SMTL ID : 7r41.1

Bovine complex I in the presence of IM1761092, active class i (Composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 15 residues within 4Å: Chain 1: V.30, P.33, T.34, T.39, K.40, L.43 Chain A: L.84, N.85, L.88, T.89, L.92, F.93, I.96, L.97 Chain H: I.309 Ligand excluded by PLIP LMT.2: 13 residues within 4Å: Chain 1: E.16, L.19, S.22, F.23, A.26 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295, A.299, M.302 Ligand excluded by PLIP LMT.20: 7 residues within 4Å: Chain J: M.1, Y.4, I.8, V.11, M.15, L.108, K.111 Ligand excluded by PLIP LMT.23: 9 residues within 4Å: Chain D: Y.53 Chain L: S.567, L.568, Q.570, M.571 Chain N: I.284, L.287, Y.291 Ligands: LMT.30 Ligand excluded by PLIP LMT.25: 11 residues within 4Å: Chain L: L.491, T.494, I.495, F.498, I.499, L.502, E.503, N.506, K.509 Chain a: V.64, L.67 Ligand excluded by PLIP LMT.27: 16 residues within 4Å: Chain 8: R.65, F.69, T.72, H.73, I.76, I.80 Chain L: M.17, M.20, M.21, T.26, Y.27, K.28, S.30, N.31, L.34, Y.35 Ligand excluded by PLIP LMT.30: 13 residues within 4Å: Chain L: L.562, K.564 Chain M: N.144, L.147, Y.148, F.151, Y.152, A.155, L.212 Chain N: Y.291 Ligands: LMT.23, 3PE.29 Chain c: Y.77 Ligand excluded by PLIP LMT.31: 7 residues within 4Å: Chain M: N.188, F.256, P.260 Ligands: LMT.47 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP LMT.32: 14 residues within 4Å: Chain 5: D.9, H.10, H.13, P.17 Chain 6: A.81, V.82, W.85, V.89, F.93 Chain M: K.19, N.21, M.22, H.30, L.33 Ligand excluded by PLIP LMT.35: 16 residues within 4Å: Chain 4: R.64, Q.70 Chain J: F.117, E.118 Chain K: M.1, M.9, T.13, L.16 Chain L: I.595 Chain N: M.72, I.76, F.80, N.91, P.92, M.93, L.97 Ligand excluded by PLIP LMT.47: 11 residues within 4Å: Chain M: N.188, S.189, W.190, F.256, M.257, P.260, F.261 Chain Y: D.85, L.130, E.131 Ligands: LMT.31 Ligand excluded by PLIP LMT.49: 10 residues within 4Å: Chain N: I.277 Chain Y: W.10, T.121, L.124, V.125, G.128, Q.129, G.132, W.133, V.135 Ligand excluded by PLIP LMT.50: 12 residues within 4Å: Chain Y: I.28, G.29, V.36, R.58, Y.59, T.62, A.63, I.66, G.67, F.70, T.105 Ligands: 3PE.48 Ligand excluded by PLIP LMT.53: 11 residues within 4Å: Chain 7: V.82, G.85, I.86, I.89, I.93, P.116, I.117, R.119, W.120 Chain f: N.59, Y.61 Ligand excluded by PLIP LMT.54: 7 residues within 4Å: Chain 9: R.55, I.59, E.62, F.63, T.67, F.70 Chain a: W.73 Ligand excluded by PLIP LMT.55: 8 residues within 4Å: Chain L: L.286, F.418 Chain b: L.128, K.131, H.132, G.135, F.136, F.139 Ligand excluded by PLIP

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

PC1.3: 8 residues within 4Å: Chain A: W.23, L.24, P.25, Q.26 Chain P: S.308, F.310, W.313 Ligands: PC1.5 1 PLIP interactions: 1 interactions with chain P pi-Cation interactions: P:F.310 PC1.5: 15 residues within 4Å: Chain A: I.20, W.23, L.24, Q.26 Chain B: I.74, R.78, R.209, L.210, W.213, R.216 Chain H: F.56 Chain P: D.90, F.310, E.311 Ligands: PC1.3 13 PLIP interactions: 2 interactions with chain P, 5 interactions with chain B, 2 interactions with chain A, 4 interactions with chain H Salt bridges: P:D.90, P:E.311, B:R.78, B:R.216 Water bridges: B:R.78, B:W.213, B:R.216 Hydrophobic interactions: A:I.20, A:W.23, H:F.56, H:F.56, H:F.56, H:F.56 PC1.6: 12 residues within 4Å: Chain B: K.69, D.72, W.76, R.79, K.205 Chain H: L.46, I.49 Chain g: F.28, R.29, N.31, W.75, V.77 9 PLIP interactions: 2 interactions with chain H, 7 interactions with chain B Hydrophobic interactions: H:L.46, H:I.49, B:D.72, B:W.76, B:W.76 Salt bridges: B:R.79, B:R.79, B:K.205, B:K.205 PC1.28: 18 residues within 4Å: Chain 6: V.98, S.103, V.106, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, W.71, I.317, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: 3PE.26, CDL.52 12 PLIP interactions: 2 interactions with chain 6, 10 interactions with chain M Hydrophobic interactions: 6:V.98, 6:V.106, M:I.67, M:W.71, M:W.71, M:I.317, M:P.443, M:L.447, M:L.449, M:L.449, M:N.450, M:I.454

