SMTL ID : 7r48.1

Bovine complex I in the presence of IM1761092, deactive class iv (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

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

LMT.1: 10 residues within 4Å: Chain 1: V.30, T.34, T.39, K.40, L.43 Chain A: N.85, L.88, T.89, F.93, I.96 5 PLIP interactions: 1 interactions with chain 1, 4 interactions with chain A Water bridges: 1:T.39 Hydrophobic interactions: A:T.89, A:F.93, A:I.96 Hydrogen bonds: A:N.85 LMT.3: 8 residues within 4Å: Chain 1: F.23, A.26, G.27 Chain A: I.96, A.103, T.107, K.109 Ligands: 3PE.2 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain 1 Hydrophobic interactions: A:I.96, A:A.103, 1:F.23, 1:F.23, 1:F.23, 1:A.26 Hydrogen bonds: A:K.109, A:K.109 LMT.5: 14 residues within 4Å: Chain A: P.25, Q.26, L.27, N.28, K.33 Chain B: I.74, R.78, E.146, R.209 Chain H: I.57, K.58, E.59 Chain P: Y.89, D.90 11 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, 1 interactions with chain P, 1 interactions with chain H Hydrophobic interactions: B:I.74, A:L.27 Hydrogen bonds: B:R.209, B:R.209, A:Q.26, A:Q.26, A:K.33, A:K.33, P:D.90, H:E.59 Salt bridges: B:R.78 LMT.20: 12 residues within 4Å: Chain 4: V.12, D.13, L.14, E.24 Chain A: N.83, T.86 Chain J: S.148, Y.149, T.151, W.152, I.155 Chain N: L.15 9 PLIP interactions: 4 interactions with chain 4, 2 interactions with chain A, 2 interactions with chain J, 1 interactions with chain N Hydrophobic interactions: 4:V.12, 4:L.14, J:T.151, J:W.152, N:L.15 Hydrogen bonds: 4:D.13, 4:E.24, A:T.86, A:T.86 LMT.23: 8 residues within 4Å: Chain D: Y.53 Chain L: S.567, L.568, Q.570, M.571 Chain N: I.284, Y.291 Ligands: LMT.28 7 PLIP interactions: 1 interactions with chain D, 2 interactions with chain L, 4 interactions with chain N Hydrogen bonds: D:Y.53, N:Y.291 Hydrophobic interactions: L:Q.570, L:Q.570, N:I.284, N:Y.291, N:Y.291 LMT.28: 15 residues within 4Å: Chain L: L.562, P.563, K.564, I.566, S.567 Chain M: N.144, L.147, Y.148, Y.152, A.155, L.212 Chain N: Y.291 Ligands: LMT.23, 3PE.27 Chain c: Y.77 12 PLIP interactions: 7 interactions with chain M, 4 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: M:Y.148, M:Y.152, M:Y.152, M:A.155, M:L.212, L:L.562, L:I.566 Hydrogen bonds: M:N.144, M:Y.148, L:S.567, N:Y.291 Salt bridges: L:K.564 LMT.29: 8 residues within 4Å: Chain M: N.188, S.189, W.190, V.193, F.256, M.257, P.260 Chain Y: D.85 8 PLIP interactions: 7 interactions with chain M, 1 interactions with chain Y Hydrophobic interactions: M:W.190, M:W.190, M:V.193, M:F.256, M:P.260 Hydrogen bonds: