SMTL ID : 8esz.1

Structure of mitochondrial complex I from Drosophila melanogaster, Helix-locked state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CDL.1: 20 residues within 4Å: Chain 8: R.6, D.7, V.8, S.9 Chain A: L.5, G.6, R.9, L.10, K.12, L.13, M.16, L.30, L.36, Y.56 Chain G: F.83 Chain L: M.1, W.2, F.3, L.6, P.7 14 PLIP interactions: 5 interactions with chain A, 5 interactions with chain L, 3 interactions with chain 8, 1 interactions with chain G Hydrophobic interactions: A:L.10, A:L.30, A:L.36, L:F.3, L:F.3, L:F.3, L:L.6, L:P.7, G:F.83 Salt bridges: A:R.9, A:R.9, 8:R.6 Hydrogen bonds: 8:D.7, 8:S.9 CDL.35: 21 residues within 4Å: Chain 7: P.109, Y.148, I.152, L.156 Chain J: I.570, I.573 Chain O: K.7, Y.8, T.24, K.26, Y.27, V.29, S.30, V.33, F.38, F.70, L.117, K.124 Ligands: PC1.32, 3PE.33, 3PE.57 14 PLIP interactions: 9 interactions with chain O, 3 interactions with chain 7, 2 interactions with chain J Hydrophobic interactions: O:T.24, O:K.26, O:V.29, O:V.33, O:F.38, O:F.70, O:K.124, 7:P.109, 7:L.156, J:I.570, J:I.573 Hydrogen bonds: O:Y.27, 7:Y.148 Salt bridges: O:K.124 CDL.40: 14 residues within 4Å: Chain J: M.1 Chain Q: F.69, Y.70, R.71, L.74, R.94, F.95, G.98, K.99, L.101, L.102, T.105 Ligands: PC1.28, 3PE.29 10 PLIP interactions: 9 interactions with chain Q, 1 interactions with chain J Hydrophobic interactions: Q:F.69, Q:L.74, Q:L.101, Q:L.102 Hydrogen bonds: Q:Y.70, J:M.1 Salt bridges: Q:R.94, Q:K.99, Q:K.99, Q:K.99 CDL.42: 27 residues within 4Å: Chain I: L.337, P.341, T.344, L.345, W.346, F.348, L.349, P.358, Y.399, W.429 Chain J: H.86, R.89, M.92, L.93, L.95, M.96, L.99, S.100, L.103, G.119, V.123 Chain T: R.52, W.55, K.59, L.62, V.66 Ligands: PC1.28 18 PLIP interactions: 7 interactions with chain J, 4 interactions with chain I, 7 interactions with chain T Hydrophobic interactions: J:L.93, J:L.93, J:L.99, J:L.103, J:V.123, I:F.348, I:L.349, I:P.358, I:W.429, T:K.59, T:L.62, T:V.66 Salt bridges: J:R.89, J:R.89, T:R.52, T:R.52, T:K.59, T:K.59 CDL.43: 25 residues within 4Å: Chain P: F.26, R.27, V.31, Q.35 Chain Q: Y.108, A.109, Y.112, Y.113, F.114, N.117 Chain T: V.70, V.73, T.74, V.77, L.78, N.81, P.86, H.106 Chain V: V.88, S.91, A.95, Y.96 Ligands: PC1.17, 3PE.38, PC1.39 20 PLIP interactions: 6 interactions with chain T, 4 interactions with chain P, 4 interactions with chain V, 6 interactions with chain Q Hydrophobic interactions: T:V.70, T:V.73, T:T.74, T:V.77, P:F.26, P:F.26, V:A.95, V:Y.96, Q:Y.108, Q:Y.112, Q:Y.112, Q:Y.113, Q:F.114 Hydrogen bonds: T:N.81, P:Q.35, V:Y.96, V:Y.96, Q:N.117 Salt bridges: T:H.106, P:R.27 CDL.59: 12 residues within 4Å: Chain 7: M.1, F.2, M.124, M.128, F.209, F.213, I.315, N.316 Chain e: K.63, S.65, F.67, H.341 10 PLIP interactions: 8 interactions with chain e, 2 interactions with chain 7 Hydrophobic interactions: e:F.67, e:F.67, 7:F.209 Hydrogen bonds: e:S.65, e:S.65, e:V.66, e:H.341, 7:N.316 Salt bridges: e:K.63, e:H.341 CDL.63: 26 residues within 4Å: Ligands: 3PE.16, PC1.51, WSF.61 Chain a: I.12 Chain b: L.9, T.12, T.13, I.15, I.16, L.18, N.19, M.20, I.21, H.22, A.25, L.28, T.29, I.32, F.78, N.79, S.81, K.83, L.84, T.85, L.86, F.87 21 PLIP interactions: 20 interactions with chain b, 1 interactions with chain a Hydrophobic interactions: b:L.9, b:T.12, b:T.13, b:I.15, b:L.18, b:L.28, b:I.32, b:I.32, b:T.85, b:L.86, b:F.87, b:F.87, a:I.12 Hydrogen bonds: b:I.21, b:H.22, b:N.79, b:S.81, b:S.81, b:L.84 Salt bridges: b:K.83, b:K.83 CDL.64: 13 residues within 4Å: Chain 2: H.236, W.238, P.335, G.336, T.337, I.339, G.340 Chain H: Y.69 Ligands: PC1.11, 3PE.16 Chain c: S.23, I.24, K.28 10 PLIP interactions: 6 interactions with chain 2, 4 interactions with chain c Hydrophobic interactions: 2:I.339, c:I.24 Hydrogen bonds: 2:T.337, 2:T.337, 2:G.340 Salt bridges: 2:H.236, 2:H.236, c:K.28, c:K.28, c:K.28

