SMTL ID : 8q49.1

Outward-facing, open2 proteoliposome complex I at 2.6 A. Initially purified in LMNG.

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

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

PC1.1: 11 residues within 4Å: Chain 4: V.12, E.24 Chain A: N.83, T.86, F.93 Chain J: S.148, Y.149, T.151, W.152, I.155 Ligands: 3PE.3 9 PLIP interactions: 2 interactions with chain A, 5 interactions with chain J, 2 interactions with chain 4 Hydrophobic interactions: A:F.93, A:F.93, J:T.151, J:W.152, J:W.152, J:I.155, 4:V.12 pi-Cation interactions: J:Y.149 Salt bridges: 4:E.24 PC1.4: 17 residues within 4Å: Chain A: L.24, L.27, N.28, V.29, S.31 Chain B: L.70, I.74, R.78, R.209, L.210, W.213, R.216 Chain H: F.56 Chain P: D.90, F.310 Ligands: PLC.6, PC1.7 10 PLIP interactions: 1 interactions with chain H, 5 interactions with chain B, 2 interactions with chain P, 2 interactions with chain A Hydrophobic interactions: H:F.56, B:L.70, B:I.74, B:W.213, P:F.310, A:L.24, A:N.28 Salt bridges: B:R.78, B:R.216, P:D.90 PC1.7: 15 residues within 4Å: Chain B: D.72, L.73, W.76, R.79, K.205 Chain H: V.39, L.46 Chain I: F.88 Ligands: PC1.4, 3PE.79 Chain g: F.28, R.29, N.31, W.75, V.77 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain g, 2 interactions with chain H Hydrophobic interactions: B:D.72, B:L.73, B:L.73, B:W.76, B:W.76, H:L.46 Water bridges: B:R.79, g:D.76, H:G.41 Salt bridges: B:R.79, B:K.205, B:K.205 PC1.16: 21 residues within 4Å: Chain 0: A.39 Chain A: L.3, M.4, L.7, F.11 Chain H: M.98, N.99, L.100, F.104, M.108 Chain J: V.35, G.38, G.42, L.45, S.50, L.54, F.57 Chain Z: F.140, I.141, Y.143, T.144 14 PLIP interactions: 1 interactions with chain Z, 4 interactions with chain H, 4 interactions with chain J, 5 interactions with chain A pi-Cation interactions: Z:F.140 Hydrophobic interactions: H:F.104, J:L.45, J:F.57, J:F.57, A:L.3, A:L.7, A:F.11, A:F.11, A:F.11 Hydrogen bonds: H:N.99, H:L.100, J:S.50 Water bridges: H:N.99 PC1.17: 15 residues within 4Å: Chain H: Q.169, E.170, Q.171, M.172, W.173, G.244, T.245, S.246, N.258, I.261, K.262, L.265, L.266, S.269 Ligands: PC1.20 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:W.173, H:I.261, H:K.262, H:L.265, H:L.266 Hydrogen bonds: H:S.246, H:N.258 Salt bridges: H:K.262, H:K.262 PC1.20: 29 residues within 4Å: Chain 1: K.15, E.16, V.18, I.25 Chain D: R.266 Chain H: I.175, W.179, A.182, M.183, M.184, F.186, I.187, T.238, Y.277, F.280, L.288, N.292, F.293, L.296, W.303 Chain I: T.60, L.61, W.63, L.66, L.70 Chain Z: L.43 Ligands: PC1.17, PC1.21, 3PE.58 19 PLIP interactions: 9 interactions with chain H, 2 interactions with chain D, 4 interactions with chain I, 3 interactions with chain 1, 1 interactions with chain Z Hydrophobic interactions: H:I.175, H:W.179, H:F.186, H:T.238, H:Y.277, H:F.280, H:F.293, H:L.296, H:W.303, I:L.61, I:W.63, I:W.63, I:L.70, 1:I.25, 1:I.25, Z:L.43 Salt