29, G.30, Y.36, V.37, V.41 Ligands: 3PE.25, 3PE.39 Chain b: N.15, R.16 16 PLIP interactions: 13 interactions with chain Y, 2 interactions with chain b, 1 interactions with chain R Hydrophobic interactions: Y:F.4, Y:L.7, Y:L.7, Y:F.15, Y:F.15, Y:F.19, Y:F.19, Y:Y.36, Y:V.37, Y:V.37, Y:V.41 Hydrogen bonds: Y:G.30, Y:G.30, b:N.15, b:R.16, R:N.113 3PE.24: 22 residues within 4Å: Chain X: P.82, D.83 Chain b: I.286, L.293, I.415, I.422, K.426 Chain c: Q.162, K.165, S.166, L.168, S.169, L.172, M.173, F.176, I.221, G.231, L.238, N.561, I.564, I.565, L.569 20 PLIP interactions: 6 interactions with chain b, 13 interactions with chain c, 1 interactions with chain X Hydrophobic interactions: b:I.286, b:L.293, b:I.415, b:I.422, b:I.422, b:K.426, c:L.168, c:L.172, c:F.176, c:F.176, c:I.221, c:I.221, c:I.564, c:I.565, c:I.565, c:L.569, c:L.569 Hydrogen bonds: c:S.166, X:D.83 Salt bridges: c:K.165 3PE.25: 15 residues within 4Å: Chain 9: Y.359 Chain Y: F.19, K.23, A.29 Ligands: 3PE.19, 3PE.37, 3PE.39, 3PE.40 Chain b: L.11, F.14, N.15, L.18, T.116, A.120, L.147 11 PLIP interactions: 5 interactions with chain b, 5 interactions with chain Y, 1 interactions with chain 9 Hydrophobic interactions: b:L.11, b:F.14, b:T.116, b:A.120, b:L.147, Y:F.19, Y:F.19, Y:F.19, 9:Y.359 Hydrogen bonds: Y:A.29 Salt bridges: Y:K.23 3PE.26: 18 residues within 4Å: Chain 5: S.14, M.15, T.16, G.18, W.19 Ligands: CDL.38 Chain b: T.366, P.370, T.374, I.377, I.378, F.381, L.462 Chain c: W.16, L.20, H.112, R.115, L.152 16 PLIP interactions: 5 interactions with chain c, 7 interactions with chain b, 4 interactions with chain 5 Hydrophobic interactions: c:L.20, c:L.20, b:T.374, b:I.377, b:I.378, b:F.381, b:L.462 Salt bridges: c:H.112, c:R.115, c:R.115 Hydrogen bonds: b:T.366, b:T.374, 5:S.14, 5:M.15, 5:T.16, 5:G.18 3PE.35: 22 residues within 4Å: Chain 3: N.5, Y.15, S.19, R.23, L.26, F.27, A.29, F.30, A.31, I.34, V.38 Chain 8: P.318, F.321, G.322, L.325 Ligands: CDL.31 Chain a: I.99, F.102, V.103, I.106, N.107, N.109 19 PLIP interactions: 9 interactions with chain 3, 7 interactions with chain a, 3 interactions with chain 8 Hydrophobic interactions: 3:L.26, 3:F.27, 3:F.27, 3:F.30, 3:F.30, 3:A.31, 3:I.34, 3:V.38, a:I.99, a:F.102, a:V.103, a:I.106, 8:P.318, 8:F.321, 8:L.325 Salt bridges: 3:R.23 Hydrogen bonds: a:N.107, a:N.109, a:N.109 3PE.37: 17 residues within 4Å: Chain 9: A.358, Y.359, L.362, P.376, L.377 Ligands: 3PE.25, 3PE.39 Chain b: S.10, F.14, L.18, G.22, Y.28, N.112, L.113, T.116, A.143, P.146 10 PLIP interactions: 7 interactions with chain b, 3 interactions with chain 9 Hydrophobic interactions: b:F.14, b:L.113, b:P.146, b:P.146, 9:L.362, 9:P.376, 9:L.377 Hydrogen bonds: b:G.22, b:N.112, b:T.116 3PE.39: 20 residues within 4Å: Chain 9: P.376, T.451, F.452, F.454 Chain Y: T.5, G.9, G.12, L.13 Ligands: 3PE.19, 3PE.25, 3PE.37, 3PE.40 Chain b: L.3, T.4, F.60, N.64, F.66, G.67, L.68, N.70 8 PLIP interactions: 3 interactions with chain b, 4 interactions with chain 9, 1 interactions with chain Y Hydrogen bonds: b:N.64, b:L.68, b:N.70 Hydrophobic interactions: 9:P.376, 9:F.452, 9:F.452, 9:F.454, Y:L.13 3PE.40: 19 residues within 4Å: Chain 9: P.376, F.454 Ligands: 3PE.25, 3PE.39 Chain b: L.3, F.38, F.55, N.56, F.57, L.59, F.60, L.68, L.123, V.124, L.126, L.127, W.130, L.140, A.143 18 PLIP interactions: 3 interactions with chain 9, 15 interactions with chain b Hydrophobic interactions: 9:P.376, 9:P.376, 9:F.454, b:F.38, b:F.38, b:F.55, b:F.57, b:F.60, b:L.123, b:L.123, b:L.123, b:V.124, b:L.127, b:L.127, b:L.127, b:W.130, b:W.130, b:A.143

