SMTL ID : 8esw.1

Structure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CDL.1: 19 residues within 4Å: Chain A: L.5, G.6, I.7, R.9, L.10, K.12, L.13, L.30, D.35, Y.56 Chain M: M.1, W.2, F.3, L.6 Chain b: R.6, D.7, V.8, S.9, I.12 16 PLIP interactions: 8 interactions with chain A, 3 interactions with chain b, 5 interactions with chain M Hydrophobic interactions: A:L.5, A:I.7, A:L.10, A:L.13, A:L.30, b:I.12, M:W.2, M:F.3, M:F.3, M:F.3 Hydrogen bonds: A:Y.56, b:S.9, M:W.2 Salt bridges: A:R.9, A:K.12, b:R.6 CDL.8: 17 residues within 4Å: Chain A: L.23, Y.27, L.28, Y.31, N.72 Chain F: G.56, Y.57, S.58, S.71, R.74, D.77, L.78 Chain I: F.26, L.49, I.52, F.56 Ligands: PC1.9 13 PLIP interactions: 4 interactions with chain I, 4 interactions with chain F, 5 interactions with chain A Hydrophobic interactions: I:F.26, I:L.49, I:I.52, I:F.56, F:L.78, A:L.23, A:Y.27, A:Y.27, A:Y.27 Hydrogen bonds: F:Y.57, F:S.58, A:N.72 Salt bridges: F:R.74 CDL.21: 23 residues within 4Å: Chain J: L.337, P.341, S.342, T.344, L.345, W.346, F.348, L.349, P.358, P.359, Y.399, W.429 Chain K: N.88, R.89, M.92, L.93, M.96, S.100, V.123 Chain U: R.52, W.55, K.59, L.62 19 PLIP interactions: 6 interactions with chain U, 9 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: U:L.62, J:T.344, J:L.345, J:L.349, J:P.358, J:P.358, J:P.359, J:W.429, J:W.429, J:W.429, K:V.123 Hydrogen bonds: U:W.55, K:N.88 Salt bridges: U:R.52, U:R.52, U:K.59, U:K.59, K:R.89, K:R.89 CDL.25: 25 residues within 4Å: Chain 8: I.155, L.156, I.159, I.160, I.163, S.281 Chain K: Y.532, F.533, G.534, H.537, L.538, K.541, L.542, Y.545, T.548, L.549 Chain P: W.35, F.100, K.104, N.106, V.108, C.112, F.116 Ligands: 3PE.18, 3PE.29 19 PLIP interactions: 4 interactions with chain 8, 12 interactions with chain K, 3 interactions with chain P Hydrophobic interactions: 8:I.155, 8:I.159, 8:I.160, 8:I.163, K:L.538, K:L.538, K:L.538, K:L.542, K:Y.545, K:Y.545, K:L.549, P:W.35, P:F.116 Hydrogen bonds: K:F.533 Salt bridges: K:H.537, K:H.537, K:K.541, K:K.541, P:K.104 CDL.33: 13 residues within 4Å: Chain K: M.1, N.13 Chain R: Y.70, R.71, L.74, F.95, G.98, K.99, L.101, L.102, T.105, I.107 Ligands: 3PE.32 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain K Hydrophobic interactions: R:I.107 Hydrogen bonds: R:R.71, K:M.1 Salt bridges: R:K.99 CDL.35: 23 residues within 4Å: Chain Q: P.22, W.25, F.26, R.27, V.31, Q.35 Chain R: T.105, A.109, Y.112, Y.113, N.117 Chain U: T.74, V.77, L.78, N.81, P.86, H.106 Chain W: S.91, F.92, A.95, Y.96 Ligands: PC1.14, PC1.31 16 PLIP interactions: 3 interactions with chain W, 5 interactions with chain U, 6 interactions with chain Q, 2 interactions with chain R Hydrophobic interactions: W:A.95, W:Y.96, U:V.77, U:L.78, Q:W.25, Q:F.26, Q:F.26, Q:F.26, R:T.105, R:Y.112 Hydrogen bonds: W:Y.96, U:N.81, U:H.106, Q:Q.35 Salt bridges: U:H.106, Q:R.27 CDL.39: 20 residues within 4Å: Chain 3: I.237, W.238, R.240, Q.241, F.242, R.243, T.322, L.325, K.326, L.329 Chain H: S.23 Chain I: S.73, N.74, Y.75, L.76, Y.79 Ligands: CDL.40 Chain a: L.80, S.81, M.82 17 PLIP interactions: 10 interactions with chain 3, 4 interactions with chain I, 1 interactions with chain H, 2 interactions with chain a Hydrophobic interactions: 3:W.238, 3:Q.241, 3:T.322, 3:L.325, 3:K.326, 3:K.326, 3:L.329, I:Y.79 Salt bridges: 3:R.240, 3:R.243, 3:K.326 Hydrogen bonds: I:S.73, I:Y.75, I:Y.79, H:S.23, a:L.80, a:M.82 CDL.40: 14 residues within 4Å: Chain 3: H.236, W.238, I.333, C.334, P.335, G.336, T.337, I.339 Chain H: F.20, S.23, I.24, K.28 Ligands: PC1.10, CDL.39 9 PLIP interactions: 5 interactions with chain 3, 4 interactions with chain H Hydrophobic interactions: 3:W.238, H:F.20 Hydrogen bonds: 3:G.336, 3:T.337 Salt bridges: 3:H.236, 3:H.236, H:K.28, H:K.28, H:K.28