bridges: D:R.266, D:R.266, 1:E.16 PC1.21: 20 residues within 4Å: Chain H: M.183, W.272 Chain I: D.55, L.62, T.64, E.65, I.67, R.68, G.71, L.74 Chain Z: R.28, G.29, L.30, S.31, G.32, M.35 Ligands: PC1.20, 3PE.57 Chain h: L.11, W.14 9 PLIP interactions: 5 interactions with chain I, 1 interactions with chain Z, 1 interactions with chain H, 2 interactions with chain h Hydrophobic interactions: I:T.64, I:L.74, H:W.272, h:L.11, h:W.14 Hydrogen bonds: I:T.64 Salt bridges: I:D.55, I:R.68, Z:R.28 PC1.26: 21 residues within 4Å: Chain L: D.163, T.166, Q.170, L.173, Y.174, I.177, G.228, L.229, M.533, H.534, A.537, P.538, N.541, L.542 Chain M: V.398, V.401, L.405 Ligands: 3PE.30 Chain b: R.114, N.115, R.116 11 PLIP interactions: 3 interactions with chain M, 8 interactions with chain L Hydrophobic interactions: M:V.398, M:V.401, M:L.405, L:Q.170, L:L.173, L:L.229, L:N.541 Hydrogen bonds: L:Q.170 Salt bridges: L:D.163, L:H.534, L:H.534 PC1.34: 9 residues within 4Å: Chain M: N.188, S.189, W.190 Chain Y: P.87, L.88, L.91, L.120, M.127 Ligands: 3PE.32 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain M Hydrophobic interactions: Y:L.91, Y:L.120 pi-Cation interactions: M:W.190 PC1.64: 19 residues within 4Å: Chain 3: R.8, T.10, F.11, Q.12, F.13, R.78 Chain 4: F.3, F.4, R.9 Chain N: W.133, L.136, Y.143, L.202, I.206, V.345, L.346, E.347 Ligands: CDL.39, 3PE.63 17 PLIP interactions: 4 interactions with chain 4, 7 interactions with chain 3, 6 interactions with chain N Hydrophobic interactions: 4:F.4, 4:F.4, 4:F.4, 3:F.11, 3:F.11, N:W.133, N:W.133, N:L.136, N:L.136, N:I.206, N:L.346 pi-Cation interactions: 4:F.3 Hydrogen bonds: 3:F.11, 3:Q.12 Salt bridges: 3:R.8, 3:R.78, 3:R.78 PC1.70: 20 residues within 4Å: Chain 6: V.98, L.99, S.103, A.107, Y.108 Chain L: W.66 Chain M: I.67, L.68, W.71, I.317, L.321, P.443, L.446, L.447, L.449, N.450, I.454 Ligands: 3PE.29, CDL.35, CDL.73 12 PLIP interactions: 10 interactions with chain M, 2 interactions with chain 6 Hydrophobic interactions: M:I.67, M:W.71, M:W.71, M:I.317, M:L.321, M:P.443, M:L.447, M:N.450, M:I.454, 6:V.98, 6:L.99 Hydrogen bonds: M:N.450 PC1.72: 9 residues within 4Å: Chain 7: V.82, I.89, I.93, W.110, P.116, R.119, W.120, R.123 Chain f: Y.61 7 PLIP interactions: 7 interactions with chain 7 Hydrophobic interactions: 7:I.89, 7:I.93, 7:P.116, 7:W.120, 7:W.120 Salt bridges: 7:R.119, 7:R.123 PC1.76: 15 residues within 4Å: Chain L: A.560, T.565, L.568, A.569 Chain Y: G.109, A.113, A.116, Y.117 Ligands: 3PE.37, 3PE.49, PLC.54, 3PE.74 Chain c: Y.77, F.80, P.82 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain L Hydrophobic interactions: Y:A.116, Y:Y.117, L:T.565 PC1.78: 6 residues within 4Å: Ligands: 3PE.79 Chain g: R.21, L.24, R.25, F.28, F.74 4 PLIP interactions: 4 interactions with chain g Hydrophobic interactions: g:F.28 Hydrogen bonds: g:R.21 Salt bridges: g:R.21 pi-Cation interactions: g:F.74