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

PC1.2: 10 residues within 4Å: Chain A: Y.27, L.28, Y.31, R.32, N.72 Chain F: K.54 Chain H: L.49, I.52, P.53 Ligands: 3PE.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:N.72 Salt bridges: A:K.24 Hydrophobic interactions: H:I.52, H:P.53 PC1.11: 15 residues within 4Å: Chain 2: D.100, P.335 Chain F: L.75, L.78, L.215, W.218, K.221 Chain H: A.59, I.60, F.63, T.64 Ligands: CDL.64 Chain c: L.25, K.27, K.28 11 PLIP interactions: 5 interactions with chain H, 5 interactions with chain F, 1 interactions with chain 2 Hydrophobic interactions: H:A.59, H:I.60, H:I.60, H:F.63, H:T.64, F:L.75, F:L.78, F:L.215, F:W.218 Salt bridges: F:K.221, 2:D.100 PC1.14: 28 residues within 4Å: Chain 4: R.271, Q.275 Chain 9: E.19, D.22, G.25, L.29 Chain G: T.65, M.66, F.68, L.71, L.72, F.75 Chain H: L.190, V.191, V.193, S.194, L.197, P.204, F.265, W.272, V.273, L.277, F.280, L.288, F.293, F.296 Chain M: Y.43 Ligands: 3PE.65 24 PLIP interactions: 6 interactions with chain G, 12 interactions with chain H, 3 interactions with chain 4, 2 interactions with chain 9, 1 interactions with chain M Hydrophobic interactions: G:T.65, G:M.66, G:F.68, G:L.71, G:L.72, G:F.75, H:L.190, H:V.191, H:V.193, H:L.197, H:P.204, H:F.265, H:W.272, H:V.273, H:L.277, H:F.293, H:F.296, H:F.296, 9:D.22, M:Y.43 Salt bridges: 4:R.271, 4:R.271, 4:R.271 Hydrogen bonds: 9:D.22 PC1.17: 21 residues within 4Å: Chain I: L.36, L.63, W.67, L.309, L.434, L.435, L.437, K.438, E.440 Chain J: W.39, E.40, L.41 Chain Q: K.124, G.125 Chain V: C.86, S.91, W.94, A.95, R.103 Ligands: PC1.39, CDL.43 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain V Hydrophobic interactions: I:L.36, I:L.63, I:W.67, I:W.67, I:L.309, I:L.437, V:W.94 Salt bridges: I:K.438, I:E.440 PC1.21: 21 residues within 4Å: Chain 7: P.252, L.331, F.332, S.335 Chain I: L.9, Y.50, F.51, L.98, L.99, L.102, F.115 Chain K: W.173, L.174, E.175 Chain Z: S.20, L.22, S.23, W.26, N.27, D.72, R.75 12 PLIP interactions: 3 interactions with chain 7, 6 interactions with chain I, 3 interactions with chain Z Hydrophobic interactions: 7:P.252, 7:F.332, 7:F.332, I:Y.50, I:F.51, I:L.98, I:L.99, I:L.102, I:F.115 Hydrogen bonds: Z:S.20, Z:S.20 Salt bridges: Z:D.72 PC1.28: 10 residues within 4Å: Chain J: M.1, I.9, L.14, M.92, L.95 Chain Q: R.71 Chain T: K.59 Ligands: 3PE.38, CDL.40, CDL.42 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain J Salt bridges: T:K.59 Hydrophobic interactions: J:I.9, J:L.14, J:L.95 PC1.32: 13 residues within 4Å: Chain 7: F.273 Chain O: Y.27, A.31, L.63, A.120, K.124, E.133, F.134, F.135 Ligands: 3PE.30, 3PE.33, CDL.35, PC1.36 13 PLIP interactions: 12 interactions with chain O, 1 interactions with chain 7 Hydrophobic interactions: O:Y.27, O:A.31, O:L.63, O:A.120, O:F.134, O:F.134, 7:F.273 Hydrogen bonds: O:E.133, O:F.134, O:F.135 Salt bridges: O:K.124, O:K.124, O:E.133 PC1.36: 15 residues within 4Å: Chain 7: Y.272, F.273, T.276, M.280 Chain I: L.149, P.153, Y.160, K.164, Y.180, L.182, C.186 Chain O: I.123, W.132 Ligands: 3PE.20, PC1.32 9 PLIP interactions: 2 interactions with chain O, 5 interactions with chain I, 2 interactions with chain 7 Hydrophobic interactions: O:I.123, O:W.132, I:L.149, I:P.153, I:Y.160, I:L.182, 7:F.273, 7:T.276 Salt bridges: I:K.164 PC1.37: 13 residues within 4Å: Chain 7: S.195, L.198, I.199, F.202 Chain N: F.6, L.7 Chain O: G.144, G.145, L.146, N.147, I.148, N.151 Ligands: PC1.58 6 PLIP interactions: 3 interactions with chain O, 3 interactions with chain 7 Hydrogen bonds: O:G.145, O:L.146, O:N.151 Hydrophobic interactions: 7:I.199, 7:F.202, 7:F.202 PC1.39: 17 residues within 4Å: Chain I: P.358, P.359, L.364, I.436 Chain J: W.39, M.51, I.111, L.115 Chain Q: Y.113, R.123, G.125, W.127 Chain V: A.95, Y.96 Ligands: PC1.17, 3PE.38, CDL.43 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain Q, 2 interactions with chain I Hydrophobic interactions: J:W.39, J:L.115, J:L.115, I:L.364, I:I.436 Salt bridges: Q:R.123 PC1.51: 18 residues within 4Å: Chain 2: R.240, R.243 Chain H: L.76, S.77, I.80, F.84, Y.121, T.122, V.125, W.128 Ligands: 3PE.16, CDL.63 Chain b: L.24, G.27, L.28, L.31, F.66, L.80 14 PLIP interactions: 7 interactions with chain H, 6 interactions with chain b, 1 interactions with chain 2 Hydrophobic interactions: H:L.76, H:I.80, H:F.84, H:Y.121, H:T.122, H:V.125, H:V.125, b:L.24, b:L.24, b:L.28, b:L.31, b:F.66, b:F.66 Salt bridges: 2:R.243 PC1.58: 16 residues within 4Å: Chain 7: I.322, F.326, L.333, L.336, F.337, Y.338 Chain O: L.146, N.147, N.151, W.153 Chain Z: C.31, F.60, I.63, F.71, Y.78 Ligands: PC1.37 14 PLIP interactions: 2 interactions with chain O, 7 interactions with chain 7, 5 interactions with chain Z Hydrogen bonds: O:L.146, O:N.147 Hydrophobic interactions: 7:I.322, 7:I.322, 7:L.333, 7:L.336, 7:F.337, 7:F.337, 7:Y.338, Z:F.60, Z:I.63, Z:F.71, Z:F.71, Z:F.71

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.87, H.96, C.111, C.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.87, B:H.96, B:C.111, B:C.114