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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(Covalent)(Non-covalent)

SF4.3: 11 residues within 4Å: Chain C: H.134, P.135, D.137, C.138, C.141, G.144, C.147, L.149, Q.150, R.189, V.242 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:H.134, C:H.134, C:C.138, C:C.141, C:C.147 SF4.4: 13 residues within 4Å: Chain C: C.190, I.191, H.192, C.193, T.194, R.195, C.196, I.220, C.240, P.241, V.242, A.244, L.245 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.190, C:C.193, C:C.196, C:C.240 SF4.7: 12 residues within 4Å: Chain 5: R.143, H.228 Chain F: A.95, C.96, C.97, G.132, T.133, G.159, S.160, C.161, C.191, P.192 6 PLIP interactions: 6 interactions with chain F, Metal complexes: F:C.96, F:C.97, F:C.161, F:C.191, F:C.191, F:C.191 SF4.11: 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 SF4.12: 13 residues within 4Å: Chain G: C.118, I.119, A.120, C.121, K.122, C.124, I.135, Y.150, A.166, 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 SF4.42: 11 residues within 4Å: Chain 7: I.220, P.238, C.394, Q.396, C.397, C.400, T.438, I.439, C.440, L.442, G.443 5 PLIP interactions: 5 interactions with chain 7, Metal complexes: 7:C.394, 7:C.397, 7:C.397, 7:C.400, 7:C.440

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

FES.5: 7 residues within 4Å: Chain C: R.72, F.73, C.74, Y.75, C.85, 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.6: 9 residues within 4Å: Chain 7: P.137 Chain E: C.128, T.130, P.132, C.133, C.169, L.170, G.171, C.173 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.128, E:C.133, E:C.169, E:C.173