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

3PE.2: 6 residues within 4Å: Chain A: M.1, L.8, T.9, T.12, L.13 Chain H: M.3 Ligand excluded by PLIP 3PE.3: 14 residues within 4Å: Chain A: L.97, V.100, A.103, Y.104, T.107, Q.108 Chain J: I.155, W.159 Chain N: N.2, I.5, I.8, L.15 Ligands: PC1.1, 3PE.60 Ligand excluded by PLIP 3PE.15: 10 residues within 4Å: Chain 0: L.6, A.10, G.13, F.17, R.25 Chain H: E.253, L.254, I.261, L.264 Ligands: CDL.81 Ligand excluded by PLIP 3PE.22: 8 residues within 4Å: Chain J: K.87, A.88, T.95, M.99 Chain Y: F.49 Ligands: 3PE.25, 3PE.48, 3PE.55 Ligand excluded by PLIP 3PE.23: 14 residues within 4Å: Chain J: E.114, V.115, V.116, F.117 Chain K: M.9, M.10, T.13, L.16 Chain L: M.599, I.600, H.605 Chain N: M.72, M.93 Ligands: 3PE.25 Ligand excluded by PLIP 3PE.25: 17 residues within 4Å: Chain J: S.21, K.23, A.88, A.92, G.96, M.99 Chain K: T.13, V.14, V.17, M.21, Y.22, R.23 Chain L: K.585 Ligands: 3PE.22, 3PE.23, 3PE.48, 3PE.55 Ligand excluded by PLIP 3PE.29: 18 residues within 4Å: Chain 8: I.81, Y.85, H.89, K.93 Chain L: N.65, W.66, H.67, W.68, S.77, L.78, N.136, F.138, Q.139, I.142 Chain M: P.371, L.449 Ligands: PC1.70, CDL.73 Ligand excluded by PLIP 3PE.30: 8 residues within 4Å: Chain L: M.211 Chain M: N.390, I.391, I.393, I.394 Ligands: PC1.26 Chain c: W.101, R.111 Ligand excluded by PLIP 3PE.32: 17 residues within 4Å: Chain L: L.558, I.561 Chain M: W.190, V.193, M.201, L.212, F.256, M.257, Y.259, P.260, F.261, L.264 Ligands: PC1.34, 3PE.74 Chain c: L.98, Y.102, K.106 Ligand excluded by PLIP 3PE.33: 15 residues within 4Å: Chain M: A.155, P.159, Y.166, S.191, F.194, M.195, A.198 Chain N: N.274, I.276, I.277, T.280 Chain Y: L.124, W.133 Ligands: 3PE.37, 3PE.49 Ligand excluded by PLIP 3PE.37: 31 residues within 4Å: Chain D: W.43, Q.46, Y.47, M.52, Y.53 Chain L: L.562, I.566, S.567, Q.570, M.571 Chain M: N.144, L.147, Y.148, F.151, Y.152, A.155, G.156, M.201, V.205 Chain N: L.163, W.167, F.281, I.284, T.285, L.287, L.288, Y.291, R.295 Ligands: 3PE.33, 3PE.49, PC1.76 Ligand excluded by PLIP 3PE.38: 11 residues within 4Å: Chain L: F.602 Chain N: N.152, T.156, L.160, W.167 Chain Y: A.2, K.3, L.6 Ligands: 3PE.49, 3PE.51, 3PE.52 Ligand excluded by PLIP 3PE.48: 14 residues within 4Å: Chain L: L.589 Chain Y: V.41, T.45, P.46, T.47, S.48, F.49, G.52, V.53, T.56 Ligands: 3PE.22, 3PE.25, 3PE.53, 3PE.55 Ligand excluded by PLIP 3PE.49: 16 residues within 4Å: Chain L: A.569, K.572, A.573, L.576 Chain N: W.167 Chain Y: I.110, Y.117, T.121, L.124 Ligands: 3PE.33, 3PE.37, 3PE.38, 3PE.50, 3PE.51, 3PE.52, PC1.76 Ligand excluded by PLIP 3PE.50: 17 residues within 4Å: Chain Y: Y.9, W.10, I.28, G.29, R.58, Y.59, T.62, A.63, G.67, F.70, L.101, T.105, M.118, V.125 Ligands: 3PE.49, 3PE.51, 3PE.52 Ligand excluded by PLIP 3PE.51: 14 