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

SF4.4: 12 residues within 4Å: Chain 4: M.380, I.384 Chain C: H.134, P.135, D.137, C.138, C.141, G.144, C.147, L.149, Q.150, V.242 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.134, C:C.138, C:C.141, C:C.147 SF4.5: 13 residues within 4Å: Chain C: C.190, I.191, H.192, C.193, T.194, R.195, C.196, I.220, L.239, C.240, P.241, V.242, L.245 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.190, C:C.193, C:C.196, C:C.240 SF4.8: 11 residues within 4Å: Chain 4: R.143, H.228 Chain F: A.95, C.96, C.97, G.132, G.159, S.160, C.161, C.191, P.192 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.96, F:C.97, F:C.161, F:C.191 SF4.12: 11 residues within 4Å: Chain G: H.106, C.128, I.133, C.157, I.158, Y.159, C.160, G.161, F.162, C.163, E.174 6 PLIP interactions: 6 interactions with chain G, Salt bridges: G:E.174 Metal complexes: G:H.106, G:C.128, G:C.157, G:C.160, G:C.163 SF4.13: 13 residues within 4Å: Chain G: C.118, I.119, A.120, C.121, K.122, L.123, C.124, I.135, Y.150, C.167, P.168, V.169, I.172 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.118, G:C.121, G:C.124, G:C.167 SF4.56: 11 residues within 4Å: Chain 6: I.220, P.238, C.394, G.395, Q.396, C.397, C.400, T.438, I.439, C.440, L.442 4 PLIP interactions: 4 interactions with chain 6, Metal complexes: 6:C.394, 6:C.397, 6:C.400, 6:C.440

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

FES.6: 9 residues within 4Å: Chain C: R.72, C.74, Y.75, A.82, G.83, C.85, R.86, C.88, C.102 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.74, C:C.85, C:C.88, C:C.102 FES.7: 9 residues within 4Å: Chain E: C.128, T.130, P.132, C.133, C.169, L.170, G.171, A.172, C.173 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.128, E:C.133, E:C.169, E:C.173