M:N.188, M:N.188, Y:D.85 LMT.31: 9 residues within 4Å: Chain 3: L.54, L.55, L.62 Chain M: W.16, L.17, S.18, K.19, N.20, K.93 4 PLIP interactions: 3 interactions with chain 3, 1 interactions with chain M Hydrophobic interactions: 3:L.55, 3:L.62 Water bridges: 3:L.54, M:K.93 LMT.32: 11 residues within 4Å: Chain 4: Q.70 Chain J: F.117, E.118 Chain K: M.1, M.9, T.13 Chain L: I.595 Chain N: F.80, N.91, P.92, M.93 8 PLIP interactions: 2 interactions with chain J, 3 interactions with chain N, 1 interactions with chain K, 1 interactions with chain 4, 1 interactions with chain L Hydrophobic interactions: J:F.117, N:F.80, K:M.9, L:I.595 Hydrogen bonds: J:E.118, N:N.91, N:N.91, 4:Q.70 LMT.43: 12 residues within 4Å: Chain N: I.277 Chain Y: W.10, D.11, T.121, L.124, V.125, G.128, Q.129, G.132, W.133, V.135 Ligands: 3PE.27 8 PLIP interactions: 7 interactions with chain Y, 1 interactions with chain N Hydrophobic interactions: Y:L.124, Y:L.124, Y:V.125, Y:V.135, N:I.277 Hydrogen bonds: Y:W.10, Y:D.11, Y:Q.129 LMT.46: 12 residues within 4Å: Chain 5: F.20, Y.24, R.28 Chain 6: F.105 Chain 7: H.109, W.110, R.123, T.124, F.125 Chain M: F.36, L.39, L.40 9 PLIP interactions: 2 interactions with chain 5, 1 interactions with chain 7, 5 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: 5:F.20, 7:F.125, M:F.36, M:F.36, M:L.39, M:L.40, M:L.40, 6:F.105 Hydrogen bonds: 5:R.28 LMT.49: 13 residues within 4Å: Chain 7: V.82, G.85, I.86, I.89, I.93, W.110, P.116, I.117, R.119, W.120, R.123 Chain f: N.59, Y.61 15 PLIP interactions: 12 interactions with chain 7, 3 interactions with chain f Hydrophobic interactions: 7:I.86, 7:I.89, 7:I.117, 7:W.120, 7:W.120, 7:W.120, 7:W.120 Hydrogen bonds: 7:P.116, 7:R.119, 7:W.120, 7:R.123, 7:R.123, f:N.59, f:N.59, f:N.59 LMT.50: 8 residues within 4Å: Chain 9: R.55, I.59, E.62, F.63, A.66, T.67, F.70 Chain a: W.73 6 PLIP interactions: 4 interactions with chain 9, 2 interactions with chain a Hydrophobic interactions: 9:F.63, 9:F.63, 9:F.70, a:W.73, a:W.73 Hydrogen bonds: 9:R.55 LMT.51: 8 residues within 4Å: Chain L: N.518 Chain b: L.128, K.131, H.132, G.135, F.136, F.139, M.140 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain b Hydrogen bonds: L:N.518 Hydrophobic interactions: b:F.136, b:F.139, b:F.139 Salt bridges: b:H.132 LMT.52: 10 residues within 4Å: Chain L: I.561, T.565 Chain Y: A.113, A.116, Y.117 Chain c: Y.77, P.78, F.80, R.81, P.82 6 PLIP interactions: 3 interactions with chain c, 3 interactions with chain Y Hydrophobic interactions: c:P.82, Y:A.113, Y:A.116, Y:Y.117 Hydrogen bonds: c:Y.77, c:P.78