residues within 4Å: Chain L: L.576, S.598, F.602 Chain N: L.160 Chain Y: A.32, V.35, V.36, Y.39, S.40, K.44, Y.59 Ligands: 3PE.38, 3PE.49, 3PE.50 Ligand excluded by PLIP 3PE.52: 17 residues within 4Å: Chain N: V.159, I.277, F.281 Chain Y: L.6, R.7, W.10, I.28, A.32, L.124, V.125, G.128, Q.129, W.133, V.135 Ligands: 3PE.38, 3PE.49, 3PE.50 Ligand excluded by PLIP 3PE.53: 8 residues within 4Å: Chain Y: V.53, A.54, G.57, R.58, F.61, R.104 Ligands: 3PE.48, 3PE.55 Ligand excluded by PLIP 3PE.55: 19 residues within 4Å: Chain L: I.593, L.596, I.597, I.600, L.601 Chain Y: A.2, V.5, Y.23, T.26, S.27, G.30, A.31, L.34, V.35, A.38 Ligands: 3PE.22, 3PE.25, 3PE.48, 3PE.53 Ligand excluded by PLIP 3PE.57: 12 residues within 4Å: Chain H: I.175, L.176, W.179 Chain I: I.67 Chain Z: R.28, G.29, L.30, M.35, V.38, G.39 Ligands: PC1.21 Chain h: W.14 Ligand excluded by PLIP 3PE.58: 10 residues within 4Å: Chain 1: L.32, S.36, Y.38 Chain H: L.310 Chain Z: L.44, Y.47, W.48, M.51, R.55 Ligands: PC1.20 Ligand excluded by PLIP 3PE.59: 18 residues within 4Å: Chain 1: L.9, V.12, E.16, L.19, V.20, S.22, F.23, A.24, A.26 Chain A: A.99, L.102, A.103, W.106, T.107 Chain H: K.291, P.295 Ligands: 3PE.60, 3PE.62 Ligand excluded by PLIP 3PE.60: 10 residues within 4Å: Chain 1: F.8, V.12, F.23, G.27, V.30 Chain A: A.103, T.107 Ligands: 3PE.3, 3PE.59, PLC.61 Ligand excluded by PLIP 3PE.62: 10 residues within 4Å: Chain 1: A.6, L.9, K.10, W.13, V.20 Chain I: D.49, M.50 Chain Z: Y.33, F.36 Ligands: 3PE.59 Ligand excluded by PLIP 3PE.63: 15 residues within 4Å: Chain 3: Q.12, F.13, L.14, V.71, Y.74, L.75 Chain 4: R.9 Chain N: L.203, I.210, M.261, L.339, L.343, V.345, L.346 Ligands: PC1.64 Ligand excluded by PLIP 3PE.67: 13 residues within 4Å: Chain 5: H.10, H.13 Chain 6: W.85, F.93 Chain M: M.22, V.25, N.26, A.29, H.30, L.33 Ligands: 3PE.68, 3PE.69, PLC.71 Ligand excluded by PLIP 3PE.68: 15 residues within 4Å: Chain 5: V.6, V.7, H.10, W.11, H.13, V.14, L.15, P.17, M.18, V.21, F.22 Chain M: M.10 Ligands: CDL.47, 3PE.67, 3PE.69 Ligand excluded by PLIP 3PE.69: 10 residues within 4Å: Chain 5: P.17, F.20, Y.24 Chain 7: F.125 Chain M: L.33, F.36, T.37, L.40 Ligands: 3PE.67, 3PE.68 Ligand excluded by PLIP 3PE.74: 19 residues within 4Å: Chain L: W.557, L.558, I.561 Chain M: Y.210 Chain Y: Y.108, G.109, A.112 Ligands: 3PE.32, PLC.54, PC1.76 Chain c: P.82, N.83, T.84, S.87, L.88, G.90, A.91, I.95, L.98 Ligand excluded by PLIP 3PE.75: 8 residues within 4Å: Chain L: M.533, L.536, M.540 Chain b: W.126, C.130, L.133 Chain c: S.9, R.10 Ligand excluded by PLIP 3PE.79: 10 residues within 4Å: Chain B: K.205 Chain H: L.15, F.19, P.42, L.46, I.49 Ligands: PC1.7, PC1.78 Chain g: F.28, W.75 Ligand excluded by PLIP 3PE.80: 4 residues within 4Å: Ligands: CDL.81 Chain h: R.6, F.7, W.10 Ligand excluded by PLIP

