SMTL ID : 7v2h.1

Active state complex I from DQ-NADH dataset

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.180, P.198, S.353, C.354, G.355, Q.356, C.357, C.360, T.398, I.399, C.400, L.402, G.403 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.354, A:C.357, A:C.360, A:C.400 SF4.4: 13 residues within 4Å: Chain B: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.77, B:C.80, B:C.83, B:C.126 SF4.5: 12 residues within 4Å: Chain B: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.133 Metal complexes: B:C.87, B:C.116, B:C.119, B:C.122 SF4.6: 13 residues within 4Å: Chain C: A.30, C.31, C.32, G.67, T.68, G.94, S.95, C.96, C.126, P.127 Chain P: R.85, R.105, H.190 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.31, C:C.32, C:C.96, C:C.126 SF4.12: 12 residues within 4Å: Chain L: H.96, P.97, D.99, C.100, C.103, Q.105, G.106, C.109, L.111, Q.112, V.200, G.201 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:H.96, L:C.100, L:C.103, L:C.109 SF4.13: 13 residues within 4Å: Chain L: M.145, C.148, I.149, Q.150, C.151, T.152, R.153, C.154, V.178, C.198, V.200, A.202, L.203 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.148, L:C.151, L:C.154, L:C.198

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: G.62, R.63, G.64, K.73, N.91, D.93, E.94, G.95, Y.179, I.180, G.182, E.183, E.184, V.217, A.218, N.219, T.222, A.401, L.402 Ligands: NAI.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.179, A:I.180, A:E.183, A:E.183, A:A.401, A:L.402 Hydrogen bonds: A:G.64, A:N.91, A:E.94, A:G.95, A:E.184, A:E.184, A:N.219, A:N.219, A:T.222 Salt bridges: A:K.73

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 17 residues within 4Å: Chain A: G.64, G.65, A.66, F.68, K.73, F.76, E.94, G.95, E.96, Y.179, E.184, K.201, F.204, G.325, T.326, A.401 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.96, A:Y.179, A:T.326 Hydrogen bonds: A:G.64, A:K.73, A:G.95, A:E.96, A:E.184, A:K.201 Salt bridges: A:K.201, A:K.201 pi-Stacking: A:F.68, A:F.204