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

3PE.2: 18 residues within 4Å: Chain 1: W.13, E.16, L.19, V.20, S.22, F.23, A.24, A.26 Chain A: A.99, L.102, W.106, T.107 Chain H: K.291, P.295, L.298, A.299, M.302 Ligands: LMT.3 15 PLIP interactions: 8 interactions with chain 1, 4 interactions with chain A, 3 interactions with chain H Hydrophobic interactions: 1:W.13, 1:L.19, 1:F.23, 1:F.23, 1:F.23, 1:F.23, 1:A.24, 1:A.26, A:A.99, A:L.102, A:W.106, A:T.107, H:P.295, H:A.299 Salt bridges: H:K.291 3PE.14: 26 residues within 4Å: Chain 0: A.39, H.40 Chain A: M.1, L.3, M.4, L.7, F.11 Chain H: M.77, M.98, N.99, F.104, M.108, L.111, W.118 Chain J: L.31, V.35, G.38, G.42, L.45, N.46, S.50, L.54, F.57 Chain Z: F.140, I.141, T.144 13 PLIP interactions: 3 interactions with chain A, 4 interactions with chain H, 5 interactions with chain J, 1 interactions with chain 0 Hydrophobic interactions: A:L.7, A:L.7, A:F.11, H:F.104, H:L.111, H:W.118, J:L.31, J:V.35, J:L.45, J:L.54 Hydrogen bonds: H:N.99, J:S.50, 0:A.39 3PE.15: 14 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, S.269 Chain I: I.67 Ligands: 3PE.17 9 PLIP interactions: 1 interactions with chain I, 8 interactions with chain H Hydrophobic interactions: I:I.67, H:L.243, H:I.261, H:K.262, H:L.265 Hydrogen bonds: H:Q.169, H:S.246 Salt bridges: H:K.262, H:K.262 3PE.17: 23 residues within 4Å: Chain 1: V.18, I.25 Chain D: R.266 Chain H: W.179, P.180, M.183, M.184, F.186, I.187, Y.277, F.280, L.288, N.292, F.293, L.296, W.303 Chain I: T.60, L.61, W.63, L.66, I.67 Chain Z: L.43 Ligands: 3PE.15 17 PLIP interactions: 9 interactions with chain H, 3 interactions with chain I, 1 interactions with chain Z, 2 interactions with chain D, 2 interactions with chain 1 Hydrophobic interactions: H:W.179, H:P.180, H:M.183, H:F.186, H:F.186, H:I.187, H:F.280, H:L.296, H:W.303, I:W.63, I:W.63, I:I.67, Z:L.43, 1:I.25, 1:I.25 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, I.177, G.228, L.229, L.280, H.534, A.537, P.538, N.541 Chain M: V.398, L.405 Chain b: N.115, R.116 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:I.177, L:L.229, L:L.280, L:A.537, L:P.538, L:P.538, L:N.541, M:L.405 Hydrogen bonds: L:D.163, L:Q.170 Water bridges: L:D.163 Salt bridges: L:H.534, L:H.534 3PE.25: 16 residues within 4Å: Chain 8: I.80, Y.84, H.88, K.92 Chain L: N.65, W.66, H.67, W.68, S.77, L.78, N.136, F.138, I.142 Chain M: L.449 Ligands: PC1.47, CDL.48 16 PLIP interactions: 9 interactions with chain L, 6 interactions with chain 8, 1 interactions with chain M Hydrophobic interactions: L:W.66, L:W.68, L:W.68, L:W.68, L:L.78, L:F.138, L:I.142, 8:I.80, 8:Y.84, M:L.449 Hydrogen bonds: L:H.67, L:H.67 Water bridges: 8:K.92 Salt bridges: 8:H.88, 8:K.92, 8:K.92 3PE.26: 6 residues within 4Å: Chain