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

SF4.5: 14 residues within 4Å: Chain B: A.90, C.91, C.92, G.127, T.128, G.154, S.155, C.156, G.185, 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 SF4.11: 11 residues within 4Å: Chain G: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.12: 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 SF4.18: 11 residues within 4Å: Chain I: H.101, C.123, I.147, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 6 PLIP interactions: 6 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:H.101, I:C.123, I:C.152, I:C.155, I:C.158 SF4.19: 13 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, 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

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

PLC.6: 6 residues within 4Å: Chain B: G.63, L.70, W.213, Y.214 Chain P: Q.137 Ligands: PC1.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.70 PLC.24: 9 residues within 4Å: Chain J: M.1, Y.4, F.7, I.8, V.11, M.15, L.97, E.100, L.108 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:V.11, J:L.97, J:E.100 pi-Cation interactions: J:Y.4 PLC.28: 12 residues within 4Å: Chain L: T.294, I.414, S.417, F.418, I.421, L.496, L.500, I.504, A.519, F.520, F.522 Chain d: W.30 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:T.294, L:I.414, L:F.418, L:I.421, L:L.496, L:L.500, L:I.504, L:F.520, L:F.522 PLC.42: 9 residues within 4Å: Chain N: I.7, I.8 Chain O: Q.25, G.27, P.28, L.29, I.32 Ligands: CDL.39, CDL.66 5 PLIP interactions: 3 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: O:L.29, O:I.32, N:I.7, N:I.8 Hydrogen bonds: O:L.29 PLC.54: 12 residues within 4Å: Chain Y: A.96, L.99, I.100, G.102, A.103, R.106, S.107, Y.108, G.111, A.112 Ligands: 3PE.74, PC1.76 9 PLIP interactions: 9 interactions with chain Y Hydrophobic interactions: Y:A.96, Y:L.99, Y:L.99, Y:I.100, Y:Y.108, Y:A.112 Hydrogen bonds: Y:G.102, Y:R.106 Salt bridges: Y:R.106 PLC.56: 5 residues within 4Å: Chain Z: L.30, S.31, S.34, A.37, V.38 2 PLIP interactions: 2 interactions with chain Z Hydrophobic interactions: Z:A.37, Z:V.38 PLC.61: 8 residues within 4Å: Chain 1: V.30, P.33, T.34, L.35 Chain A: N.85, T.89, L.92 Ligands: 3PE.60 3 PLIP interactions: 2 interactions with chain 1, 1 interactions with chain A Hydrophobic interactions: 1:V.30, 1:T.34, A:L.92 PLC.65: 8 residues within 4Å: Chain 3: L.54, L.55, L.58, I.65 Chain 5: W.11 Chain M: W.16, L.17, S.18 2 PLIP interactions: 1 interactions with chain 3, 1 interactions with chain 5 Hydrophobic interactions: 3:I.65, 5:W.11 PLC.71: 9 residues within 4Å: Chain 6: I.84, W.85, M.87, R.88, F.92 Chain 7: F.73, Y.74, L.77 Ligands: 3PE.67 3 PLIP interactions: 3 interactions with chain 6 Hydrophobic interactions: 6:W.85, 6:F.92 Salt bridges: 6:R.88

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

FES.8: 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.13: 9 residues within 4Å: Chain G: R.62, 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.10: 19 residues within 4Å: Chain F: G.87, R.88, G.89, A.91, 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 17 PLIP interactions: 17 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:D.118, F:E.119, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244 Water bridges: F:E.121 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.14: 5 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:I.223, G:V.228, G:L.231

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.27: 11 residues within 4Å: Chain 8: K.63, R.66, H.67, F.70, H.74 Chain L: T.26, K.28, N.31, L.34, Y.35, T.38 11 PLIP interactions: 5 interactions with chain 8, 6 interactions with chain L Hydrophobic interactions: 8:R.66, L:T.26, L:K.28, L:N.31, L:L.34, L:Y.35, L:Y.35 Hydrogen bonds: 8:K.63, 8:R.66, 8:R.66 Salt bridges: 8:H.67

2 x ZN: ZINC ION(Non-covalent)