10 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.7: 16 residues within 4Å: Chain 7: I.20, L.24, P.25, Q.26 Chain C: L.10, V.14, L.150, W.153, R.156 Chain I: D.55, F.275 Ligands: PLX.8, PLX.32 Chain f: A.52, L.53, F.56 13 PLIP interactions: 4 interactions with chain f, 1 interactions with chain I, 6 interactions with chain C, 2 interactions with chain 7 Hydrophobic interactions: f:A.52, f:L.53, f:F.56, f:F.56, I:F.275, C:L.10, C:V.14, C:L.150, C:L.150, C:W.153, 7:I.20, 7:I.20 Salt bridges: C:R.156 PEE.20: 17 residues within 4Å: Chain 7: A.99, A.103, W.106, T.107, K.109 Chain S: F.7, L.8, E.15, L.18, V.19, S.21, F.22, A.23, G.25, G.26 Chain f: K.291, P.295 15 PLIP interactions: 8 interactions with chain S, 5 interactions with chain 7, 2 interactions with chain f Hydrophobic interactions: S:F.7, S:L.8, S:L.18, S:V.19, S:V.19, S:F.22, S:F.22, S:A.23, 7:A.103, 7:W.106, 7:W.106, f:P.295 Hydrogen bonds: 7:W.106 Salt bridges: 7:K.109, f:K.291 PEE.22: 19 residues within 4Å: Chain 6: I.276, I.277 Chain T: L.123, E.130, W.132 Ligands: PLX.24, PEE.37 Chain e: Y.152, A.155, G.156, P.159, V.162, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 14 PLIP interactions: 8 interactions with chain e, 1 interactions with chain 6, 5 interactions with chain T Hydrophobic interactions: e:A.155, e:V.162, e:F.194, e:F.194, e:L.197, e:A.198, e:M.201, 6:I.276, T:L.123, T:L.123, T:W.132, T:W.132 Hydrogen bonds: e:S.191, T:E.130 PEE.25: 10 residues within 4Å: Chain 6: W.167 Chain 9: F.568, I.569, M.573 Chain T: I.109, A.112, A.113, Y.116, M.117, T.120 6 PLIP interactions: 1 interactions with chain 6, 4 interactions with chain T, 1 interactions with chain 9 Hydrophobic interactions: 6:W.167, T:I.109, T:A.112, T:A.113, T:Y.116, 9:I.569 PEE.31: 14 residues within 4Å: Chain 7: V.11, S.15, V.18, L.19, F.22, W.23, L.27 Ligands: UQ.11, PLX.32, CDL.40 Chain f: R.62, I.72, L.77, S.80 8 PLIP interactions: 3 interactions with chain f, 5 interactions with chain 7 Hydrophobic interactions: f:I.72, f:L.77, 7:V.11, 7:V.11, 7:V.18, 7:L.19, 7:W.23 Salt bridges: f:R.62 PEE.37: 19 residues within 4Å: Chain 6: L.163, L.170, M.284, T.285, L.287, L.288, Y.291, R.295 Chain 9: L.562, S.567, Q.570 Chain P: Q.13, M.19, Y.20 Ligands: PEE.22 Chain e: N.144, F.151, Y.152, A.155 17 PLIP interactions: 2 interactions with chain 9, 1 interactions with chain P, 10 interactions with chain 6, 4 interactions with chain e Hydrophobic interactions: 9:L.562, 9:L.562, 6:L.163, 6:L.287, 6:L.288, 6:L.288, 6:L.288, 6:Y.291, 6:Y.291, 6:Y.291, e:F.151, e:F.151, e:Y.152, e:A.155 Hydrogen bonds: P:Q.13, 6:Y.291 Salt bridges: 6:R.295 PEE.38: 16 residues within 4Å: Chain 0: N.85, R.86 Chain 9: T.166, Q.170, L.173, Y.174, I.180, G.228, L.229, L.280, M.533, H.534, T.538, N.541 Chain e: M.401, L.405 12 PLIP interactions: 10 interactions with chain 9, 1 interactions with chain 0, 1 interactions with chain e Hydrophobic interactions: 9:L.173, 9:L.173, 9:I.180, 9:L.229, 9:L.229, 9:L.280, 9:N.541, 0:R.86, e:L.405 Hydrogen bonds: 9:Q.170 Salt bridges: 9:H.534, 9:H.534 PEE.39: 14 residues within 4Å: Chain 9: N.65, W.66, H.67, W.68, S.77, L.78, N.136 Chain Z: I.80, Y.83, Y.84, H.88 Ligands: CDL.27, PLX.28, CDL.35 12 PLIP interactions: 6 interactions with chain Z, 6 interactions with chain 9 Hydrophobic interactions: Z:I.80, Z:I.80, Z:Y.83, Z:Y.84, Z:Y.84, 9:W.66, 9:W.68, 9:L.78, 9:L.78 Salt bridges: Z:H.88 Hydrogen bonds: 9:H.67, 9:H.67 PEE.41: 21 residues within 4Å: Chain 7: I.3 Chain Q: A.39 Chain U: F.138, I.139, W.140, Y.141, T.142 Ligands: CDL.40 Chain a: I.12, V.35, V.39, C.41, G.42, L.45, N.46, S.50, F.57 Chain f: M.98, N.99, F.104, M.108 13 PLIP interactions: 7 interactions with chain a, 3 interactions with chain f, 1 interactions with chain U, 2 interactions with chain 7 Hydrophobic interactions: a:I.12, a:V.35, a:V.39, a:L.45, a:F.57, f:F.104, 7:I.3, 7:I.3 Hydrogen bonds: a:S.50, a:S.50, f:N.99, f:N.99, U:Y.141 PEE.45: 22 residues within 4Å: Chain B: T.24, L.25, W.27, L.30, L.34 Chain P: R.233 Chain S: V.17, I.24 Chain U: L.41 Chain f: P.180, M.183, M.184, F.186, I.187, L.190, F.198, I.273, Y.277, L.288, S.292, F.293, L.296 17 PLIP interactions: 2 interactions with chain P, 9 interactions with chain f, 1 interactions with chain U, 4 interactions with chain B, 1 interactions with chain S Salt bridges: P:R.233, P:R.233 Hydrophobic interactions: f:F.186, f:F.186, f:L.190, f:F.198, f:I.273, f:I.273, f:Y.277, f:F.293, f:L.296, U:L.41, B:W.27, B:W.27, B:W.27, B:L.34, S:I.24