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

PC1.9: 12 residues within 4Å: Chain A: Y.31, R.32, D.34, M.73, Y.75 Chain F: Y.57, L.78, W.81 Chain I: K.46, V.47, G.48 Ligands: CDL.8 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain I, 1 interactions with chain F Hydrogen bonds: A:Y.31, I:G.48 Salt bridges: A:D.34, F:K.84 PC1.10: 16 residues within 4Å: Chain 3: D.100, P.335 Chain F: L.75, L.78, L.79, T.214, L.215, W.218, K.221 Chain H: L.25, K.27, K.28 Chain I: A.59, I.60, F.63 Ligands: CDL.40 14 PLIP interactions: 7 interactions with chain F, 2 interactions with chain H, 4 interactions with chain I, 1 interactions with chain 3 Hydrophobic interactions: F:L.75, F:L.78, F:L.79, F:L.79, F:L.215, F:W.218, H:L.25, H:L.25, I:A.59, I:I.60, I:I.60, I:F.63 Salt bridges: F:K.221, 3:D.100 PC1.13: 28 residues within 4Å: Chain 5: R.271, Q.275 Chain G: T.65, M.66, F.68, L.71, L.72, F.75 Chain I: P.187, L.190, V.191, V.193, S.194, V.269, W.272, L.277, F.280, K.284, Y.287, L.288, C.292, F.293, F.296 Chain N: I.40, Y.43 Chain d: D.22, G.25, L.29 15 PLIP interactions: 7 interactions with chain I, 3 interactions with chain d, 1 interactions with chain N, 3 interactions with chain G, 1 interactions with chain 5 Hydrophobic interactions: I:V.191, I:V.193, I:V.269, I:W.272, I:W.272, I:F.280, d:D.22, d:L.29, N:I.40, G:L.71, G:L.72, G:F.75 Hydrogen bonds: I:S.194, d:D.22, 5:R.271 PC1.14: 18 residues within 4Å: Chain J: L.63, W.67, P.431, L.434, L.435, L.437, K.438 Chain K: W.39, E.40, L.41 Chain R: G.125 Chain W: C.86, S.91, W.94, A.95, R.103 Ligands: PC1.31, CDL.35 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain W Hydrophobic interactions: J:L.63, J:W.67, J:W.67, J:P.431, J:L.434, J:L.435, J:L.437, W:W.94 Salt bridges: J:K.438 PC1.15: 17 residues within 4Å: Chain 0: I.40, W.44, K.48, V.50, F.51 Chain 1: W.11, L.14 Chain 8: F.329 Chain J: L.9, I.12, P.13, F.16, I.17, L.91, I.95 Ligands: 3PE.17 Chain f: Y.382 15 PLIP interactions: 2 interactions with chain 1, 2 interactions with chain f, 1 interactions with chain 8, 7 interactions with chain J, 3 interactions with chain 0 Hydrophobic interactions: 1:W.11, 1:L.14, 8:F.329, J:L.9, J:I.12, J:P.13, J:F.16, J:I.17, J:L.91, J:I.95, 0:I.40, 0:I.40, 0:V.50 Hydrogen bonds: f:Y.382, f:Y.382 PC1.27: 10 residues within 4Å: Chain 8: F.273 Chain P: Y.27, A.31, A.120, K.124, E.133, F.134, F.135 Ligands: 3PE.26, 3PE.29 12 PLIP interactions: 11 interactions with chain P, 1 interactions with chain 8 Hydrophobic interactions: P:Y.27, P:A.31, P:A.120, P:K.124, P:F.134, P:F.134, 8:F.273 Hydrogen bonds: P:F.134, P:F.135 Salt bridges: P:K.124, P:K.124, P:E.133 PC1.30: 17 residues within 4Å: Chain 8: S.195, L.198, F.202, F.339 Chain O: T.4, P.5, F.6 Chain P: Y.143, G.144, G.145, I.148, N.151, W.153 Chain U: Y.162, R.163, P.164 Ligands: PC1.45 7 PLIP interactions: 1 interactions with chain O, 4 interactions with chain 8, 2 