ZN.31: 4 residues within 4Å: Chain 6: D.63 Chain M: H.82, E.335, H.338 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain 6 Metal complexes: M:H.82, M:H.338, 6:D.63 ZN.44: 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

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.35: 26 residues within 4Å: Chain 7: L.68, R.72 Chain L: M.22, S.23, F.24, K.116, K.119, Y.120, L.123, T.127, I.149, M.150, L.153 Chain M: P.353, L.354, T.357, W.358, L.360, L.364, P.371, L.442, L.445, L.446, T.448, L.449 Ligands: PC1.70 18 PLIP interactions: 1 interactions with chain 7, 8 interactions with chain L, 9 interactions with chain M Salt bridges: 7:R.72, L:K.116, L:K.119, L:K.119, L:K.119 Hydrophobic interactions: L:L.123, L:T.127, L:I.149, L:L.153, M:T.357, M:W.358, M:L.360, M:L.364, M:L.442, M:L.445, M:L.446, M:L.449 Hydrogen bonds: M:P.353 CDL.36: 32 residues within 4Å: Chain 3: F.33, F.36, C.40, L.43, A.47, V.53 Chain M: I.9, P.13, W.16, T.90, R.91, L.94, T.97, M.98, S.101, L.104, F.105, V.127, I.131, R.135 Chain N: P.238, I.239, V.242, L.245, A.246, P.256, L.257, T.301, T.334, M.335, P.338 Ligands: CDL.47 27 PLIP interactions: 12 interactions with chain M, 8 interactions with chain N, 5 interactions with chain 3, 2 interactions with chain O Hydrophobic interactions: M:I.9, M:P.13, M:W.16, M:L.94, M:T.97, M:L.104, M:F.105, M:V.127, M:I.131, M:R.135, N:I.239, N:V.242, N:L.245, N:A.246, N:P.256, N:L.257, N:T.301, N:P.338, 3:F.33, 3:F.36, 3:F.36, 3:L.43, 3:L.43 Hydrogen bonds: M:T.90, M:R.91, O:K.326, O:K.326 CDL.39: 23 residues within 4Å: Chain N: F.6, I.7, L.10, M.14, K.46, S.125, L.128, I.129, T.132, W.133, I.209, I.210, S.213, T.217, M.220, K.322, T.324, F.325, M.329 Chain O: P.28, H.280 Ligands: PLC.42, PC1.64 18 PLIP interactions: 18 interactions with chain N Hydrophobic interactions: N:I.7, N:L.10, N:L.10, N:L.128, N:L.128, N:I.129, N:W.133, N:W.133, N:I.209, N:I.209, N:I.210, N:K.322, N:F.325 Hydrogen bonds: N:K.46, N:S.125, N:T.324 Water bridges: N:K.46 Salt bridges: N:K.322 CDL.47: 25 residues within 4Å: Chain 3: T.27, P.29, R.30, A.32, F.33, F.36 Chain 5: L.26, K.29, K.33 Chain M: L.2, I.5, I.6, L.55, F.56, F.105, M.108, I.120 Chain N: P.256, P.338 Chain X: F.169, W.170, T.171, M.172 Ligands: CDL.36, 3PE.68 15 PLIP interactions: 7 interactions with chain M, 1 interactions with chain N, 4 interactions with chain 3, 2 interactions with chain 5, 1 interactions with chain X Hydrophobic interactions: M:L.2, M:I.5, M:I.6, M:I.6, M:F.56, M:F.105, M:I.120, N:P.256, 3:R.30, 3:F.33, 3:F.33, 3:F.36, X:F.169 Salt bridges: 5:K.29, 5:K.33 CDL.66: 20 residues within 4Å: Chain 2: K.43, T.47, T.50 Chain 3: V.34, D.45, R.49, R.60, L.63, Y.64, S.67, F.68, F.70, G.72, L.75 Chain N: F.325, T.328, M.336, L.339, M.342 Ligands: PLC.42 10 PLIP interactions: 7 interactions with chain 3, 2 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: 3:V.34, 3:Y.64, 3:F.68, 3:F.70, N:L.339 Hydrogen bonds: 3:R.49, 3:R.60, N:F.325 Salt bridges: 3:R.60, 2:K.43 CDL.73: 23 residues within 4Å: Chain 6: T.104, A.107, Y.108 Chain 7: A.83, I.86, T.87, N.90, E.95, H.115 Chain 8: W.80, I.81, Y.84, Y.85, H.89 Chain L: L.12, F.80 Chain M: L.446 Ligands: 3PE.29, PC1.70 Chain f: V.48, R.49, I.52, H.56 23 PLIP interactions: 2 interactions with chain 6, 11 interactions with chain 8, 5 interactions with chain 7, 2 interactions with chain f, 2 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: 6:A.107, 6:Y.108, 8:W.80, 8:W.80, 8:W.80, 8:I.81, 8:Y.84, 8:Y.84, 8:Y.85, 8:Y.85, 8:Y.85, 7:A.83, f:V.48, L:L.12, L:F.80, M:L.446 Hydrogen bonds: 8:Y.84, 7:N.90, 7:N.90, 7:E.95 Salt bridges: 8:H.89, 7:H.115, f:R.49 CDL.81: 18 residues within 4Å: Chain 0: M.1, W.2, F.3, L.6, P.7 Chain H: Y.43 Ligands: 3PE.15, 3PE.80 Chain g: L.3, V.6, R.9, G.10, Q.13 Chain h: S.3, A.4, T.5, F.7, I.8 12 PLIP interactions: 1 interactions with chain H, 3 interactions with chain g, 4 interactions with chain 0, 4 interactions with chain h Hydrophobic interactions: H:Y.43, g:L.3, 0:W.2, 0:L.6, 0:L.6, h:F.7 Hydrogen bonds: g:R.9, h:S.3, h:T.5 Salt bridges: g:R.9 Water bridges: 0:W.2, h:R.12