3 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.12: 19 residues within 4Å: Chain 9: L.391, Y.396, I.400 Chain J: Y.82, K.92, D.93, H.97, L.131, G.133, W.134, G.136, A.145, T.162, F.163, W.164 Chain b: F.177, V.184, D.205, I.209 18 PLIP interactions: 10 interactions with chain J, 4 interactions with chain b, 4 interactions with chain 9 Hydrophobic interactions: J:L.131, J:W.134, J:W.134, J:W.134, J:F.163, J:W.164, b:F.177, b:I.209, b:I.209, 9:L.391, 9:Y.396, 9:Y.396, 9:Y.396 Hydrogen bonds: J:Y.82, J:G.133, J:A.145, J:F.163, b:D.205 LMN.14: 12 residues within 4Å: Chain 6: Y.48, T.49, R.50, G.53, L.57 Chain J: L.114, V.115, P.116, I.119 Chain X: K.31, P.35 Ligands: CDL.42 6 PLIP interactions: 3 interactions with chain 6, 3 interactions with chain J Hydrophobic interactions: 6:Y.48, 6:L.57, J:V.115, J:I.119 Hydrogen bonds: 6:R.50, J:V.115 LMN.27: 13 residues within 4Å: Chain 6: Y.69, Y.72, Q.73 Ligands: 3PE.11 Chain b: L.204, D.205, T.208, L.212, I.216, M.219, L.272, Y.273, M.276 5 PLIP interactions: 4 interactions with chain b, 1 interactions with chain 6 Hydrophobic interactions: b:L.212, b:I.216 Hydrogen bonds: b:T.208, b:L.272, 6:Q.73

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 4 residues within 4Å: Chain M: C.97, H.110, C.125, C.128 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.97, M:H.110, M:C.125, M:C.128

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

ZMP.17: 18 residues within 4Å: Chain N: D.65, S.66, L.67 Chain O: Q.22, T.25, F.32, I.52, I.56, E.59, F.60, H.63, R.64, Q.72, L.75, G.79, F.96, Y.99, F.100 15 PLIP interactions: 15 interactions with chain O Hydrophobic interactions: O:Q.22, O:T.25, O:F.32, O:F.32, O:I.52, O:I.56, O:E.59, O:F.60, O:Q.72, O:L.75, O:F.96, O:F.96, O:Y.99, O:F.100 Salt bridges: O:R.64 ZMP.18: 16 residues within 4Å: Chain P: D.88, S.89, L.90 Chain Q: F.7, N.11, K.12, S.22, I.43, K.46, F.47, N.50, A.51, I.53, L.59, T.66, H.69 8 PLIP interactions: 7 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: Q:K.12, Q:I.43, Q:A.51, Q:T.66 Hydrogen bonds: Q:N.11, Q:A.51, P:S.89 Salt bridges: Q:K.12