interactions with chain P pi-Cation interactions: O:F.6 Hydrophobic interactions: 8:F.202, 8:F.202, 8:F.339, 8:F.339 Hydrogen bonds: P:G.145, P:N.151 PC1.31: 18 residues within 4Å: Chain J: P.358, L.363, I.436 Chain K: W.39, L.41, M.51, I.111, L.115 Chain R: Y.113, R.123, G.125, G.126, W.127 Chain W: A.95, Y.96 Ligands: PC1.14, 3PE.32, CDL.35 8 PLIP interactions: 4 interactions with chain K, 2 interactions with chain R, 2 interactions with chain J Hydrophobic interactions: K:L.41, K:M.51, K:I.111, K:L.115, R:W.127, J:L.363, J:I.436 Salt bridges: R:R.123 PC1.34: 9 residues within 4Å: Chain J: L.199, V.248, I.252 Chain S: V.77, I.80, A.81, W.85, K.88 Ligands: 3PE.16 6 PLIP interactions: 3 interactions with chain J, 3 interactions with chain S Hydrophobic interactions: J:L.199, J:V.248, J:I.252, S:V.77, S:I.80, S:A.81 PC1.37: 20 residues within 4Å: Chain 0: S.20, L.22, S.23, W.26, N.27, D.72, R.75 Chain 8: L.331, F.332, S.335 Chain J: L.2, L.9, Y.50, F.51, L.98, L.99, L.102, F.115 Chain L: W.173, E.175 15 PLIP interactions: 3 interactions with chain 8, 6 interactions with chain J, 3 interactions with chain L, 3 interactions with chain 0 Hydrophobic interactions: 8:L.331, 8:F.332, 8:F.332, J:L.2, J:L.9, J:L.98, J:L.99, J:L.102, J:F.115, L:W.173, 0:L.22 Hydrogen bonds: L:E.175, L:E.175, 0:S.20 Salt bridges: 0:D.72 PC1.44: 17 residues within 4Å: Chain 8: N.270, Y.272, F.273, T.276 Chain J: L.149, I.156, Y.160, Y.180, L.182, L.183, C.186 Chain P: I.123, W.132, E.133, F.134, P.136 Ligands: 3PE.28 13 PLIP interactions: 7 interactions with chain J, 3 interactions with chain P, 3 interactions with chain 8 Hydrophobic interactions: J:L.149, J:I.156, J:Y.160, J:Y.160, J:L.182, J:L.182, J:L.183, P:I.123, P:W.132, P:F.134, 8:Y.272, 8:Y.272, 8:T.276 PC1.45: 17 residues within 4Å: Chain 0: C.31, G.35, F.60, G.64, F.71, K.74, Y.78 Chain 8: I.322, F.326, L.333, L.336, F.337, Y.338, F.339 Chain P: N.151, W.153 Ligands: PC1.30 9 PLIP interactions: 7 interactions with chain 8, 2 interactions with chain 0 Hydrophobic interactions: 8:I.322, 8:L.333, 8:L.336, 8:F.337, 8:F.337, 8:Y.338, 8:F.339, 0:F.71, 0:F.71 PC1.46: 20 residues within 4Å: Chain H: M.1, S.3, I.4, A.8 Chain I: F.84, F.87, L.88, F.91, Y.103, S.104, F.105, F.111, C.114, L.118 Chain N: S.154 Chain a: I.35, L.39, F.48, Y.52, F.55 16 PLIP interactions: 8 interactions with chain I, 6 interactions with chain a, 2 interactions with chain H Hydrophobic interactions: I:F.84, I:F.87, I:L.88, I:F.91, I:F.111, I:F.111, I:L.118, a:I.35, a:L.39, a:Y.52, a:F.55, a:F.55, H:I.4, H:A.8 pi-Cation interactions: I:F.105 Hydrogen bonds: a:Y.52 PC1.47: 15 residues within 4Å: Chain 3: R.309, Y.389 Chain a: N.19, M.20, I.21, H.22, A.25, L.28, I.32, F.78, N.79, L.80, S.81, L.84, T.85 8 PLIP interactions: 8 interactions with chain a Hydrophobic interactions: a:A.25, a:L.28, a:L.28, a:I.32, a:L.80 Hydrogen bonds: a:I.21, a:H.22, a:N.79