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

3PE.9: 11 residues within 4Å: Chain A: Y.31, D.34, M.73 Chain F: Y.57, W.81, K.84 Chain H: K.46, G.48, F.56 Ligands: PC1.2, 3PE.10 Ligand excluded by PLIP 3PE.10: 8 residues within 4Å: Chain F: Y.57, S.58, W.70, R.74, L.75, D.77, L.78 Ligands: 3PE.9 Ligand excluded by PLIP 3PE.16: 16 residues within 4Å: Chain 2: I.237 Chain H: Y.69, P.70, L.71, Y.75, L.76, Y.79, F.84 Ligands: PC1.51, CDL.63, CDL.64 Chain b: L.28, I.32 Chain c: I.17, F.20, I.24 Ligand excluded by PLIP 3PE.18: 16 residues within 4Å: Chain 7: M.280, L.283, I.284, F.287 Chain I: Q.138, L.141, Y.142, F.145, Y.146, L.149 Chain J: G.535, Q.536, L.538, Y.539, L.542 Ligands: 3PE.27 Ligand excluded by PLIP 3PE.19: 9 residues within 4Å: Chain I: Y.245, F.247, W.249, I.252 Chain O: L.90 Chain R: F.69, V.77 Ligands: 3PE.20, 3PE.41 Ligand excluded by PLIP 3PE.20: 10 residues within 4Å: Chain I: F.185, Y.245 Chain O: K.86, I.87, L.115, I.119, V.122, M.126 Ligands: 3PE.19, PC1.36 Ligand excluded by PLIP 3PE.22: 16 residues within 4Å: Chain 7: S.233, I.235, T.239, M.242, F.329 Chain I: I.12, F.16, N.87, L.88, L.91, I.95 Chain Z: I.40, W.44, V.50 Ligands: 3PE.46 Chain e: Y.382 Ligand excluded by PLIP 3PE.23: 13 residues within 4Å: Chain J: L.23, L.24, Y.27, F.28, M.33, Y.35, F.55 Chain P: F.11, A.12, V.15, L.16 Chain Q: K.134 Ligands: 3PE.38 Ligand excluded by PLIP 3PE.24: 15 residues within 4Å: Chain J: F.258, L.262, N.265, F.266, Y.385, F.386, L.390, S.393, V.464, F.471, F.482, N.484, K.485, S.486, L.496 Ligand excluded by PLIP 3PE.25: 18 residues within 4Å: Chain I: L.265, F.389 Chain J: N.138, M.141, L.142, L.145, I.149, F.202, S.506, T.507, M.510, I.511, P.514, L.515 Chain W: E.115, D.116, R.117, S.119 Ligand excluded by PLIP 3PE.26: 13 residues within 4Å: Chain 3: W.61, H.62, E.66 Chain J: F.22, L.26, I.435, S.438, M.439, W.442 Chain S: P.73, V.75, Y.76 Ligands: 3PE.29 Ligand excluded by PLIP 3PE.27: 15 residues within 4Å: Chain J: Y.532, F.533, G.534, H.537, L.538, K.541, M.544, Y.545 Chain O: N.106, V.108, A.109, C.112, F.116 Ligands: 3PE.18, 3PE.33 Ligand excluded by PLIP 3PE.29: 18 residues within 4Å: Chain J: L.4, S.8, F.11, V.12, N.13, S.16, M.17, L.72, F.75, K.78, R.424, G.428, M.432, I.435 Chain Q: W.96, A.103 Ligands: 3PE.26, CDL.40 Ligand excluded by PLIP 3PE.30: 13 residues within 4Å: Chain 7: L.151, I.152, I.155, L.156, I.159, I.160, I.163, L.277 