6 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.20: 18 residues within 4Å: Chain 8: L.183, W.295 Chain I: K.76, L.79, A.81, E.82, F.84, Y.88, L.91 Chain T: A.25, R.26, G.27, F.28, R.29, P.30, Y.33 Ligands: PLC.21, CDL.23 9 PLIP interactions: 6 interactions with chain I, 2 interactions with chain T, 1 interactions with chain 8 Hydrophobic interactions: I:L.79, I:A.81, I:F.84, I:F.84, I:L.91, T:Y.33, T:Y.33, 8:L.183 Salt bridges: I:K.76 PLC.21: 9 residues within 4Å: Chain I: Y.88 Chain T: A.25, R.26, G.27, F.28, Y.33 Chain W: L.28 Ligands: PLC.20, CDL.23 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain T Hydrophobic interactions: I:Y.88 Hydrogen bonds: T:G.27 Salt bridges: T:R.26, T:R.26 PLC.28: 13 residues within 4Å: Chain 3: A.35, A.39, L.51, Y.52 Chain 8: I.326, T.330, F.334 Chain T: G.42, F.45, Y.46, L.49, G.50, Q.53 9 PLIP interactions: 2 interactions with chain 3, 3 interactions with chain 8, 4 interactions with chain T Hydrophobic interactions: 3:A.39, 3:L.51, 8:I.326, 8:I.326, 8:F.334, T:F.45, T:F.45, T:F.45, T:Y.46 PLC.30: 14 residues within 4Å: Chain 4: L.24, N.25, S.26, I.27 Chain 8: Y.21, N.40, F.41, V.42, G.43, Y.44, L.47, L.48 Chain D: I.13 Chain K: W.70 4 PLIP interactions: 2 interactions with chain 8, 1 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: 8:L.47, 8:L.48, D:I.13 Hydrogen bonds: K:W.70 PLC.43: 7 residues within 4Å: Chain 5: Y.51 Chain 7: Y.35 Ligands: CDL.38 Chain b: I.463, I.466 Chain c: L.64, F.65 7 PLIP interactions: 3 interactions with chain c, 3 interactions with chain b, 1 interactions with chain 5 Hydrophobic interactions: c:L.64, c:F.65, c:F.65, b:I.463, b:I.463, b:I.466 Hydrogen bonds: 5:Y.51 PLC.44: 9 residues within 4Å: Chain Q: W.29, S.31 Chain c: C.297, V.427, K.431, F.536, N.537, I.543, Y.547 6 PLIP interactions: 5 interactions with chain c, 1 interactions with chain Q Hydrophobic interactions: c:V.427, c:F.536 Salt bridges: c:K.431, c:K.431 pi-Cation interactions: c:Y.547 Hydrogen bonds: Q:S.31

