SMTL ID : 7qsl.1

Bovine complex I in lipid nanodisc, Active-apo

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.76 Å

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

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

3PE.1: 13 residues within 4Å: Chain 1: V.30, P.33, T.34, T.39 Chain A: N.85, L.88, T.89, L.92, F.93, I.96, L.97 Chain J: L.162 Ligands: 3PE.3 Ligand excluded by PLIP 3PE.3: 11 residues within 4Å: Chain A: N.83, T.86, T.89, M.90, F.93 Chain J: S.148, T.151, W.152, I.155 Chain N: L.15 Ligands: 3PE.1 Ligand excluded by PLIP 3PE.14: 11 residues within 4Å: Chain H: Q.169, E.170, W.173, G.244, T.245, S.246, N.258, I.261, K.262, L.265, L.266 Ligand excluded by PLIP 3PE.16: 20 residues within 4Å: Chain 1: I.25 Chain D: R.266 Chain H: W.179, P.180, M.183, M.184, F.186, I.187, Y.277, 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 Ligand excluded by PLIP 3PE.20: 15 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, G.228, H.534, A.537, P.538, N.541 Chain M: L.405 Chain b: N.115, R.116, V.117 Ligand excluded by PLIP 3PE.22: 17 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, I.142 Chain M: L.449 Ligands: PC1.26, CDL.50 Ligand excluded by PLIP 3PE.23: 19 residues within 4Å: Chain M: A.155, P.159, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: I.276, I.277, T.280, I.284 Chain Y: W.133 Ligands: PC1.28, 3PE.29, 3PE.42, PC1.53 Ligand excluded by PLIP 3PE.24: 19 residues within 4Å: Chain 3: F.36, C.40, L.43, I.44, A.47, P.52, V.53, L.54 Chain M: W.16, T.97, M.98, S.101, V.127 Chain N: I.239, P.256, M.335 Chain O: Y.327 Ligands: 3PE.25, CDL.39 Ligand excluded by PLIP 3PE.25: 22 residues within 4Å: Chain 3: F.33 Chain M: N.88, T.90, R.91, L.94, M.98, I.131, R.135 Chain N: P.238, I.239, V.242, L.243, L.245, A.246, L.249, L.257, T.301, T.334, M.335 Chain O: Q.317 Ligands: 3PE.24, CDL.39 Ligand excluded by PLIP 3PE.27: 17 residues within 4Å: Chain L: L.558, I.561 Chain M: W.190, V.193, M.201, Y.210, G.211, F.256, M.257, P.260, F.261, L.264 Ligands: PC1.28, 3PE.54 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.29: 24 residues within 4Å: Chain D: M.52, Y.53 Chain L: P.563, S.567, Q.570, M.571 Chain M: N.144, L.147, Y.148, F.151, Y.152, A.155, M.201, V.205 Chain N: L.163, W.167, I.284, T.285, L.287, L.288, Y.291, R.295 Ligands: 3PE.23, PC1.53 Ligand excluded by PLIP 3PE.35: 10 residues within 4Å: Chain P: N.219, I.220, W.222, F.223, Y.291, I.301, W.313, T.314, R.355 Ligands: PC1.2 Ligand excluded by PLIP 3PE.40: 16 residues within 4Å: Chain L: L.576, Q.580, I.597, S.598 Chain N: P.110, H.112, L.160, I.164 Chain Y: V.36, Y.39, S.40, L.43, K.44, Y.59 Ligands: 3PE.41, 3PE.43 Ligand excluded by PLIP 3PE.41: 14 residues within 4Å: Chain Y: Y.9, I.28, A.32, R.58, Y.59, T.62, A.63, G.67, F.70, L.101, T.105, M.118, V.125 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.42: 9 residues within 4Å: Chain N: I.277, F.281 Chain Y: W.10, L.124, V.125, Q.129, W.133, V.135 Ligands: 3PE.23 Ligand excluded by PLIP 3PE.43: 10 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, L.160, W.167 Chain Y: A.2, K.3, A.32, V.36 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.45: 15 residues within 4Å: Chain H: M.183, W.272 Chain I: L.62, T.64, E.65, I.67, R.68, G.71, L.74 Chain Z: R.28, G.29, L.30, M.35 Chain h: W.14, A.15 Ligand excluded by PLIP 3PE.46: 14 residues within 4Å: Chain 1: V.12, E.16, L.19, V.20, S.22, F.23, A.24, A.26 Chain A: A.99, A.103, W.106, T.107 Chain H: K.291, P.295 Ligand excluded by PLIP 3PE.47: 9 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, Y.74 Chain 4: R.9 Chain N: M.336 Ligands: PC1.48, CDL.49 Ligand excluded by PLIP 3PE.54: 14 residues within 4Å: Chain L: W.557 Chain Y: Y.108, G.109, A.112 Ligands: 3PE.27 Chain c: P.82, N.83, T.84, S.87, G.90, A.91, G.94, I.95, L.98 Ligand excluded by PLIP