Chain J: Y.545, T.548 Chain O: W.35 Ligands: PC1.32, 3PE.33 Ligand excluded by PLIP 3PE.33: 15 residues within 4Å: Chain 7: F.112, L.156, I.160 Chain J: K.541, Y.545, M.552 Chain O: W.35, F.38, F.100, K.104, A.109 Ligands: 3PE.27, 3PE.30, PC1.32, CDL.35 Ligand excluded by PLIP 3PE.34: 9 residues within 4Å: Chain N: P.10, L.11, D.13, L.14 Chain O: I.155, M.156 Chain b: F.139, F.143, I.146 Ligand excluded by PLIP 3PE.38: 15 residues within 4Å: Chain J: Y.35, F.53, F.55 Chain P: L.16 Chain Q: G.106, I.107, G.110, A.111, F.114, W.127, V.129 Ligands: 3PE.23, PC1.28, PC1.39, CDL.43 Ligand excluded by PLIP 3PE.41: 9 residues within 4Å: Chain I: L.199, F.247, V.248, I.252 Chain R: L.73, V.77, I.80, K.88 Ligands: 3PE.19 Ligand excluded by PLIP 3PE.46: 14 residues within 4Å: Chain 0: W.11 Chain 7: F.325 Chain I: L.9, F.10, I.12, P.13, F.16 Chain Z: V.33, V.36, I.40, V.50, F.51 Ligands: 3PE.22 Chain e: Y.382 Ligand excluded by PLIP 3PE.50: 13 residues within 4Å: Chain 0: L.16, F.19, A.20, H.23, K.27 Chain I: I.34, L.37 Chain T: R.114, Y.115, I.116, L.117, N.118 Chain V: F.80 Ligand excluded by PLIP 3PE.57: 8 residues within 4Å: Chain 7: F.92, M.95, Y.148, I.152 Chain J: W.567, L.574 Chain O: M.37 Ligands: CDL.35 Ligand excluded by PLIP 3PE.62: 15 residues within 4Å: Chain 7: N.4, S.5, S.6, L.9, T.12 Ligands: 3PE.66 Chain b: I.157, K.161 Chain c: H.106, Q.110 Chain e: I.70, L.328, A.330, E.331, E.334 Ligand excluded by PLIP 3PE.65: 17 residues within 4Å: Chain 9: L.12, A.16, E.19, I.20, V.24, S.27, A.28, L.31 Chain H: K.291 Ligands: PC1.14, 3PE.66 Chain c: L.98, L.101, I.102, Y.105, W.108, N.114 Ligand excluded by PLIP 3PE.66: 12 residues within 4Å: Chain 7: L.9 Chain 9: R.15 Ligands: 3PE.62, 3PE.65 Chain b: N.150, L.153, I.154, I.157 Chain c: I.102, Y.105, H.106, N.109 Ligand excluded by PLIP

1 x U10: UBIQUINONE-10(Covalent)

U10.15: 31 residues within 4Å: Chain 4: P.94, H.97, M.190, T.194, F.205 Chain F: W.88, T.91, G.93, A.98, M.101, M.102, A.105, D.112, V.117, F.118, R.119 Chain H: L.21, A.25, T.28, E.31, R.32, L.35, R.41, P.55, D.58, A.59, L.62, E.211, F.231, M.232, R.274 14 PLIP interactions: 7 interactions with chain H, 6 interactions with chain F, 1 interactions with chain 4 Hydrophobic interactions: H:L.21, H:A.25, H:L.35, H:L.62, H:F.231, H:F.231, H:F.231, F:W.88, F:W.88, F:T.91, F:A.105, F:V.117, F:F.118, 4:F.205