7 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.8: 15 residues within 4Å: Chain C: K.9, D.12, L.13, W.16, R.19, K.145 Chain M: F.27, R.28, N.30, W.74, V.76 Ligands: PEE.7 Chain f: L.46, I.49, L.53 7 PLIP interactions: 2 interactions with chain f, 5 interactions with chain C Hydrophobic interactions: f:L.46, f:I.49, C:W.16, C:W.16 Salt bridges: C:R.19, C:K.145, C:K.145 PLX.24: 15 residues within 4Å: Chain T: P.86, L.87, F.90, A.122 Ligands: PEE.22 Chain e: N.188, S.189, W.190, I.193, M.201, G.211, L.212, P.260, F.261, L.264 12 PLIP interactions: 8 interactions with chain e, 4 interactions with chain T Hydrophobic interactions: e:W.190, e:W.190, e:I.193, e:L.212, e:P.260, e:F.261, e:L.264, T:L.87, T:F.90, T:F.90, T:A.122 pi-Cation interactions: e:W.190 PLX.28: 18 residues within 4Å: Chain 2: S.53, A.57, Y.58 Chain 9: M.20, N.23, W.66 Ligands: CDL.27, CDL.35, PEE.39 Chain e: L.39, P.64, V.67, W.71, I.317, P.443, L.446, L.449, N.450 9 PLIP interactions: 8 interactions with chain e, 1 interactions with chain 9 Hydrophobic interactions: e:L.39, e:V.67, e:I.317, e:P.443, e:L.446, e:L.449, e:N.450, 9:N.23 Hydrogen bonds: e:N.450 PLX.30: 20 residues within 4Å: Chain 4: S.5, R.10, P.12, L.13, F.15, M.36, F.73, L.77, R.80 Chain 5: P.1, F.2, F.3 Chain 6: L.203, T.210, L.332, V.336, M.339, A.342, L.343, S.345 11 PLIP interactions: 6 interactions with chain 4, 5 interactions with chain 6 Hydrophobic interactions: 4:F.15, 4:F.73, 4:F.73, 4:L.77, 6:L.203, 6:L.332, 6:L.332, 6:V.336, 6:M.339 Salt bridges: 4:R.10, 4:R.80 PLX.32: 12 residues within 4Å: Chain 7: L.16, I.20, W.23, L.24, P.25 Chain I: L.269, V.272, S.273, F.275, W.278 Ligands: PEE.7, PEE.31 9 PLIP interactions: 4 interactions with chain I, 5 interactions with chain 7 Hydrophobic interactions: I:L.269, I:V.272, I:F.275, 7:L.16, 7:L.16, 7:I.20, 7:I.20 pi-Cation interactions: I:F.275 Hydrogen bonds: 7:W.23 PLX.33: 11 residues within 4Å: Chain 5: L.13 Chain 7: N.83, T.86, M.90, F.93 Chain a: S.148, Y.149, T.151, W.152, I.155, W.159 10 PLIP interactions: 3 interactions with chain 7, 6 interactions with chain a, 1 interactions with chain 5 Hydrophobic interactions: 7:F.93, a:T.151, a:W.152, a:I.155, a:I.155, a:W.159, 5:L.13 Hydrogen bonds: 7:N.83, 7:T.86 pi-Cation interactions: a:Y.149 PLX.42: 17 residues within 4Å: Chain 2: F.42, L.51, T.54, F.55 Chain Y: V.31, I.35, R.72, T.73, F.74, Y.75, D.76 Chain b: F.19, C.23, R.27 Chain e: L.36, I.37, S.40 13 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain b, 4 interactions with chain e, 5 interactions with chain Y Hydrophobic interactions: 2:F.42, 2:T.54, 2:F.55, e:L.36, e:I.37, Y:V.31, Y:I.35, Y:F.74, Y:F.74 Salt bridges: b:R.27, Y:D.76 Hydrogen bonds: e:S.40, e:S.40