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

PC1.2: 12 residues within 4Å: Chain A: T.15, V.18, I.19, F.22, W.23, L.27 Chain H: R.62, I.72 Chain P: W.222 Ligands: PC1.4, CDL.15, 3PE.35 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain A Hydrophobic interactions: H:I.72, A:T.15, A:I.19 Salt bridges: H:R.62 pi-Cation interactions: A:W.23 PC1.4: 13 residues within 4Å: Chain A: I.20, W.23, L.24, P.25, Q.26 Chain P: L.304, F.305, I.307, S.308, F.310, W.313 Ligands: PC1.2, PC1.33 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain P Hydrophobic interactions: A:I.20, A:W.23, A:L.24, P:L.304, P:F.305, P:F.305, P:I.307, P:F.310, P:W.313 pi-Cation interactions: P:F.310 PC1.6: 16 residues within 4Å: Chain B: K.69, L.70, D.72, L.73, W.76, R.79, K.205 Chain H: V.39, L.46, I.49, I.53 Chain g: F.28, R.29, N.31, W.75, V.77 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:L.70, B:D.72, B:L.73, B:W.76, B:W.76, H:I.53 Salt bridges: B:R.79, B:K.205, B:K.205 PC1.26: 19 residues within 4Å: Chain 6: V.98, L.99, G.102, S.103, V.106, A.107, Y.108 Chain L: W.66 Chain M: P.64, I.67, L.68, W.71, P.443, L.446, L.449, N.450, I.454 Ligands: 3PE.22, CDL.50 9 PLIP interactions: 6 interactions with chain M, 3 interactions with chain 6 Hydrophobic interactions: M:W.71, M:W.71, M:P.443, M:L.446, M:I.454, 6:L.99, 6:V.106, 6:V.106 Hydrogen bonds: M:N.450 PC1.28: 11 residues within 4Å: Chain M: N.188, S.189, W.190, F.194, M.201 Chain Y: D.86, P.87, L.88, M.127 Ligands: 3PE.23, 3PE.27 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:W.190, M:F.194 pi-Cation interactions: M:W.190 PC1.33: 19 residues within 4Å: Chain A: L.24, Q.26 Chain B: G.63, V.66, V.67, L.70, I.74, L.210, W.213, Y.214, R.216 Chain H: A.52, I.53, F.56, I.57 Chain P: D.90, F.310, E.311 Ligands: PC1.4 18 PLIP interactions: 4 interactions with chain H, 10 interactions with chain B, 2 interactions with chain A, 2 interactions with chain P Hydrophobic interactions: H:I.53, H:F.56, H:F.56, H:I.57, B:V.66, B:V.66, B:V.67, B:L.70, B:L.70, B:L.210, B:W.213, B:Y.214, A:L.24, A:Q.26 Water bridges: B:R.78 Salt bridges: B:R.216, P:D.90, P:E.311 PC1.44: 24 residues within 4Å: Chain 0: A.39, H.40 Chain A: M.1, L.3, L.7, F.11 Chain H: L.81, M.98, N.99, L.100, F.104, M.108, L.111 Chain J: I.34, V.35, G.38, V.39, L.45, S.50, L.54 Chain Z: F.140, I.141, W.142, Y.143 10 PLIP interactions: 1 interactions with chain Z, 4 interactions with chain H, 3 interactions with chain J, 2 interactions with chain A pi-Cation interactions: Z:F.140 Hydrophobic interactions: H:L.81, H:L.111, J:I.34, J:L.45, A:L.7, A:F.11 Hydrogen bonds: H:N.99, H:L.100, J:S.50 PC1.48: 14 residues within 4Å: Chain 3: R.8, F.11, Q.12, F.13, R.78 Chain 4: F.3, F.4, R.9 Chain N: L.136, Y.143, L.202, V.345, L.346 Ligands: 3PE.47 12 PLIP interactions: 4 interactions with chain 4, 7 interactions with chain 3, 1 interactions with chain N Hydrophobic interactions: 4:F.3, 4:F.4, 4:F.4, 3:F.11, N:L.346 pi-Cation interactions: 4:F.3 Hydrogen bonds: 3:F.11, 3:Q.12, 3:R.78 Water bridges: 3:R.8 Salt bridges: 3:R.8, 3:R.78 PC1.51: 12 residues within 4Å: Chain 7: T.78, P.81, V.82, I.89, I.93, W.110, P.116, I.117, R.119, W.120, R.123 Chain f: Y.61 10 PLIP interactions: 10 interactions with chain 7 Hydrophobic interactions: 7:T.78, 7:P.81, 7:I.89, 7:I.93, 7:I.117, 7:W.120, 7:W.120, 7:W.120 Salt bridges: 7:R.119, 7:R.123 PC1.53: 14 residues within 4Å: Chain L: T.565, I.566, A.569, Q.570 Chain Y: G.109, I.110, A.113, Y.117 Ligands: 3PE.23, 3PE.29 Chain c: Y.77, P.78, F.80, P.82 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain Y Hydrophobic interactions: L:T.565, L:I.566, L:A.569, Y:A.113, Y:Y.117, Y:Y.117