L: F.602, F.604 Chain N: N.152, T.156 Chain Y: A.2, K.3 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain N, 1 interactions with chain Y Hydrophobic interactions: L:F.602, L:F.602 Hydrogen bonds: N:N.152 Salt bridges: Y:K.3 3PE.27: 20 residues within 4Å: Chain M: A.155, G.156, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: N.274, I.276, I.277, T.280, F.281, I.284 Chain Y: E.131, W.133 Ligands: LMT.28, LMT.43 16 PLIP interactions: 2 interactions with chain Y, 9 interactions with chain M, 5 interactions with chain N Hydrophobic interactions: Y:W.133, M:P.159, M:Y.166, M:F.194, M:F.194, M:M.195, M:L.197, M:M.201, N:I.276, N:T.280, N:F.281, N:I.284 Water bridges: Y:Q.134 Hydrogen bonds: M:S.191, M:S.191, N:N.274 3PE.30: 19 residues within 4Å: Chain 3: F.33 Chain M: T.90, L.94, M.98, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, A.246, L.249, P.256, L.257, T.301, T.334, M.335, P.338 Ligands: 3PE.44 12 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain M, 8 interactions with chain N Hydrophobic interactions: 3:F.33, 3:F.33, M:L.94, M:I.131, N:I.239, N:V.242, N:L.249, N:P.256, N:L.257, N:T.301, N:P.338 Hydrogen bonds: N:I.239 3PE.33: 14 residues within 4Å: Chain N: F.6, K.46, S.125, L.128, I.129, T.132, W.133, I.209, S.213, T.217, K.322, M.323, T.324, M.329 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:L.128, N:I.129, N:W.133, N:W.133, N:I.209, N:T.217 Hydrogen bonds: N:S.125, N:T.324 Water bridges: N:S.125 Salt bridges: N:K.46 3PE.42: 13 residues within 4Å: Chain D: E.57 Chain L: L.576, Q.580, T.594, S.598 Chain N: P.110, L.160 Chain Y: V.36, Y.39, S.40, L.43, K.44, Y.59 10 PLIP interactions: 1 interactions with chain D, 6 interactions with chain Y, 2 interactions with chain N, 1 interactions with chain L Hydrogen bonds: D:E.57, Y:S.40 Hydrophobic interactions: Y:V.36, Y:V.36, Y:Y.39, Y:L.43, N:P.110, N:L.160, L:T.594 Salt bridges: Y:K.44 3PE.44: 17 residues within 4Å: Chain 3: F.36, C.40, L.43, I.44, A.47, V.53, L.54 Chain M: I.9, P.13, W.16, M.98 Chain N: I.239, M.335 Chain O: K.326, Y.327 Ligands: 3PE.30, CDL.45 12 PLIP interactions: 8 interactions with chain 3, 3 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: 3:F.36, 3:F.36, 3:L.43, 3:I.44, 3:V.53, 3:L.54, 3:L.54, M:I.9, M:W.16, M:W.16 Hydrogen bonds: 3:V.53 Salt bridges: O:K.326 3PE.53: 16 residues within 4Å: Chain L: L.553, W.557, L.558 Chain M: Y.210, L.264 Chain Y: Y.108, G.109, A.112 Chain c: P.82, N.83, T.84, S.87, L.88, G.90, A.91, I.95 11 PLIP interactions: 4 interactions with chain c, 2 interactions with chain M, 1 interactions with chain Y, 4 interactions with chain L Hydrophobic interactions: c:L.88, c:I.95, c:I.95, M:Y.210, M:L.264, Y:A.112, L:L.553, L:W.557, L:W.557, L:L.558 Hydrogen bonds: c:T.84

