SMTL ID : 8rgp.1

Closed Complex I from murine brain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: A.98, C.99, C.100, G.135, T.136, G.162, S.163, C.164, G.193, C.194, P.195 Chain C: R.138, H.223 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.99, A:C.100, A:C.164, A:C.194 SF4.8: 13 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.379, E:C.382, E:C.385, E:C.425 SF4.9: 11 residues within 4Å: Chain F: H.124, P.125, D.127, C.128, C.131, Q.133, C.137, L.139, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.124, F:C.128, F:C.131, F:C.137 SF4.10: 13 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.176, F:C.179, F:C.182, F:C.226 SF4.13: 12 residues within 4Å: Chain G: H.101, C.123, P.124, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:E.169 Metal complexes: G:C.123, G:C.152, G:C.155, G:C.158 SF4.14: 13 residues within 4Å: Chain G: C.113, I.114, A.115, C.116, K.117, C.119, I.130, Y.145, C.162, P.163, V.164, A.166, I.167 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.113, G:C.116, G:C.119, G:C.162

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

3PE.2: 10 residues within 4Å: Chain A: K.77, D.80, L.81, W.84, R.87, K.213 Chain O: R.29, N.31, W.75 Chain S: L.46 10 PLIP interactions: 1 interactions with chain S, 8 interactions with chain A, 1 interactions with chain O Hydrophobic interactions: S:L.46, A:D.80, A:L.81, A:W.84, A:W.84 Salt bridges: A:R.87, A:R.87, A:K.213, A:K.213 Hydrogen bonds: O:R.29 3PE.5: 22 residues within 4Å: Chain 1: Y.117 Chain C: W.43, Q.46, Y.53 Chain V: I.562, P.563, S.567, H.570 Chain W: N.144, I.147, Y.148, F.151, Y.152, I.155, I.205, G.211, V.212 Chain X: F.163, M.284, L.288, F.291 Ligands: PC1.27 17 PLIP interactions: 6 interactions with chain X, 7 interactions with chain W, 1 interactions with chain 1, 2 interactions with chain V, 1 interactions with chain C Hydrophobic interactions: X:F.163, X:M.284, X:L.288, X:F.291, X:F.291, X:F.291, W:F.151, W:Y.152, W:Y.152, W:Y.152, W:I.155, W:I.205, 1:Y.117, V:I.562, V:P.563 Hydrogen bonds: W:N.144, C:Q.46 3PE.20: 18 residues within 4Å: Chain 4: F.8, L.9, A.12, E.16, L.19, V.20, F.23, S.24, W.26 Chain R: T.96, S.99, L.100, A.103, W.106, T.107 Chain S: K.291, P.295 Ligands: PC1.15 14 PLIP interactions: 4 interactions with chain R, 8 interactions with chain 4, 2 interactions with chain S Hydrophobic interactions: R:T.96, R:L.100, R:A.103, 4:F.8, 4:L.9, 4:A.12, 4:L.19, 4:F.23, 4:F.23, 4:W.26, 4:W.26, S:P.295 Hydrogen bonds: R:T.107 Salt bridges: S:K.291 3PE.22: 10 residues within 4Å: Chain T: L.17, A.20, F.91, L.94 Chain U: L.14, L.17, M.21, F.22, R.23 Chain V: K.585 10 PLIP interactions: 4 interactions with chain T, 5 interactions with chain U, 1 interactions with chain V Hydrophobic interactions: T:L.17, T:A.20, T:F.91, T:L.94, U:L.14, U:L.17, U:L.17, U:M.21 Salt bridges: U:R.23, V:K.585 3PE.23: 16 residues within 4Å: Chain V: Q.170, L.173, Y.174, I.177, G.228, L.229, L.283, I.533, H.534, T.537, P.538, S.541, L.542 Chain W: L.277 Chain e: N.115, R.116 13 PLIP interactions: 11 interactions with chain V, 1 interactions with chain e, 1 interactions with chain W Hydrophobic interactions: V:L.173, V:Y.174, V:I.177, V:L.229, V:L.283, V:I.533, V:T.537, V:P.538, V:L.542, e:R.116, W:L.277 Salt bridges: V:H.534, V:H.534 3PE.26: 16 residues within 4Å: Chain 1: L.101, G.109, T.110, M.113, G.114, V.116, Y.117, A.121 Chain V: K.560, T.561, S.565, T.568, L.569, N.572 Ligands: CDL.33, CDL.43 12 PLIP interactions: 3 interactions with chain V, 9 interactions with chain 1 Hydrophobic interactions: V:T.561, V:L.569, 1:L.101, 1:V.116, 1:V.116, 1:Y.117, 1:Y.117, 1:A.121 Salt bridges: V:K.560 Hydrogen bonds: 1:T.110, 1:T.110, 1:T.110 3PE.28: 24 residues within 4Å: Chain 9: V.96, T.101, V.104, A.105 Chain V: W.66, H.67, W.68 Chain W: L.39, L.42, P.64, I.67, W.71, P.371, P.443, I.445, L.446, L.447, T.449, S.450, K.452, L.453, I.454 Ligands: CDL.24, CDL.40 19 PLIP interactions: 15 interactions with chain W, 2 interactions with chain V, 2 interactions with chain 9 Hydrophobic interactions: W:L.39, W:L.42, W:P.64, W:I.67, W:W.71, W:W.71, W:P.443, W:I.445, W:I.445, W:L.446, W:T.449, W:L.453, W:L.453, W:I.454, 9:T.101, 9:V.104 Salt bridges: W:K.452 Hydrogen bonds: V:H.67, V:W.68 3PE.29: 7 residues within 4Å: Chain W: W.190, N.193, L.197, Y.256, M.257, P.260 Chain f: Y.102 5 PLIP interactions: 3 interactions with chain W, 2 interactions with chain f Hydrophobic interactions: W:L.197, W:P.260, f:Y.102, f:Y.102 Hydrogen bonds: W:N.193 3PE.34: 9 residues within 4Å: Chain 1: L.99, G.102, A.103, H.106, S.107, Y.108, A.111 Ligands: CDL.35, CDL.43 3 PLIP interactions: 3 interactions with chain 1 Hydrophobic interactions: 1:L.99, 1:L.99, 1:A.103 3PE.36: 25 residues within 4Å: Chain 2: F.140, T.141, Y.143, T.144 Chain 3: A.39 Chain R: M.1, L.3, Y.4, I.7, F.8, I.11 Chain S: T.76, L.77, L.81, S.84, L.98, N.99, F.104, T.108 Chain T: F.37, L.41, L.44, S.49, F.56 Ligands: PC1.21 16 PLIP interactions: 6 interactions with chain R, 5 interactions with chain T, 3 interactions with chain S, 2 interactions with chain 2 Hydrophobic interactions: R:Y.4, R:I.7, R:I.7, R:F.8, R:I.11, R:I.11, T:F.37, T:F.37, T:L.44, T:F.56, S:L.77, S:L.81 Hydrogen bonds: T:S.49, S:N.99, 2:Y.143, 2:T.144 3PE.39: 4 residues within 4Å: Chain 6: H.8, L.11, Y.75, R.78 5 PLIP interactions: 5 interactions with chain 6 Hydrophobic interactions: 6:Y.75 Hydrogen bonds: 6:L.11 Salt bridges: 6:H.8, 6:R.78, 6:R.78 3PE.41: 10 residues within 4Å: Chain 8: P.17, F.20 Chain 9: F.91, I.95, F.103 Chain W: K.3, L.33, L.36, T.40 Chain a: F.125 7 PLIP interactions: 3 interactions with chain 9, 2 interactions with chain 8, 2 interactions with chain W Hydrophobic interactions: 9:F.91, 9:I.95, 9:F.103, 8:P.17, 8:F.20, W:L.33, W:L.36 3PE.42: 14 residues within 4Å: Chain V: L.9, F.12, T.65, W.66, M.78 Ligands: CDL.24, CDL.40 Chain a: E.95, K.114 Chain b: F.81, V.82, Y.85, H.89, K.93 12 PLIP interactions: 7 interactions with chain b, 4 interactions with chain V, 1 interactions with chain a Hydrophobic interactions: b:F.81, b:V.82, b:Y.85, b:Y.85, b:Y.85, V:L.9, V:F.12, V:F.12, V:W.66 Salt bridges: b:H.89, b:K.93 Hydrogen bonds: a:E.95 3PE.44: 5 residues within 4Å: Ligands: CDL.43 Chain f: P.84, K.85, L.88, A.91 2 PLIP interactions: 2 interactions with chain f Hydrophobic interactions: f:P.84, f:A.91