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

SF4.5: 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: 13 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, 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: 13 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, 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: 9 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, C.176, L.177, G.178, A.179, C.180 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 23 PLIP interactions: 23 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:N.116, F:E.119, F:G.120, F:G.207, F:E.209, F:E.209, F:N.244, F:N.244, F:T.247 Water bridges: F:A.91, F:T.95, F:K.98, F:G.207, 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: 4 interactions with chain G Metal complexes: G:I.223, G:C.226, G:V.228, G:L.231

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 12 residues within 4Å: Chain H: R.62, A.68, S.69, I.72 Chain J: Y.28, I.82, W.83, L.84 Chain P: W.222, R.286, T.358 Ligands: PC1.2 16 PLIP interactions: 8 interactions with chain H, 5 interactions with chain J, 3 interactions with chain P Hydrophobic interactions: H:I.72, J:Y.28, J:W.83, J:W.83, P:W.222 Hydrogen bonds: H:A.68, H:S.69, J:W.83, J:L.84 Water bridges: H:R.62, H:R.62, H:S.67, H:M.70, P:Y.359 Salt bridges: H:R.62, P:R.286 CDL.19: 25 residues within 4Å: Chain J: S.21, K.23, A.92, T.95, G.96, M.99 Chain K: M.10, T.13, V.14, V.17, G.18, M.21, Y.22, R.23 Chain L: K.585, L.589 Chain Y: A.38, V.41, T.45, P.46, S.48, F.49, G.52, V.53, T.56 11 PLIP interactions: 3 interactions with chain Y, 2 interactions with chain L, 3 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: Y:A.38, Y:F.49, Y:V.53, L:L.589, J:A.92, J:T.95, K:T.13, K:V.17 Salt bridges: L:K.585, J:K.23, K:R.23 CDL.21: 18 residues within 4Å: Chain 7: L.68, L.71, R.72, I.75 Chain L: M.22, S.23, N.25, K.116, K.119, Y.120, L.123, T.127, I.149, M.150, L.153 Chain M: L.354, T.357, L.445 17 PLIP interactions: 11 interactions with chain L, 4 interactions with chain 7, 2 interactions with chain M Hydrophobic interactions: L:T.127, L:I.149, L:L.153, 7:L.68, 7:L.71, 7:I.75, M:L.354 Hydrogen bonds: L:S.23, L:N.25, L:Y.120, M:T.357 Salt bridges: L:K.116, L:K.119, L:K.119, L:K.119, L:K.119, 7:R.72 CDL.30: 20 residues within 4Å: Chain N: P.3, F.6, I.7, L.10, K.46, S.125, L.128, I.129, T.132, W.133, I.209, S.213, T.217, K.322, M.323, T.324, F.325, M.329 Chain O: P.28, H.280 14 PLIP interactions: 13 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.7, N:L.128, N:L.128, N:I.129, N:W.133, N:I.209, N:F.325, O:P.28 Hydrogen bonds: N:S.125, N:M.323, N:T.324, N:T.324 Water bridges: N:S.125, N:K.321 CDL.39: 25 residues within 4Å: Chain 3: T.27, P.29, R.30, A.32, F.33, F.36 Chain 5: F.22, L.26, K.29, N.30 Chain M: L.55, L.104, F.105, M.108, I.120, L.121 Chain N: P.256, L.337, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: 3PE.24, 3PE.25 19 PLIP interactions: 5 interactions with chain M, 4 interactions with chain N, 5 interactions with chain 3, 3 interactions with chain 5, 2 interactions with chain X Hydrophobic interactions: M:L.55, M:L.104, M:F.105, M:I.120, M:L.121, N:P.256, N:L.337, N:P.338, N:P.338, 3:A.32, 3:F.33, 3:F.33, 3:F.36, 3:F.36, 5:F.22, 5:L.26 Salt bridges: 5:K.29 Hydrogen bonds: X:T.171, X:T.171 CDL.49: 21 residues within 4Å: Chain 2: K.43, L.46, T.47, T.50 Chain 3: V.34, D.45, R.60, L.63, Y.64, S.67, F.68, F.70, V.71, L.75 Chain N: M.323, T.324, F.325, T.328, M.336, M.342 Ligands: 3PE.47 16 PLIP interactions: 13 interactions with chain 3, 1 interactions with chain N, 2 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:L.63, 3:L.63, 3:Y.64, 3:F.68, 3:F.68, 3:F.70, 3:F.70, 3:V.71, 3:L.75, 2:L.46 Hydrogen bonds: 3:R.60, 3:Y.64, N:F.325 Salt bridges: 3:R.60, 2:K.43 CDL.50: 25 residues within 4Å: Chain 6: T.104, A.107, Y.108 Chain 7: A.83, I.86, T.87, N.90, V.91, E.95, H.115 Chain 8: W.79, I.80, I.81, Y.83, Y.84, H.88 Chain L: L.9 Chain M: L.449 Ligands: 3PE.22, PC1.26 Chain f: P.44, V.45, V.48, R.49, I.52 25 PLIP interactions: 10 interactions with chain 8, 1 interactions with chain M, 6 interactions with chain f, 1 interactions with chain L, 5 interactions with chain 7, 2 interactions with chain 6 Hydrophobic interactions: 8:W.79, 8:W.79, 8:I.80, 8:I.81, 8:Y.83, 8:Y.83, 8:Y.83, 8:Y.84, 8:Y.84, M:L.449, f:P.44, f:V.45, f:V.48, f:V.48, f:V.48, L:L.9, 7:A.83, 7:I.86, 6:A.107 Salt bridges: 8:H.88, f:R.49, 7:H.115 Hydrogen bonds: 7:N.90, 7:N.90, 6:Y.108 CDL.56: 19 residues within 4Å: Chain 0: W.2, F.3, L.6, P.7, A.10 Chain H: Y.43 Chain I: F.78 Chain g: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 Chain h: S.3, A.4, T.5, F.7, I.8 17 PLIP interactions: 8 interactions with chain 0, 2 interactions with chain g, 5 interactions with chain h, 2 interactions with chain I Hydrophobic interactions: 0:W.2, 0:F.3, 0:F.3, 0:L.6, 0:L.6, 0:P.7, 0:A.10, h:F.7, h:F.7, h:I.8, I:F.78, I:F.78 Water bridges: 0:W.2 Hydrogen bonds: g:R.9, h:S.3, h:T.5 Salt bridges: g:R.9