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

SF4.4: 13 residues within 4Å: Chain B: A.90, C.91, C.92, G.127, T.128, G.154, S.155, C.156, C.186, P.187 Chain D: R.118, R.138, H.223 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.91, B:C.92, B:C.156, B:C.186 SF4.9: 13 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.10: 13 residues within 4Å: Chain D: I.379 Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.127 Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.11: 14 residues within 4Å: Chain G: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, C.226, P.227, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.17: 12 residues within 4Å: Chain I: H.101, C.123, P.124, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:C.123, I:C.152, I:C.155, I:C.158 SF4.18: 14 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, L.118, C.119, I.130, Y.145, C.162, P.163, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.113, I:C.116, I:C.119, I:C.162

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

FES.7: 10 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, C.176, L.177, G.178, A.179, C.180, M.185 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.135, E:C.140, E:C.176, E:C.180 FES.12: 10 residues within 4Å: Chain G: R.62, F.63, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 18 residues within 4Å: Chain F: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 25 PLIP interactions: 25 interactions with chain F Hydrophobic interactions: F:Y.204, F:Y.204, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:G.89, F:N.116, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247 Water bridges: F:G.87, F:G.87, F:A.91, F:G.92, F:K.98, F:K.98, F:N.116, F:E.119, F:E.121, F:G.207 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.13: 5 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:I.223, G:C.226, G:V.228, H2O.18