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.22: 30 residues within 4Å: Chain 3: P.37, L.41 Chain 8: Y.332 Chain 9: I.3, L.4, I.7 Chain U: H.27, F.28, K.29, F.87, S.129, S.130, F.153, P.154, W.155, F.156, F.158, V.159, N.160 Ligands: CDL.31 Chain a: N.85, Y.86, F.88, T.89, I.90, L.92, L.93 Chain d: F.160, L.163, V.164 31 PLIP interactions: 5 interactions with chain 9, 5 interactions with chain a, 16 interactions with chain U, 1 interactions with chain 8, 3 interactions with chain d, 1 interactions with chain 3 Hydrophobic interactions: 9:I.3, 9:I.3, 9:L.4, 9:L.4, 9:I.7, a:Y.86, a:F.88, a:I.90, a:L.92, a:L.93, U:F.87, U:F.153, U:P.154, U:W.155, U:W.155, U:F.156, U:F.158, U:F.158, U:F.158, d:F.160, d:L.163, d:V.164, 3:L.41 Hydrogen bonds: U:S.129, U:S.130, U:S.130, U:F.158, U:N.160, 8:Y.332 Salt bridges: U:K.29, U:K.29 CDL.23: 20 residues within 4Å: Chain 4: S.4, L.5 Chain 8: F.291 Chain D: A.2, I.3, F.5, L.8, L.9, G.12 Chain I: L.91, E.92, F.95 Chain W: G.16, S.17, W.21, L.24, R.25, L.28 Ligands: PLC.20, PLC.21 17 PLIP interactions: 4 interactions with chain W, 7 interactions with chain D, 1 interactions with chain 8, 1 interactions with chain 4, 4 interactions with chain I Hydrophobic interactions: W:W.21, W:L.24, W:L.28, D:F.5, D:L.8, D:L.8, D:L.9, 8:F.291, 4:L.5, I:F.95, I:F.95, I:F.95, I:F.95 Hydrogen bonds: W:W.21, D:A.2, D:A.2, D:I.3 CDL.31: 23 residues within 4Å: Chain 3: N.5, G.7, F.8, W.9, Y.15, F.30 Chain 9: L.4, I.7, S.8, T.11, F.12, M.15 Chain U: K.73, V.77, T.79, M.80, F.83, A.84, F.87, P.154 Ligands: CDL.22, 3PE.35 Chain a: V.103 16 PLIP interactions: 3 interactions with chain 9, 8 interactions with chain U, 4 interactions with chain 3, 1 interactions with chain a Hydrophobic interactions: 9:L.4, 9:I.7, 9:F.12, U:T.79, U:M.80, U:F.83, U:F.83, U:A.84, U:P.154, 3:F.8, 3:F.30, a:V.103 Hydrogen bonds: U:R.76, 3:N.5, 3:F.8 Salt bridges: U:K.73 CDL.38: 38 residues within 4Å: Chain 5: M.15, I.36 Chain 7: Y.20, K.23, W.24, V.27, L.31 Chain R: Y.169, A.173, L.176, L.179, L.180, M.183 Ligands: 3PE.26, PLC.43 Chain b: T.87, L.90, V.333, F.337, Q.371, T.374, Y.375, I.448, K.451, F.452, N.455, I.456, I.458, I.459, S.460, L.462, I.463, I.464, I.470, M.471 Chain c: C.13, L.17, F.21 33 PLIP interactions: 5 interactions with chain R, 16 interactions with chain b, 7 interactions with chain 7, 5 interactions with chain c Hydrophobic interactions: R:L.176, R:L.176, R:L.179, R:L.180, b:T.87, b:L.90, b:V.333, b:T.374, b:Y.375, b:I.456, b:I.458, b:I.459, b:L.462, b:I.463, b:I.464, b:I.464, b:I.470, 7:W.24, 7:W.24, 7:W.24, 7:W.24, 7:V.27, 7:L.31, c:L.17, c:F.21, c:F.21, c:F.21, c:F.21 Hydrogen bonds: R:Y.169, b:K.451, b:N.455 Salt bridges: b:K.451, 7:K.23 CDL.42: 22 residues within 4Å: Chain 6: Y.48 Chain J: P.116, A.117, G.120, W.121, L.124, C.125, A.128, C.129, F.132 Ligands: LMN.14, T7X.41 Chain c: R.586, L.587, G.591, I.592, R.594, L.595, K.598, I.647, F.654, S.655 16 PLIP interactions: 6 interactions with chain c, 10 interactions with chain J Hydrophobic interactions: c:L.587, c:I.592, c:I.647, c:F.654, J:A.117, J:W.121, J:W.121, J:W.121, J:W.121, J:L.124, J:L.124, J:L.124, J:A.128, J:F.132 Hydrogen bonds: c:R.594 Salt bridges: c:R.586

1 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.29: 18 residues within 4Å: Chain 8: L.16, A.20, T.23, E.26, R.27, L.30, A.50, D.53, A.54, L.57, F.224, V.225, F.228, Y.232, R.297 Chain K: W.77, I.106, R.108 13 PLIP interactions: 13 interactions with chain 8 Hydrophobic interactions: 8:L.16, 8:T.23, 8:D.53, 8:A.54, 8:L.57, 8:F.224, 8:V.225, 8:F.228, 8:F.228, 8:F.228, 8:F.228, 8:F.228 pi-Cation interactions: 8:R.297

4 x T7X: Phosphatidylinositol(Non-covalent)