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

GTP.31: 21 residues within 4Å: Chain O: 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.32 16 PLIP interactions: 16 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:Y.106, O:Q.120, O:R.127, O:E.214 Salt bridges: 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.32: 3 residues within 4Å: Chain O: K.58, S.59 Ligands: GTP.31 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.34: 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.148, I.167, S.168, H.169, Y.180, K.184, P.203, A.204, I.206, R.212 26 PLIP interactions: 25 interactions with chain P, 1 interactions with chain B 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:L.129, P:R.132, P:K.184, P:I.206, P:I.206, P:R.212 Water bridges: P:G.63, P:R.85, P:T.136 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

1 x ZN: ZINC ION(Non-covalent)

ZN.36: 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.37: 18 residues within 4Å: Chain T: S.112, L.113 Chain W: K.29, V.32, L.35, W.39, I.54, G.59, K.62, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.106 11 PLIP interactions: 9 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:W.39, W:I.54, W:K.62, W:M.66, W:F.106, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 EHZ.38: 20 residues within 4Å: Chain L: Y.513, H.514 Chain U: S.112 Chain d: H.12, Q.13, V.16, H.26, L.27, W.30, L.44, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67, E.70, G.74 7 PLIP interactions: 7 interactions with chain d Hydrophobic interactions: d:V.16, d:L.27, d:L.44, d:F.48, d:A.67 Hydrogen bonds: d:H.51, d:K.52

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.52: 11 residues within 4Å: Chain 8: K.62, R.65, H.66, I.68, F.69, T.72, H.73 Chain L: N.31, L.34, Y.35, T.38 10 PLIP interactions: 7 interactions with chain 8, 3 interactions with chain L Hydrophobic interactions: 8:R.65, 8:I.68, 8:F.69, 8:F.69, L:N.31, L:Y.35 Hydrogen bonds: 8:R.65 Salt bridges: 8:K.62, 8:H.66, L:K.37

1 x MYR: MYRISTIC ACID(Covalent)

MYR.55: 9 residues within 4Å: Chain L: N.400, L.409, L.413, Y.485, L.486, T.489 Chain b: Q.154 Chain e: G.2, L.5 7 PLIP interactions: 5 interactions with chain L, 1 interactions with chain e, 1 interactions with chain b Hydrophobic interactions: L:L.409, L:L.413, L:Y.485, L:L.486, L:T.489, e:L.5 Hydrogen bonds: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, I. et al., Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Nat Commun (2022)

Release Date

2022-05-25

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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