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: 12 residues within 4Å: 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 SF4.18: 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 SF4.19: 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 PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 12 residues within 4Å: Chain B: K.69, D.72, L.73, W.76, R.79, K.205 Chain H: V.39 Chain g: F.28, R.29, N.31, W.75, V.77 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.72, B:L.73, B:W.76, B:W.76 Salt bridges: B:R.79, B:R.79, B:K.205, B:K.205 PC1.47: 18 residues within 4Å: Chain 6: S.103, V.106, A.107, Y.108 Chain L: T.16, W.66 Chain M: P.64, I.67, L.68, W.71, P.443, L.446, L.449, N.450, I.454 Ligands: CDL.24, 3PE.25, CDL.48 8 PLIP interactions: 1 interactions with chain L, 6 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: L:T.16, M:W.71, M:W.71, M:P.443, M:N.450, M:I.454, 6:V.106 Hydrogen bonds: M:N.450

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:E.208, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:G.89, F:N.116, F:E.119, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247, F:T.247 Water bridges: F:G.92, F:G.92, F:G.92, F:K.98, F:N.116, F:D.127, 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 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:I.223, G:C.226, G:V.228, G:L.231, H2O.27

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

I49.16: 12 residues within 4Å: Chain B: W.83 Chain H: A.18, T.21, E.24, R.25, P.48, D.51, A.52, L.55, F.224, M.225, Y.228 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:T.21, H:D.51, H:L.55, H:F.224, B:W.83 Hydrogen bonds: H:T.21, H:Y.228, H:R.274 Salt bridges: H:E.24 I49.35: 13 residues within 4Å: Chain 3: M.82, Y.83, R.86 Chain 7: R.157, R.161, W.168, F.169 Chain N: Y.196, N.197, P.198, S.344, E.347 Chain Y: V.141 6 PLIP interactions: 3 interactions with chain 7, 3 interactions with chain N Hydrophobic interactions: 7:W.168 Hydrogen bonds: 7:R.157, 7:R.161, N:Y.196, N:Y.196 Salt bridges: N:E.347

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 23 residues within 4Å: Chain J: V.18, S.21, K.23, A.92, G.96 Chain K: M.10, T.13, V.14, V.17, G.18, M.21, Y.22, R.23 Chain L: K.585, L.589, L.596 Chain Y: V.41, T.45, P.46, S.48, F.49, G.52, V.53 15 PLIP interactions: 3 interactions with chain Y, 5 interactions with chain K, 4 interactions with chain L, 3 interactions with chain J Hydrophobic interactions: Y:V.41, Y:V.53, K:T.13, K:V.17, K:V.17, K:M.21, L:L.589, L:L.596, J:V.18, J:A.92 Hydrogen bonds: Y:G.52 Salt bridges: K:R.23, L:K.585, L:K.585, J:K.23 CDL.24: 24 residues within 4Å: Chain 6: L.99, V.100 Chain 7: L.68, L.71, R.72 Chain L: I.19, M.22, F.24, K.116, K.119, Y.120, L.123, T.127, I.149, M.150, L.153 Chain M: L.354, T.357, L.360, L.369, L.442, L.445 Ligands: PC1.47, CDL.48 16 PLIP interactions: 1 interactions with chain 6, 9 interactions with chain L, 4 interactions with chain M, 2 interactions with chain 7 Hydrophobic interactions: 6:V.100, L:I.19, L:T.127, L:I.149, L:L.153, M:L.360, M:L.369, M:L.445, 7:L.71 Hydrogen bonds: L:Y.120, M:T.357 Salt bridges: L:K.116, L:K.119, L:K.119, L:K.119, 7:R.72 CDL.34: 19 residues within 4Å: Chain 2: K.43, T.47, T.50, L.54 Chain 3: V.34, D.45, R.49, R.60, L.63, Y.64, S.67, F.68, G.72, L.75 Chain N: T.324, F.325, L.332, M.336, M.342 17 PLIP interactions: 10 interactions with chain 3, 5 interactions with chain N, 2 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:L.63, 3:L.63, 3:Y.64, 3:Y.64, 3:L.75, N:F.325, N:L.332, 2:L.54 Hydrogen bonds: 3:R.60, N:F.325 Water bridges: 3:R.51, 3:R.51, N:L.326, N:L.326 Salt bridges: 3:R.60, 2:K.43 CDL.45: 24 residues within 4Å: Chain 3: T.27, P.29, R.30, A.32, F.33, F.36 Chain 5: L.26, K.29, N.30 Chain M: L.2, M.12, L.55, L.104, F.105, M.108, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: 3PE.44 20 PLIP interactions: 4 interactions with chain X, 4 interactions with chain N, 3 interactions with chain 5, 3 interactions with chain M, 6 interactions with chain 3 Hydrophobic interactions: X:F.169, N:P.256, N:P.256, N:L.337, N:P.338, M:L.55, M:F.105, M:L.121, 3:R.30, 3:F.33, 3:F.33, 3:F.33, 3:F.36, 3:F.36 Hydrogen bonds: X:T.171, X:T.171, X:M.172, 5:L.26, 5:N.30 Salt bridges: 5:K.29 CDL.48: 23 residues within 4Å: Chain 6: T.104, A.107, Y.108 Chain 7: I.86, T.87, N.90, E.95, H.115 Chain 8: I.80, Y.83, Y.84, H.88 Chain L: L.9, L.12, N.65, F.80 Ligands: CDL.24, 3PE.25, PC1.47 Chain f: V.48, R.49, I.52, H.56 17 PLIP interactions: 2 interactions with chain f, 4 interactions with chain 7, 3 interactions with chain 6, 5 interactions with chain 8, 3 interactions with chain L Hydrophobic interactions: f:V.48, 6:A.107, 6:Y.108, 8:I.80, 8:Y.83, 8:Y.84, 8:Y.84, L:L.9, L:F.80, L:F.80 Salt bridges: f:R.49, 7:H.115, 8:H.88 Hydrogen bonds: 7:N.90, 7:N.90, 7:E.95, 6:Y.108 CDL.55: 19 residues within 4Å: Chain 0: 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, R.9, G.10, Q.13 Chain h: S.3, A.4, T.5, F.7, I.8, L.11 17 PLIP interactions: 5 interactions with chain g, 6 interactions with chain 0, 5 interactions with chain h, 1 interactions with chain I Hydrophobic interactions: g:V.6, 0:W.2, 0:L.6, 0:P.7, 0:I.9, 0:A.10, h:F.7, h:F.7, h:I.8, h:L.11, I:F.78 Hydrogen bonds: g:R.9, g:G.10, h:T.5 Water bridges: g:Q.13, 0:W.2 Salt bridges: g:R.9