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

3PE.16: 9 residues within 4Å: Chain J: Y.245, F.247, V.248, W.249 Chain P: L.90, F.94 Chain S: K.88 Ligands: 3PE.28, PC1.34 6 PLIP interactions: 2 interactions with chain J, 2 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: J:W.249, J:W.249, P:L.90, P:F.94 Salt bridges: S:K.88, S:K.88 3PE.17: 18 residues within 4Å: Chain 0: V.33, G.37, I.40, W.44, V.50 Chain 8: S.233, I.235, T.239, M.242, F.325, F.329, F.332 Chain J: F.16, N.87, L.88, L.91 Ligands: PC1.15 Chain f: F.375 12 PLIP interactions: 4 interactions with chain 0, 2 interactions with chain J, 6 interactions with chain 8 Hydrophobic interactions: 0:V.33, 0:I.40, 0:W.44, 0:V.50, J:L.88, J:L.91, 8:I.235, 8:F.325, 8:F.325, 8:F.329, 8:F.332 Hydrogen bonds: 8:S.233 3PE.18: 16 residues within 4Å: Chain 8: M.280, L.283, I.284, F.287 Chain J: Q.138, Y.142, F.145, Y.146, L.149 Chain K: F.533, G.535, Q.536, L.538, Y.539, L.542 Ligands: CDL.25 9 PLIP interactions: 3 interactions with chain 8, 1 interactions with chain K, 5 interactions with chain J Hydrophobic interactions: 8:L.283, 8:I.284, 8:F.287, J:F.145, J:F.145, J:Y.146, J:Y.146, J:L.149 Hydrogen bonds: K:Q.536 3PE.19: 14 residues within 4Å: Chain K: S.20, L.23, L.24, Y.27, F.28, Y.35, F.55, M.63 Chain Q: F.11, A.12, V.15, L.16 Chain R: K.134 Ligands: 3PE.32 6 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain K, 1 interactions with chain R Hydrophobic interactions: Q:F.11, Q:A.12, Q:L.16, K:L.24, K:F.55 Salt bridges: R:K.134 3PE.20: 19 residues within 4Å: Chain K: F.258, N.265, F.266, F.379, F.386, G.389, L.390, V.464, F.471, I.475, F.482, N.484, K.485, S.486, M.489, L.492, F.495, L.496 Chain X: C.142 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:F.258, K:F.258, K:F.379, K:F.386, K:L.390, K:V.464, K:V.464, K:F.471, K:F.471, K:L.492, K:F.495, K:L.496 Hydrogen bonds: K:K.485, K:S.486, K:S.486 Salt bridges: K:K.485 3PE.22: 11 residues within 4Å: Chain 4: W.58, H.62 Chain K: I.435, S.438, M.439, W.442, L.443 Chain Q: P.7, F.11 Chain T: P.73, Y.76 9 PLIP interactions: 2 interactions with chain Q, 4 interactions with chain K, 1 interactions with chain 4, 2 interactions with chain T Hydrophobic interactions: Q:P.7, Q:F.11, K:I.435, K:L.443, T:P.73, T:Y.76 Hydrogen bonds: K:S.438, K:S.438 Salt bridges: 4:H.62 3PE.23: 22 residues within 4Å: Chain J: S.385, F.386, F.389, F.390 Chain K: N.138, M.141, L.142, L.145, F.202, I.505, S.506, T.507, M.510, I.511, P.514 Chain X: E.85, E.115, D.116, R.117, W.118, S.119, F.135 12 PLIP interactions: 5 interactions with chain X, 4 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: X:R.117, X:F.135, K:L.142, K:F.202, K:I.505, K:P.514, J:F.386, J:F.389, J:F.390 Hydrogen bonds: X:W.118, X:S.119, X:S.119 3PE.24: 11 residues within 4Å: Chain J: W.378, M.381, S.385 Chain K: L.156, F.180, M.184, S.187, M.190, L.191, M.194, W.244 7 PLIP interactions: 4 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:L.156, K:F.180, K:L.191, K:W.244, J:W.378, J:W.378, J:W.378 3PE.26: 13 residues within 4Å: Chain P: Y.8, Y.9, T.24, Y.27, A.67, F.70, Y.89, A.96, L.117, A.120, K.124 Ligands: PC1.27, 3PE.29 11 PLIP interactions: 11 interactions with chain P Hydrophobic interactions: P:T.24, P:Y.27, P:A.67, P:F.70, P:Y.89, P:A.96, P:L.117, P:A.120, P:K.124 Hydrogen bonds: P:Y.27 Salt bridges: P:K.124 3PE.28: 12 residues within 4Å: Chain J: F.185, Y.245 Chain P: D.85, K.86, I.87, L.90, L.115, I.119, V.122, M.126 Ligands: 3PE.16, PC1.44 9 PLIP interactions: 5 interactions with chain P, 4 interactions with chain J Hydrophobic interactions: P:L.90, P:L.115, P:I.119, P:V.122, J:F.185, J:Y.245 Salt bridges: P:K.86, J:K.244 Hydrogen bonds: J:Y.245 3PE.29: 12 residues within 4Å: Chain 8: I.152 Chain P: R.5, K.7, K.26, Y.27, V.29, S.30, A.34 Ligands: CDL.25, 3PE.26, PC1.27, 3PE.43 8 PLIP interactions: 7 interactions with chain P, 1 interactions with chain 8 Hydrophobic interactions: P:Y.27, P:V.29, 8:I.152 Hydrogen bonds: P:R.5, P:Y.27, P:Y.27 Salt bridges: P:K.7, P:K.26 3PE.32: 16 residues within 4Å: Chain K: Y.35, I.37, F.53, F.55 Chain Q: L.16, I.19 Chain R: G.110, A.111, Y.113, F.114, K.115, V.129, H.131 Ligands: 3PE.19, PC1.31, CDL.33 11 PLIP interactions: 1 interactions with chain Q, 5 interactions with chain R, 5 interactions with chain K Hydrophobic interactions: Q:I.19, R:A.111, R:Y.113, R:F.114, R:F.114, R:V.129, K:Y.35, K:I.37, K:F.53, K:F.55, K:F.55 3PE.43: 14 residues within 4Å: Chain 8: M.95, Y.148, L.149, I.152 Chain K: L.563, F.566, W.567, I.570, L.574 Chain P: S.30, A.34, M.37, F.38 Ligands: 3PE.29 8 PLIP interactions: 2 interactions with chain 8, 4 interactions with chain K, 2 interactions with chain P Hydrophobic interactions: 8:Y.148, 8:I.152, K:F.566, K:W.567, K:I.570, K:L.574, P:M.37, P:F.38