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

3PE.14: 25 residues within 4Å: Chain 0: A.39, H.40 Chain A: M.1, L.3, M.4, F.11 Chain H: M.77, M.98, N.99, F.104, M.108, W.118 Chain J: L.9, I.34, V.35, G.38, L.45, N.46, S.50, L.54 Chain Z: F.140, I.141, W.142, Y.143, T.144 13 PLIP interactions: 6 interactions with chain J, 5 interactions with chain H, 1 interactions with chain A, 1 interactions with chain 0 Hydrophobic interactions: J:L.9, J:I.34, J:V.35, J:L.45, J:L.45, H:F.104, H:W.118, A:F.11 Hydrogen bonds: J:S.50, H:N.99, H:N.99, 0:A.39 Water bridges: H:L.100 3PE.15: 15 residues within 4Å: Chain H: Q.169, E.170, W.173, L.243, G.244, T.245, S.246, N.258, I.261, K.262, L.265, L.266, S.269, W.272 Ligands: 3PE.16 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:L.243, H:K.262, H:L.265, H:L.265, H:L.266, H:W.272 Hydrogen bonds: H:E.170, H:S.246, H:N.258 Salt bridges: H:K.262, H:K.262 3PE.16: 24 residues within 4Å: Chain 1: E.16, V.18, I.25, L.28 Chain D: R.266 Chain H: W.179, P.180, A.182, M.183, I.187, Y.277, F.280, L.288, N.292, F.293, L.296 Chain I: T.60, L.61, W.63, L.66, I.67, L.70 Chain Z: L.43 Ligands: 3PE.15 15 PLIP interactions: 5 interactions with chain H, 4 interactions with chain 1, 2 interactions with chain D, 1 interactions with chain Z, 3 interactions with chain I Hydrophobic interactions: H:W.179, H:P.180, H:I.187, H:Y.277, H:F.280, 1:I.25, 1:I.25, 1:L.28, Z:L.43, I:L.61, I:I.67, I:L.70 Hydrogen bonds: 1:E.16 Salt bridges: D:R.266, D:R.266 3PE.22: 17 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, G.228, F.529, M.533, H.534, A.537, P.538, N.541 Chain M: V.401, L.405 Chain b: Q.84, N.115, R.116 14 PLIP interactions: 2 interactions with chain b, 10 interactions with chain L, 2 interactions with chain M Hydrophobic interactions: b:R.116, L:L.173, L:Y.174, L:F.529, L:A.537, L:P.538, L:P.538, L:N.541, M:V.401, M:L.405 Hydrogen bonds: b:Q.84, L:Q.170 Salt bridges: L:H.534, L:H.534 3PE.26: 19 residues within 4Å: Chain 8: I.80, Y.83, Y.84, H.88, K.92 Chain L: N.65, W.66, H.67, W.68, S.77, L.78, N.136, F.138, Q.139, I.142 Chain M: L.449 Ligands: CDL.24, PC1.28, CDL.52 18 PLIP interactions: 10 interactions with chain L, 7 interactions with chain 8, 1 interactions with chain M Hydrophobic interactions: L:W.66, L:W.66, L:W.68, L:W.68, L:F.138, L:F.138, L:Q.139, L:I.142, 8:I.80, 8:Y.83, 8:Y.83, 8:Y.84, 8:Y.84, M:L.449 Hydrogen bonds: L:W.66, L:H.67 Salt bridges: 8:K.92, 8:K.92 3PE.29: 16 residues within 4Å: Chain M: A.163, Y.166, S.191, F.194, M.195, A.198, M.201 Chain N: N.274, I.276, I.277, T.280, I.284 Chain Y: L.124, E.131, W.133 Ligands: LMT.30 15 PLIP interactions: 3 interactions with chain Y, 7 interactions with chain M, 5 interactions with chain N Hydrophobic interactions: Y:L.124, Y:W.133, M:Y.166, M:F.194, M:F.194, M:M.195, M:A.198, M:M.201, N:I.276, N:I.277, N:T.280, N:I.284 Hydrogen bonds: Y:E.131, M:S.191, N:N.274 3PE.33: 21 residues within 4Å: Chain 3: F.36, C.40, L.43, I.44, A.47, V.53, L.54 Chain M: I.9, M.12, W.16, L.94, T.97, M.98, S.101, L.104, F.105 Chain N: I.239 Chain O: K.326, Y.327 Ligands: 3PE.34, 3PE.46 15 PLIP interactions: 8 interactions with chain M, 6 interactions with chain 3, 1 interactions with chain O Hydrophobic interactions: M:I.9, M:W.16, M:W.16, M:W.16, M:L.94, M:T.97, M:L.104, M:F.105, 3:F.36, 3:L.43, 3:L.43, 3:I.44, 3:V.53 Hydrogen bonds: 3:V.53 Salt bridges: O:K.326 3PE.34: 19 residues within 4Å: Chain M: T.90, R.91, L.94, M.98, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, L.243, A.246, P.256, T.301, T.334, M.335 Chain O: Q.317 Ligands: 3PE.33, 3PE.46 10 PLIP interactions: 4 interactions with chain M, 5 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: M:L.94, M:V.127, M:I.131, M:I.131, N:V.242, N:L.243, N:A.246, N:P.256, N:T.301 Hydrogen bonds: O:Q.317 3PE.36: 13 residues within 4Å: Chain N: K.46, S.125, L.128, I.129, T.132, W.133, I.209, I.210, S.213, T.217, M.220, T.324, M.329 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:I.129, N:W.133, N:I.209, N:I.210, N:T.217 Hydrogen bonds: N:K.46, N:S.125 3PE.37: 4 residues within 4Å: Chain L: F.602, F.604 Chain N: N.152, T.156 6 PLIP interactions: 4 interactions with chain L, 1 interactions with chain N, 1 interactions with chain Y Hydrophobic interactions: L:F.602, L:F.602, L:F.602, L:F.604 Hydrogen bonds: N:N.152 Salt bridges: Y:K.3 3PE.42: 10 residues within 4Å: Chain A: W.23, L.27 Chain P: N.219, I.220, W.222, F.223, Y.291, L.293, W.313, T.314 16 PLIP interactions: 14 interactions with chain P, 2 interactions with chain A Hydrophobic interactions: P:N.219, P:I.220, P:W.222, P:W.222, P:W.222, P:F.223, P:F.223, P:F.223, P:Y.291, P:L.293, P:W.313, P:W.313, P:T.314, A:W.23 Hydrogen bonds: P:N.219, A:L.27 3PE.46: 20 residues within 4Å: Chain 3: P.29, R.30, F.33, F.36, Y.39 Chain 5: K.33 Chain M: L.55, F.105, M.108, L.117, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: 3PE.33, 3PE.34 16 PLIP interactions: 5 interactions with chain 3, 4 interactions with chain X, 4 interactions with chain N, 1 interactions with chain 5, 2 interactions with chain M Hydrophobic interactions: 3:R.30, 3:F.33, 3:F.33, 3:F.36, 3:Y.39, X:F.169, X:F.169, N:P.256, N:L.337, N:P.338, N:P.338, M:F.105, M:L.121 Hydrogen bonds: X:T.171, X:T.171 Salt bridges: 5:K.33 3PE.48: 16 residues within 4Å: Chain D: E.57 Chain L: L.576, V.577, Q.580, T.594, I.597, S.598 Chain N: P.110, L.160, I.164 Chain Y: V.36, Y.39, S.40, L.43, K.44 Ligands: LMT.50 12 PLIP interactions: 2 interactions with chain N, 2 interactions with chain L, 2 interactions with chain D, 6 interactions with chain Y Hydrophobic interactions: N:P.110, N:I.164, L:T.594, L:I.597, Y:Y.39, Y:Y.39, Y:Y.39, Y:L.43 Hydrogen bonds: D:E.57, D:E.57, Y:S.40 Salt bridges: Y:K.44 3PE.51: 16 residues within 4Å: Chain 2: K.43, L.46, T.47, T.50, L.54 Chain 3: D.45, R.60, L.63, Y.64, S.67, F.68, V.71, L.75 Chain N: T.328, M.336, M.342 10 PLIP interactions: 8 interactions with chain 3, 2 interactions with chain 2 Hydrophobic interactions: 3:L.63, 3:Y.64, 3:Y.64, 3:Y.64, 3:F.68, 3:V.71, 3:L.75, 2:L.54 Salt bridges: 3:R.60, 2:K.43