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

GTP.36: 21 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, E.214, Y.221 Ligands: MG.37 19 PLIP interactions: 19 interactions with chain O Hydrogen bonds: O:C.55, O:S.56, O:G.57, O:K.58, O:S.59, O:Y.106, O:Q.120, O:Q.120, 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 pi-Stacking: O:F.157, O:F.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.37: 2 residues within 4Å: Chain O: S.59 Ligands: GTP.36 No protein-ligand interaction detected (PLIP)

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

NDP.38: 27 residues within 4Å: Chain A: Y.30 Chain B: R.216 Chain P: G.60, A.61, 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 33 PLIP interactions: 29 interactions with chain P, 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: P:P.203, 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:C.86, P:L.129, P:G.131, P:K.184, P:I.206, A:Y.30 Water bridges: P:G.63, P:G.63, P:R.85, P:R.85, P:R.132, P:E.133, P:E.133, P:T.136, P:R.212, B:R.216, B:R.216 Salt bridges: P:R.85, P:R.132, P:R.132, B:R.216 pi-Cation interactions: P:R.85, P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.39: 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.40: 18 residues within 4Å: Chain T: D.111, S.112, L.113 Chain W: K.29, V.32, L.35, W.39, I.54, G.59, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.106 17 PLIP interactions: 15 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:V.32, W:L.35, W:W.39, W:W.39, W:I.54, W:V.63, W:M.66, W:F.67, W:F.67, W:F.106, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 Water bridges: W:M.66 EHZ.41: 21 residues within 4Å: Chain L: Y.513 Chain U: D.111, S.112 Chain d: H.12, Q.13, V.16, A.23, H.26, L.27, W.30, R.47, F.48, H.51, K.52, E.54, A.60, L.63, L.64, A.67, E.70, G.74 12 PLIP interactions: 11 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:Q.13, d:V.16, d:A.23, d:H.26, d:F.48, d:E.54 Hydrogen bonds: d:Q.13, d:R.47, d:H.51, d:K.52, U:S.112 Salt bridges: d:K.52

1 x MYR: MYRISTIC ACID(Covalent)

MYR.54: 11 residues within 4Å: Chain L: A.406, W.407, L.410, Y.485, L.486 Chain b: V.146, Y.153, Q.154 Chain e: G.1, H.3, L.4 7 PLIP interactions: 4 interactions with chain L, 2 interactions with chain b, 1 interactions with chain e Hydrophobic interactions: L:A.406, L:W.407, L:L.410, L:L.486, b:V.146, e:L.4 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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