2 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.9: 20 residues within 4Å: Chain D: K.16, V.19, L.22, W.26, T.33, K.49, V.50, M.53, F.54, N.57, A.58, V.60, V.66, L.69, V.70, G.73, F.93 Chain F: D.43, S.44, L.45 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:W.26, D:W.26, D:T.33, D:K.49, D:V.50, D:M.53, D:F.54, D:A.58, D:F.93, D:F.93 Hydrogen bonds: D:K.16, D:K.16, F:L.45 Salt bridges: D:K.16 8Q1.26: 19 residues within 4Å: Chain V: D.43, S.44, L.45 Chain d: H.11, Q.12, V.15, A.22, H.25, L.26, W.29, M.43, R.46, F.47, H.50, K.51, A.66, E.69, F.70, G.73 12 PLIP interactions: 10 interactions with chain d, 2 interactions with chain V Hydrophobic interactions: d:Q.12, d:H.25, d:L.26, d:F.47, d:E.69, d:F.70 Hydrogen bonds: d:H.11, d:H.50, d:K.51, V:S.44, V:L.45 Salt bridges: d:K.51

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

NDP.10: 25 residues within 4Å: Chain C: R.156 Chain I: G.25, A.26, T.27, G.28, F.29, L.30, R.50, C.51, W.73, L.94, V.95, G.96, R.97, F.104, V.109, F.110, I.132, S.133, H.134, Y.145, K.149, P.168, D.170, I.171 19 PLIP interactions: 18 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:P.168, I:I.171 Hydrogen bonds: I:G.25, I:T.27, I:T.27, I:T.27, I:F.29, I:L.30, I:C.51, I:L.94, I:Y.145, I:K.149, I:I.171 Salt bridges: I:R.50, I:R.97, I:R.97, C:R.156 pi-Cation interactions: I:R.50, I:R.50

2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.11: 4 residues within 4Å: Chain I: S.184, W.187, W.278 Ligands: PEE.31 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:W.187, I:W.278, I:W.278 Hydrogen bonds: I:S.184 pi-Stacking: I:W.278 UQ.46: 15 residues within 4Å: Chain C: W.23, D.47, V.52, R.54 Chain f: I.11, L.14, L.15, A.18, T.21, R.25, D.51, A.52, L.55, F.224, M.225 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain f Hydrophobic interactions: C:W.23, C:W.23, C:V.52, f:I.11, f:L.14, f:L.14, f:L.15, f:A.18, f:T.21, f:D.51, f:A.52, f:L.55, f:F.224, f:F.224, f:F.224 pi-Cation interactions: f:R.274

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

FES.14: 9 residues within 4Å: Chain L: R.34, C.36, Y.37, G.45, N.46, C.47, R.48, C.50, C.64 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.36, L:C.47, L:C.50, L:C.64 FES.17: 9 residues within 4Å: Chain N: C.103, T.105, P.107, C.108, C.144, L.145, G.146, A.147, C.148 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.103, N:C.108, N:C.144, N:C.148

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 5 residues within 4Å: Chain L: Q.105, I.195, C.198, V.200, L.203 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:I.195, L:C.198, L:V.200, L:L.203