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.40: 19 residues within 4Å: Chain O: C.55, S.56, G.57, K.58, S.59, E.76, L.102, Y.106, L.119, Q.120, L.123, R.127, R.149, D.154, F.157, M.161, K.209, E.214 Ligands: MG.41 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:Q.120, O:Q.120, O:R.127, O:R.127, O:R.149, O:E.214 Salt bridges: O:K.58, O:K.58, O:R.149, O:K.209 pi-Stacking: O:F.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.41: 3 residues within 4Å: Chain O: S.59, E.76 Ligands: DGT.40 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.59

1 x FVH: [[(2~{R},3~{S},4~{R},5~{R})-5-[(3~{R})-3-aminocarbonylpiperidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

FVH.43: 27 residues within 4Å: 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.148, I.167, S.168, H.169, Y.180, K.184, P.203, A.204, I.206, R.212 24 PLIP interactions: 1 interactions with chain B, 23 interactions with chain P Salt bridges: B:R.216, P:R.85, P:R.132, P:R.132, P:R.212, P:R.212 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:G.131, P:Y.180, P:K.184, P:I.206 Water bridges: P:R.85, P:R.132 pi-Cation interactions: P:R.85

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.45: 19 residues within 4Å: Chain T: D.111, S.112, L.113 Chain W: M.25, K.29, V.32, R.33, L.35, W.39, K.62, V.63, M.66, F.67, N.70, A.71, I.73, V.79, L.82, F.107 14 PLIP interactions: 12 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:R.33, W:L.35, W:W.39, W:W.39, W:W.39, W:K.62, W:V.63, W:M.66, W:F.67, W:F.107, T:L.113 Hydrogen bonds: W:M.66, T:S.112 EHZ.46: 19 residues within 4Å: Chain U: D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, H.26, L.27, R.47, F.48, H.51, K.52, E.54, A.60, L.63, A.67, E.70, G.74 9 PLIP interactions: 8 interactions with chain d, 1 interactions with chain U Hydrophobic interactions: d:V.16, d:H.26, d:L.27, d:F.48, d:A.60, d:E.70 Hydrogen bonds: d:R.47, U:S.112 Salt bridges: d:K.52

1 x MYR: MYRISTIC ACID(Covalent)

MYR.77: 5 residues within 4Å: Chain L: L.413, L.486 Chain b: Q.154 Chain e: G.2, L.5 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain b Hydrophobic interactions: L:L.413, L:L.486 Hydrogen bonds: b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grba, D.N. et al., Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science (2024)

Release Date

2024-06-05

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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