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 17 residues within 4Å: Chain H: R.62, S.67, A.68, S.69, L.73, I.76 Chain J: M.15, G.16, G.19, Y.28, V.35, I.82, W.83, L.84 Chain P: W.222, R.286, T.358 15 PLIP interactions: 6 interactions with chain J, 8 interactions with chain H, 1 interactions with chain P Hydrophobic interactions: J:V.35, J:W.83, J:W.83, H:L.73, H:L.73, H:I.76 Hydrogen bonds: J:W.83, J:L.84, H:S.69, H:S.69 Water bridges: J:Y.28, H:A.68, H:A.68 Salt bridges: H:R.62, P:R.286 CDL.21: 24 residues within 4Å: Chain J: S.21, K.23, A.88, A.92, G.96, M.99 Chain K: M.10, V.14, V.17, M.21, Y.22, R.23 Chain L: K.585, L.589, L.596 Chain Y: A.38, V.41, T.45, P.46, S.48, F.49, G.52, V.53, T.56 11 PLIP interactions: 1 interactions with chain J, 5 interactions with chain K, 2 interactions with chain Y, 3 interactions with chain L Salt bridges: J:K.23, K:R.23, L:K.585 Hydrophobic interactions: K:V.14, K:V.17, K:M.21, Y:V.53, L:L.589, L:L.596 Water bridges: K:S.24 Hydrogen bonds: Y:G.52 CDL.24: 24 residues within 4Å: Chain 6: L.99, V.100, S.103 Chain 7: L.68, L.71, R.72 Chain L: S.23, N.25, K.116, K.119, Y.120, L.123, T.127, I.142, G.146, M.150, L.153 Chain M: L.354, T.357, L.360, L.361, L.445 Ligands: 3PE.26, CDL.52 17 PLIP interactions: 1 interactions with chain 6, 4 interactions with chain M, 3 interactions with chain 7, 9 interactions with chain L Hydrophobic interactions: 6:V.100, M:L.360, M:L.361, M:L.445, 7:L.68, 7:L.71, L:T.127, L:I.142, L:L.153 Hydrogen bonds: M:T.357, L:N.25, L:Y.120 Salt bridges: 7:K.69, L:K.116, L:K.119, L:K.119, L:K.119 CDL.52: 23 residues within 4Å: Chain 6: A.107, Y.108 Chain 7: I.86, T.87, N.90, V.91, E.95, H.115 Chain 8: Y.83, Y.84, H.88 Chain L: L.9, L.12, L.13, N.65 Chain M: L.446, L.449 Ligands: CDL.24, 3PE.26, PC1.28 Chain f: R.49, I.52, H.56 17 PLIP interactions: 2 interactions with chain 6, 2 interactions with chain L, 5 interactions with chain 8, 2 interactions with chain M, 1 interactions with chain f, 5 interactions with chain 7 Hydrophobic interactions: 6:A.107, L:L.9, L:L.12, 8:Y.83, 8:Y.83, 8:Y.84, 8:Y.84, M:L.446, M:L.449, 7:I.86 Hydrogen bonds: 6:Y.108, 7:N.90, 7:N.90, 7:E.95 Salt bridges: 8:H.88, f:R.49, 7:H.115 CDL.57: 21 residues within 4Å: Chain 0: M.1, W.2, F.3, L.6, P.7, I.9, A.10 Chain H: Y.43 Chain I: F.78 Chain g: L.3, V.6, L.7, R.9, G.10, Q.13 Chain h: S.3, A.4, T.5, F.7, I.8, L.11 10 PLIP interactions: 4 interactions with chain h, 3 interactions with chain 0, 2 interactions with chain g, 1 interactions with chain I Hydrophobic interactions: h:F.7, h:F.7, h:L.11, 0:P.7, 0:I.9, 0:A.10 Hydrogen bonds: h:T.5, g:R.9 Salt bridges: g:R.9 Water bridges: I:F.78