11 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.16: 15 residues within 4Å: Chain H: S.2, A.3, T.4, I.7 Chain M: L.2, V.5, L.6, R.8, Q.12, Y.22 Chain Q: W.2, F.3, E.4, L.6 Chain f: Y.43 10 PLIP interactions: 2 interactions with chain H, 3 interactions with chain M, 4 interactions with chain Q, 1 interactions with chain f Hydrophobic interactions: H:I.7, M:L.2, Q:W.2, Q:F.3, Q:F.3, Q:E.4, f:Y.43 Hydrogen bonds: H:T.4, M:Q.12 Salt bridges: M:R.8 CDL.21: 26 residues within 4Å: Chain 6: P.110, H.112, F.113, L.153, M.157, L.160, I.164 Chain 9: M.576, V.577, Q.580, S.598, L.601 Chain T: S.24, I.27, G.28, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, S.62, I.65, G.66 18 PLIP interactions: 11 interactions with chain T, 5 interactions with chain 6, 2 interactions with chain 9 Hydrophobic interactions: T:I.27, T:I.27, T:T.31, T:I.34, T:Y.38, T:Y.38, T:Y.38, T:L.42, T:Y.58, T:I.65, 6:P.110, 6:F.113, 6:L.153, 6:L.160, 6:I.164, 9:V.577 Hydrogen bonds: T:Y.58, 9:Q.580 CDL.23: 18 residues within 4Å: Chain 9: W.557, L.558 Chain T: Y.107, G.108, A.111, C.114 Chain c: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, L.97, F.98 Chain e: Y.210, L.264 13 PLIP interactions: 6 interactions with chain c, 2 interactions with chain T, 3 interactions with chain 9, 2 interactions with chain e Hydrophobic interactions: c:P.83, c:P.83, c:L.87, c:A.90, c:L.97, c:F.98, 9:W.557, 9:W.557, 9:L.558, e:Y.210, e:L.264 Hydrogen bonds: T:Y.107, T:G.108 CDL.27: 30 residues within 4Å: Chain 1: R.42, P.43, A.47, I.51, H.55 Chain 2: V.50, S.53, T.54, A.57, Y.58 Chain 9: T.13, N.65 Chain Y: R.21, I.24, L.25, G.28, A.32, T.36, N.39, V.40, E.44, H.64 Chain Z: W.79, Y.83, Y.84, H.88 Ligands: PLX.28, CDL.35, PEE.39 Chain e: L.446 18 PLIP interactions: 6 interactions with chain Z, 7 interactions with chain Y, 2 interactions with chain 1, 2 interactions with chain 2, 1 interactions with chain e Hydrophobic interactions: Z:W.79, Z:Y.83, Z:Y.83, Z:Y.84, Z:Y.84, Y:R.21, Y:I.24, Y:L.25, 1:P.43, 1:I.51, 2:V.50, e:L.446 Salt bridges: Z:H.88, Y:H.64 Hydrogen bonds: Y:N.39, Y:N.39, Y:E.44, 2:Y.58 CDL.29: 24 residues within 4Å: Chain 6: P.3, Y.6, T.7, T.8, I.10, M.11, M.14, S.15, M.18, K.46, Q.125, L.128, L.129, T.132, W.133, L.136, I.209, M.217, K.321, L.325, M.329 Chain a: W.159 Chain i: P.5, V.9 15 PLIP interactions: 13 interactions with chain 6, 2 interactions with chain a Hydrophobic interactions: 6:T.8, 6:I.10, 6:M.18, 6:L.128, 6:L.129, 6:W.133, 6:L.136, 6:I.209, 6:L.325, a:W.159, a:W.159 Hydrogen bonds: 6:T.7, 6:Q.125 Salt bridges: 6:K.46, 6:K.321 CDL.34: 25 residues within 4Å: Chain 8: A.13, I.14, A.17, M.21, Y.22, R.23 Chain 9: K.585, L.589, I.593, M.596 Chain T: A.37, P.45, A.46, S.47, F.48, G.51, V.52 Chain a: S.21, S.22, K.23, T.88, A.92, S.95, G.96, M.99 14 PLIP interactions: 4 interactions with chain 8, 2 interactions with chain T, 4 interactions with chain 9, 4 interactions with chain a Hydrophobic interactions: 8:A.13, 8:I.14, 8:M.21, T:F.48, T:V.52, 9:L.589, 9:L.589, 9:I.593, a:T.88, a:A.92 Salt bridges: 8:R.23, 9:K.585, a:K.23 Hydrogen bonds: a:T.88 CDL.35: 31 residues within 4Å: Chain 9: T.16, I.19, M.20, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, M.150, L.153 Chain Y: L.17 Ligands: CDL.27, PLX.28, PEE.39 Chain e: P.353, L.354, T.357, W.358, V.361, T.365, L.369, P.370, P.371, S.372, L.445, L.446, T.448, L.449 20 PLIP interactions: 9 interactions with chain e, 11 interactions with chain 9 Hydrophobic interactions: e:W.358, e:V.361, e:T.365, e:P.371, e:L.445, e:L.446, e:L.449, 9:T.16, 9:I.19, 9:L.78, 9:I.126, 9:I.130, 9:L.153 Hydrogen bonds: e:P.353, e:T.357, 9:Y.120 Salt bridges: 9:R.116, 9:K.119, 9:K.119, 9:K.119 CDL.36: 18 residues