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

ZMP.36: 19 residues within 4Å: Chain V: H.11, V.15, L.18, A.22, R.46, F.47, N.50, R.51, K.53, D.54, G.58, L.61, L.62, G.65, E.68, L.69, T.72 Chain Z: D.107, S.108 13 PLIP interactions: 12 interactions with chain V, 1 interactions with chain Z Hydrophobic interactions: V:V.15, V:L.18, V:A.22, V:F.47, V:F.47, V:R.51, V:K.53, V:E.68, V:L.69, V:T.72 Hydrogen bonds: V:H.11, V:H.11, Z:S.108 ZMP.49: 21 residues within 4Å: Chain e: R.26, A.29, L.30, L.32, W.36, I.40, K.59, L.60, E.63, F.64, H.67, R.68, I.76, L.79, G.83, I.100, Y.103, W.104 Chain g: D.107, S.108, L.109 13 PLIP interactions: 11 interactions with chain e, 2 interactions with chain g Hydrophobic interactions: e:W.36, e:W.36, e:I.40, e:K.59, e:L.60, e:F.64, e:I.76, e:I.100, e:Y.103, e:W.104, g:L.109 Salt bridges: e:R.26 Hydrogen bonds: g:S.108

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

NDP.38: 23 residues within 4Å: Chain 3: G.70, 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, D.222, I.223, R.229 Chain F: K.221 21 PLIP interactions: 20 interactions with chain 3, 1 interactions with chain F Hydrophobic interactions: 3:W.197, 3:P.220 Hydrogen bonds: 3:G.70, 3:T.72, 3:F.74, 3:V.75, 3:L.139, 3:G.141, 3:K.201, 3:D.222, 3:D.222, 3:I.223, 3:R.229 Salt bridges: 3:R.95, 3:R.142, 3:R.142, 3:R.229, 3:R.229, F:K.221 pi-Cation interactions: 3:R.95, 3:R.95

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.41: 17 residues within 4Å: Chain 7: G.102, R.103, G.104, F.108, K.113, N.131, D.133, E.134, G.135, G.222, E.223, E.224, V.257, T.258, N.259, A.441, L.442 14 PLIP interactions: 14 interactions with chain 7 Hydrophobic interactions: 7:E.223, 7:A.441, 7:L.442 Hydrogen bonds: 7:R.103, 7:G.104, 7:F.108, 7:N.131, 7:D.133, 7:E.134, 7:G.135, 7:G.222, 7:E.224, 7:N.259 Salt bridges: 7:K.113

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

DGT.48: 18 residues within 4Å: Chain f: I.91, A.93, G.94, K.95, S.96, V.144, F.147, F.159, Q.160, R.167, E.188, R.189, D.194, F.197, M.201, R.249, E.254, F.260 14 PLIP interactions: 14 interactions with chain f Hydrogen bonds: f:K.95, f:S.96, f:Q.160, f:Q.160, f:R.167, f:E.188, f:E.188, f:E.254 Salt bridges: f:K.95, f:K.95, f:K.95, f:R.189, f:R.249 pi-Stacking: f: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 3: H
NADH-ubiquinone oxidoreductase chain 1: I
NADH-ubiquinone oxidoreductase chain 4: J
NADH-ubiquinone oxidoreductase chain 5: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: P
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: Q
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: R
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: S
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: Y
Acyl carrier protein, mitochondrial: Zg
NADH dehydrogenase [ubiquinone] 1 subunit C2: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 1
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: 2
NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A: 3
GEO11417p1: 4
Complex I-49kD: 5
NADH dehydrogenase [ubiquinone] flavoprotein 3: 6
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: 7
NADH-ubiquinone oxidoreductase chain 2: 8
NADH-ubiquinone oxidoreductase chain 4L: 9
NADH-ubiquinone oxidoreductase chain 6: a
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: b
NADH dehydrogenase (Ubiquinone) 13 kDa B subunit: c
RH45008p: d
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AN

B
S6

C
S1

D
S3

E
V2

F
S7

G
S8

H
3

I
1

J
4

K
5

L
A8

M
A1

N
AO

O
S5

P
AM

Q
BL

R
B6

S
B4

T
B7

U
B5

V
B9

W
BM

X
B8

Y
B3

Z
AC

g
AB

0
C2

1
B1

2
S4

3
A9

4
B2

5
S2

6
V3

7
V1

8
2

9
4L

a
6

b
A7

c
A5

d
A3

e
A6

f
AL

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 3

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-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase (Ubiquinone) 13 kDa B subunit

RH45008p

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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

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