T7X.32: 15 residues within 4Å: Chain 9: I.33, L.36, S.437, V.438, Y.441 Chain U: W.59, L.60 Chain Y: K.18, R.25, Y.32, F.38, S.39, A.42, L.46 Ligands: PSC.33 13 PLIP interactions: 8 interactions with chain Y, 5 interactions with chain 9 Hydrophobic interactions: Y:F.38, Y:A.42, Y:L.46, Y:L.46, 9:I.33, 9:L.36, 9:Y.441 Hydrogen bonds: Y:R.25, Y:R.25, 9:S.437, 9:S.437 Salt bridges: Y:K.18, Y:R.25 T7X.34: 23 residues within 4Å: Chain 9: L.167, Y.170, D.196, N.198, L.199, I.202, A.203, L.206, N.256, S.257, L.258, V.259 Chain J: N.140 Chain L: L.8, F.12 Chain c: I.625, L.629, V.632, L.633 Chain d: V.103, L.104, S.107, G.108 20 PLIP interactions: 3 interactions with chain d, 9 interactions with chain 9, 5 interactions with chain c, 2 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: d:V.103, d:L.104, 9:L.167, 9:Y.170, 9:L.199, 9:L.199, 9:A.203, 9:L.206, c:I.625, c:L.629, c:L.629, c:V.632, c:L.633, L:L.8, L:F.12 Salt bridges: d:K.121 Hydrogen bonds: 9:S.257, 9:L.258, 9:V.259, J:N.140 T7X.36: 15 residues within 4Å: Chain 8: V.55, L.59 Chain E: W.305, W.306 Chain K: L.64, A.68, I.203, T.204 Chain a: V.21, I.23, L.24, L.25, A.26, V.27, Y.28 12 PLIP interactions: 4 interactions with chain 8, 4 interactions with chain K, 2 interactions with chain E, 2 interactions with chain a Hydrophobic interactions: 8:V.55, 8:V.55, 8:L.59, 8:L.59, K:L.64, K:L.64, K:A.68, K:I.203, E:W.305, a:V.21 Hydrogen bonds: E:W.305, a:L.24 T7X.41: 15 residues within 4Å: Chain 9: L.407, L.411 Chain C: A.36, L.37 Chain J: L.131 Ligands: 3PE.11, CDL.42 Chain b: F.165, Y.166, M.169, F.170, S.173 Chain c: G.588, P.589, I.592 3 PLIP interactions: 1 interactions with chain b, 1 interactions with chain 9, 1 interactions with chain J Hydrophobic interactions: b:F.170, 9:L.407, J:L.131

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.33: 19 residues within 4Å: Chain 9: L.36, S.40, Y.43, Y.67, M.70, Y.311, T.314, L.378, L.449, G.453, Y.456, I.460, I.463, F.464, Y.467 Chain Y: V.49, L.50, V.53 Ligands: T7X.32 10 PLIP interactions: 9 interactions with chain 9, 1 interactions with chain Y Hydrophobic interactions: 9:M.70, 9:Y.311, 9:Y.311, 9:T.314, 9:L.378, 9:Y.456, 9:Y.456, 9:I.460, Y:L.50 pi-Cation interactions: 9:Y.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galemou Yoga, E. et al., Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Nat Commun (2020)

Release Date

2020-10-28

Peptides

Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I): A
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I): B
Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I): C
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I): D
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I): E
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I): F
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I): G
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I): H
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I): I
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I): J
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I): K
Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I): L
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I): M
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I): N
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I): O
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I): P
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I): Q
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I): R
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I): S
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I): T
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I): U
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I): V
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I): W
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I): X
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I): Y
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I): Z
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I): 0
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I): 1
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I): 2
Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I): 3
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I): 4
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I): 5
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I): 6
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I): 7
Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I): 8
Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I): 9
Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I): a
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I): b
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I): c
Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I): d
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I): e
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I): f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
O

O
P

P
Q

Q
R

R
S

S
U

T
W

U
X

V
Y

W
Z

X
a

Y
b

Z
c

0
d

1
e

2
f

3
g

4
h

5
i

6
j

7
n

8
1

9
2

a
3

b
4

c
5

d
6

e
8

f
9

Membrane

We predict this structure to be a membrane protein.
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Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Related Entries With Identical Sequence