1 x I49: 1-carbamimidoyl-3-[2-(3-chloranyl-4-iodanyl-phenyl)ethyl]guanidine(Non-covalent)

I49.38: 9 residues within 4Å: Chain 3: M.82, R.86 Chain 7: R.157, W.168, F.169 Chain N: Y.196, N.197, P.198, E.347 6 PLIP interactions: 5 interactions with chain N, 1 interactions with chain 3 Hydrogen bonds: N:Y.196, N:Y.196, N:N.197, N:T.199 Salt bridges: N:E.347 Hydrophobic interactions: 3:R.86

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

GTP.39: 22 residues within 4Å: Chain O: N.53, I.54, C.55, S.56, G.57, K.58, S.59, E.76, L.102, F.105, Y.106, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214, Y.221 Ligands: MG.40 21 PLIP interactions: 21 interactions with chain O Hydrogen bonds: O:N.53, O:C.55, O:S.56, O:G.57, O:K.58, O:S.59, O:Y.106, O:Q.120, O:R.127, O:R.127, O:R.149, O:E.214, O:E.214, O:Y.221 Salt bridges: O:K.58, O:K.58, O:K.58, O:R.149, O:K.209 pi-Stacking: O:F.157, O:F.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.40: 2 residues within 4Å: Chain O: S.59 Ligands: GTP.39 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.59

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

NDP.41: 26 residues within 4Å: Chain B: R.216 Chain P: 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.167, S.168, H.169, Y.180, K.184, P.203, A.204, E.205, I.206, R.212 26 PLIP interactions: 25 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:I.206 Hydrogen bonds: P:G.60, P:T.62, P:T.62, P:T.62, P:F.64, P:L.65, P:R.85, P:R.85, P:L.129, P:G.131, P:K.184, P:I.206, P:I.206 Water bridges: P:G.63, P:G.66, P:R.85, P:R.85 Salt bridges: P:R.85, P:R.132, P:R.132, P:R.212, P:R.212, B:R.216 pi-Cation interactions: P:R.85, P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.43: 5 residues within 4Å: Chain R: C.87, G.89, H.96, C.112, C.115 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.87, R:H.96, R:C.112, R:C.115

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

EHZ.44: 19 residues within 4Å: Chain T: D.111, S.112, L.113 Chain W: M.25, K.29, V.32, L.35, W.39, G.59, K.62, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.106 12 PLIP interactions: 10 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:W.39, W:K.62, W:M.66, W:F.67, W:F.106, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 Salt bridges: W:K.29 EHZ.45: 20 residues within 4Å: Chain L: Y.513 Chain U: D.111, S.112 Chain d: H.12, Q.13, H.26, L.27, W.30, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, L.64, A.67, F.71, G.74 10 PLIP interactions: 9 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:H.26, d:L.44, d:F.48, d:E.54, d:A.67 Hydrogen bonds: d:Q.13, d:H.51, d:K.52, U:S.112

1 x MYR: MYRISTIC ACID(Covalent)

MYR.56: 7 residues within 4Å: Chain L: N.400, L.409, L.486 Chain b: Q.154 Chain e: G.2, H.4, L.5 4 PLIP interactions: 1 interactions with chain e, 2 interactions with chain L, 1 interactions with chain b Hydrophobic interactions: e:L.5, L:L.409, L:L.486 Hydrogen bonds: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bridges, H.R. et al., Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Science (2023)

Release Date

2023-02-08

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: I
NADH-ubiquinone oxidoreductase chain 6: J
NADH-ubiquinone oxidoreductase chain 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: S
Acyl carrier protein, mitochondrial: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: 1
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C2: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
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
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

h
r

i
s

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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