3 x C14: TETRADECANE(Non-covalent)

C14.31: 2 residues within 4Å: Chain H: L.314 Chain M: L.51 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: M:L.51, H:L.314 C14.44: 8 residues within 4Å: Chain I: L.37 Chain T: L.76, V.84, I.108, F.111 Chain V: W.89, F.92, Y.93 10 PLIP interactions: 6 interactions with chain T, 3 interactions with chain V, 1 interactions with chain I Hydrophobic interactions: T:L.76, T:V.84, T:I.108, T:F.111, T:F.111, T:F.111, V:W.89, V:F.92, V:Y.93, I:L.37 C14.47: 3 residues within 4Å: Chain Z: P.28, I.29, V.65 3 PLIP interactions: 3 interactions with chain Z Hydrophobic interactions: Z:P.28, Z:I.29, Z:V.65

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

ZMP.45: 20 residues within 4Å: Chain U: H.11, K.12, V.15, A.22, N.25, L.43, R.46, F.47, N.50, R.51, G.58, L.61, L.62, G.65, E.68, L.69, T.72 Chain Y: D.107, S.108, L.109 11 PLIP interactions: 9 interactions with chain U, 2 interactions with chain Y Hydrophobic interactions: U:K.12, U:V.15, U:A.22, U:F.47, U:L.69, U:T.72 Hydrogen bonds: U:R.51, U:G.65, Y:S.108, Y:L.109 Salt bridges: U:K.12 ZMP.68: 14 residues within 4Å: Chain f: R.26, W.36, I.40, C.56, L.60, E.63, F.64, H.67, I.76, L.79, G.83, Y.103, W.104 Chain g: S.108 12 PLIP interactions: 11 interactions with chain f, 1 interactions with chain g Hydrophobic interactions: f:R.26, f:W.36, f:W.36, f:I.40, f:E.63, f:E.63, f:F.64, f:F.64, f:I.76, f:Y.103, f:W.104 Hydrogen bonds: g:S.108

1 x OCT: N-OCTANE(Non-covalent)

OCT.48: 4 residues within 4Å: Chain 0: I.21, F.24 Chain I: F.6 Chain Z: I.29 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain Z, 2 interactions with chain 0 Hydrophobic interactions: I:F.6, Z:I.29, 0:I.21, 0:F.24

4 x D12: DODECANE(Non-covalent)

D12.49: 2 residues within 4Å: Chain 0: L.10, W.11 2 PLIP interactions: 2 interactions with chain 0 Hydrophobic interactions: 0:L.10, 0:W.11 D12.53: 5 residues within 4Å: Chain 2: F.242, S.244, M.313 Ligands: D12.54 Chain b: L.86 1 PLIP interactions: 1 interactions with chain b Hydrophobic interactions: b:L.86 D12.54: 5 residues within 4Å: Chain 2: Y.315, W.319, D.320, T.322 Ligands: D12.53 2 PLIP interactions: 2 interactions with chain 2 Hydrophobic interactions: 2:Y.315, 2:W.319 D12.60: 3 residues within 4Å: Chain 9: T.38 Chain c: M.87, I.94 2 PLIP interactions: 1 interactions with chain c, 1 interactions with chain 9 Hydrophobic interactions: c:I.94, 9:T.38

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

NDP.52: 25 residues within 4Å: Chain 2: G.70, A.71, T.72, G.73, F.74, V.75, R.95, Y.118, L.120, L.139, V.140, G.141, R.142, F.149, V.154, L.177, S.178, W.197, K.201, P.220, A.221, I.223, R.229, R.349 Chain F: K.221 27 PLIP interactions: 26 interactions with chain 2, 1 interactions with chain F Hydrophobic interactions: 2:P.220, 2:I.223 Hydrogen bonds: 2:G.70, 2:T.72, 2:T.72, 2:T.72, 2:G.73, 2:F.74, 2:V.75, 2:R.95, 2:L.139, 2:G.141, 2:R.142, 2:W.197, 2:K.201, 2:I.223, 2:I.223, 2:R.229, 2:R.349 Salt bridges: 2:R.95, 2:R.142, 2:R.142, 2:R.229, 2:R.229, F:K.221 pi-Cation interactions: 2:R.95, 2:R.95