within 4Å: Chain 0: F.106, F.109 Chain 9: I.293, T.294, L.410, I.414, S.417, L.418, A.421, R.425, M.496, L.500, A.501, L.504, N.505, S.517, T.519, Y.520 18 PLIP interactions: 14 interactions with chain 9, 4 interactions with chain 0 Hydrophobic interactions: 9:I.293, 9:L.410, 9:I.414, 9:L.418, 9:A.421, 9:L.500, 9:L.500, 9:T.519, 0:F.106, 0:F.109, 0:F.109, 0:F.109 Hydrogen bonds: 9:S.517, 9:S.517, 9:Y.520, 9:Y.520 Salt bridges: 9:R.425, 9:R.425 CDL.40: 22 residues within 4Å: Chain I: W.187, R.251 Ligands: PEE.31, PEE.41 Chain a: I.12, I.15, Y.28, L.31, G.32, I.34, V.35, G.38, V.82, W.83, V.84, F.93, L.97 Chain f: S.67, I.68, S.69, I.73, L.77 20 PLIP interactions: 5 interactions with chain f, 14 interactions with chain a, 1 interactions with chain I Hydrophobic interactions: f:I.68, f:L.77, a:I.12, a:I.15, a:L.31, a:V.35, a:V.35, a:W.83, a:W.83, a:W.83, a:V.84, a:F.93, a:L.97 Hydrogen bonds: f:I.68, f:S.69, f:S.69, a:Y.28, a:W.83, a:V.84 Salt bridges: I:R.251 CDL.43: 13 residues within 4Å: Chain 4: T.29, P.31, V.34, Y.35 Chain 6: P.256, P.338 Ligands: CDL.44 Chain b: R.28, K.32 Chain g: F.168, W.169, T.170, M.171 10 PLIP interactions: 3 interactions with chain 6, 2 interactions with chain b, 4 interactions with chain g, 1 interactions with chain 4 Hydrophobic interactions: 6:P.256, 6:P.338, 6:P.338, g:F.168, g:F.168, 4:Y.35 Salt bridges: b:R.28, b:K.32 Hydrogen bonds: g:T.170, g:T.170 CDL.44: 31 residues within 4Å: Chain 4: Y.41, C.42, L.45, I.46, A.49, V.55, V.56 Chain 6: P.238, V.239, S.242, L.243, M.245, V.246, T.334, L.335 Ligands: CDL.43 Chain b: L.14 Chain e: P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.104, V.127, I.131, R.135 Chain i: K.303, Y.304 22 PLIP interactions: 7 interactions with chain e, 3 interactions with chain i, 7 interactions with chain 4, 1 interactions with chain b, 4 interactions with chain 6 Hydrophobic interactions: e:W.16, e:T.97, e:L.104, e:V.127, e:I.131, 4:L.45, 4:I.46, 4:I.46, 4:A.49, 4:V.55, 4:V.56, b:L.14, 6:L.243, 6:V.246, 6:L.335, 6:L.335 Hydrogen bonds: e:T.90, i:K.303, i:Y.304, i:Y.304, 4:V.55 Salt bridges: e:R.91

1 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.18: 11 residues within 4Å: Chain C: G.28, L.29, A.30, A.33, M.37, F.53 Chain P: P.56, H.59, Y.108, F.167, I.423 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain P Hydrophobic interactions: C:A.33, C:F.53, P:F.167 Hydrogen bonds: P:H.59, P:Y.108

1 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain R: C.59, G.61, H.68, C.84, C.87 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.59, R:H.68, R:C.84

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.47: 15 residues within 4Å: Chain i: I.31, C.32, S.33, K.35, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, D.131, F.134, M.138, E.191 12 PLIP interactions: 12 interactions with chain i Hydrogen bonds: i:N.30, i:C.32, i:Y.83, i:Q.97, i:Q.97, i:R.104, i:R.104, i:E.191 Salt bridges: i:K.35, i:R.126 pi-Stacking: i:F.134, i:F.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., The coupling mechanism of mammalian mitochondrial complex I. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-03-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

V
X

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
S

R
T

S
U

T
V

U
W

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
l

a
m

b
n

c
o

d
p

e
r

f
s

g
u

h
v

i
w

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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 7

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

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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

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