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.55: 20 residues within 4Å: Chain 6: G.102, R.103, G.104, F.108, K.113, N.131, D.133, E.134, G.135, Y.219, I.220, G.222, E.223, E.224, V.257, T.258, N.259, T.262, A.441, L.442 16 PLIP interactions: 16 interactions with chain 6 Hydrophobic interactions: 6:Y.219, 6:Y.219, 6:I.220, 6:A.441, 6:L.442 Hydrogen bonds: 6:R.103, 6:G.104, 6:G.104, 6:F.108, 6:D.133, 6:E.134, 6:G.135, 6:E.224, 6:N.259, 6:T.262 Salt bridges: 6:K.113

1 x WSF: (2R)-3-{[(S)-hydroxy(3-methylbutoxy)phosphoryl]oxy}-2-(octanoyloxy)propyl decanoate(Non-covalent)

WSF.61: 20 residues within 4Å: Chain H: F.87, Y.103, S.104, F.105, F.111, C.114, L.118 Chain M: S.154 Ligands: CDL.63 Chain b: I.35, F.36, C.38, L.39, F.48, Y.52, F.55 Chain c: M.1, I.4, I.5, A.8 16 PLIP interactions: 8 interactions with chain b, 3 interactions with chain H, 5 interactions with chain c Hydrophobic interactions: b:I.35, b:I.35, b:F.36, b:L.39, b:Y.52, b:F.55, b:F.55, H:F.87, H:F.87, H:Y.103, c:I.4, c:I.4, c:I.4, c:I.5, c:A.8 Hydrogen bonds: b:Y.52

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

DGT.67: 20 residues within 4Å: Chain e: P.90, I.91, A.93, G.94, K.95, S.96, V.144, F.147, F.159, Q.160, M.163, R.167, E.188, R.189, D.194, F.197, M.201, R.249, E.254, F.260 13 PLIP interactions: 13 interactions with chain e Hydrophobic interactions: e:I.91 Hydrogen bonds: e:A.93, e:G.94, e:K.95, e:S.96, e:R.167, e:E.254 Salt bridges: e:K.95, e:K.95, e:K.95, e:R.189, e:R.249 pi-Stacking: e:F.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Padavannil, A. et al., Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state. Elife (2023)

Release Date

2023-03-29

Peptides

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: B
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: D
NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A: E
LD31474p: F
NADH dehydrogenase (ubiquinone) 23 kDa subunit: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH-ubiquinone oxidoreductase chain 4: I
NADH-ubiquinone oxidoreductase chain 5: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: M
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: O
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: P
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: Q
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: R
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: S
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: X
Acyl carrier protein, mitochondrial: Yg
NADH dehydrogenase [ubiquinone] 1 subunit C2: Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: 1
NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A: 2
GEO11417p1: 3
Complex I-49kD: 4
NADH dehydrogenase [ubiquinone] flavoprotein 3: 5
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: 6
NADH-ubiquinone oxidoreductase chain 2: 7
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: 8
RH45008p: 9
NADH-ubiquinone oxidoreductase chain 4L: a
NADH-ubiquinone oxidoreductase chain 6: b
NADH-ubiquinone oxidoreductase chain 3: c
NADH dehydrogenase (Ubiquinone) 13 kDa B subunit: d
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AN

B
S6

C
S1

D
S3

E
V2

F
S7

G
S8

H
1

I
4

J
5

K
A8

L
A1

M
AO

N
S5

O
AM

P
BL

Q
B6

R
B4

S
B7

T
B5

U
B9

V
BM

W
B8

X
B3

Y
AC

g
AB

Z
C2

0
B1

1
S4

2
A9

3
B2

4
S2

5
V3

6
V1

7
2

8
A7

9
A3

a
4L

b
6

c
3

d
A5

e
AL

f
A6

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

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

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

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

NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A

LD31474p

NADH dehydrogenase (ubiquinone) 23 kDa subunit

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

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

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

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

NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A

GEO11417p1

Complex I-49kD

NADH dehydrogenase [ubiquinone] flavoprotein 3

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase chain 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

RH45008p

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 3

NADH dehydrogenase (Ubiquinone) 13 kDa B subunit

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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