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

PC1.3: 13 residues within 4Å: Chain A: I.82, R.86, L.218, W.221, R.224 Chain H: D.90, F.310, E.311 Chain R: V.20, L.24, Q.26 Chain S: F.56 Ligands: UQ.4 9 PLIP interactions: 2 interactions with chain A, 3 interactions with chain H, 1 interactions with chain S, 3 interactions with chain R Hydrophobic interactions: A:I.82, S:F.56, R:V.20, R:L.24, R:L.24 Salt bridges: A:R.224, H:D.90, H:E.311 Hydrogen bonds: H:E.311 PC1.15: 25 residues within 4Å: Chain 2: I.40 Chain 4: E.16, V.21 Chain C: R.266 Chain G: I.60, L.61, W.63, L.66, I.67 Chain S: W.179, P.180, A.182, F.186, I.187, P.197, T.238, I.273, Y.277, F.280, L.288, N.292, F.293, L.296 Ligands: 3PE.20, PC1.37 20 PLIP interactions: 2 interactions with chain 4, 13 interactions with chain S, 2 interactions with chain G, 1 interactions with chain 2, 2 interactions with chain C Hydrophobic interactions: 4:V.21, S:W.179, S:P.180, S:F.186, S:F.186, S:F.186, S:P.197, S:T.238, S:I.273, S:I.273, S:F.280, S:F.280, S:F.293, S:L.296, G:W.63, G:L.66, 2:I.40 Salt bridges: 4:E.16, C:R.266, C:R.266 PC1.21: 9 residues within 4Å: Chain H: R.286 Chain S: S.67, M.68, S.69, I.73 Chain T: L.30, T.81, W.82 Ligands: 3PE.36 5 PLIP interactions: 3 interactions with chain S, 2 interactions with chain T Hydrogen bonds: S:M.68, S:S.69, S:S.69 Hydrophobic interactions: T:L.30, T:W.82 PC1.27: 22 residues within 4Å: Chain 1: L.124, E.131, W.133 Chain V: T.566 Chain W: I.155, G.156, P.159, I.162, L.166, S.191, L.194, L.195, L.197, A.198, M.201, I.205 Chain X: L.276, I.277, T.280, L.281, M.284 Ligands: 3PE.5 13 PLIP interactions: 7 interactions with chain W, 3 interactions with chain 1, 3 interactions with chain X Hydrophobic interactions: W:P.159, W:I.162, W:L.194, W:L.197, W:A.198, W:I.205, 1:L.124, 1:W.133, 1:W.133, X:I.277, X:T.280, X:L.281 Hydrogen bonds: W:S.191 PC1.37: 21 residues within 4Å: Chain 2: R.28, G.29, L.30, G.32, M.35 Chain G: D.55, R.59, M.62, T.64, E.65, I.67, R.68, G.71, L.74 Chain P: W.14 Chain S: L.175, M.183, L.243, L.266, W.272 Ligands: PC1.15 14 PLIP interactions: 3 interactions with chain 2, 6 interactions with chain G, 4 interactions with chain S, 1 interactions with chain P Hydrogen bonds: 2:R.28, 2:L.30, G:T.64 Salt bridges: 2:R.28, G:D.55, G:R.68 Hydrophobic interactions: G:M.62, G:I.67, G:L.74, S:L.175, S:L.243, S:L.266, S:W.272, P:W.14

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

UQ.4: 34 residues within 4Å: Chain A: W.91, T.94, F.95, G.96, L.97, A.98, A.101, M.104, M.105, A.108, V.120, F.121, R.122 Chain C: H.92, G.93, Y.141, M.185, T.189, F.200, I.456, V.457 Chain S: L.14, R.25, L.28, Q.32, R.34, F.49, D.51, A.52, L.55, F.224, M.225, R.274 Ligands: PC1.3 20 PLIP interactions: 7 interactions with chain A, 9 interactions with chain S, 4 interactions with chain C Hydrophobic interactions: A:W.91, A:W.91, A:T.94, A:A.101, A:A.108, A:V.120, A:F.121, S:L.14, S:R.25, S:L.28, S:F.49, S:F.49, S:D.51, S:A.52, S:L.55, S:F.224, C:F.200, C:F.200 Hydrogen bonds: C:H.92, C:Y.141

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

FES.6: 9 residues within 4Å: Chain D: C.134, T.136, P.138, C.139, C.175, L.176, G.177, A.178, C.179 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.134, D:C.139, D:C.175, D:C.179 FES.11: 9 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.64, F:C.75, F:C.78, F:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.7: 19 residues within 4Å: Chain E: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, Y.204, I.205, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Y.204, E:Y.204, E:I.205, E:E.208, E:A.426, E:L.427 Hydrogen bonds: E:R.88, E:G.89, E:K.98, E:N.116, E:D.118, E:E.119, E:G.120, E:E.209, E:E.209, E:N.244, E:N.244, E:T.247 Salt bridges: E:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.12: 5 residues within 4Å: Chain F: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:I.223, F:C.226, F:V.228, F:L.231

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

NDP.16: 25 residues within 4Å: Chain A: R.224 Chain H: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, A.110, L.129, I.130, G.131, R.132, E.133, F.139, F.145, V.167, S.168, H.169, K.184, P.203, S.204, I.206, R.212 23 PLIP interactions: 22 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:P.203, H:I.206, H:I.206 Hydrogen bonds: H:G.60, H:T.62, H:T.62, H:T.62, H:F.64, H:L.65, H:R.85, H:C.86, H:L.129, H:G.131, H:K.184, H:I.206, H:R.212 Salt bridges: H:R.85, H:R.132, H:R.132, H:R.212, A:R.224 pi-Cation interactions: H:R.85, H:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 5 residues within 4Å: Chain J: C.79, D.80, H.88, C.104, C.107 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.79, J:H.88, J:C.104, J:C.107

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

ZMP.18: 16 residues within 4Å: Chain L: S.112 Chain N: K.32, V.35, L.38, W.42, V.66, M.69, F.70, M.71, N.73, A.74, H.75, V.76, V.82, L.85, F.109 13 PLIP interactions: 11 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: N:L.38, N:W.42, N:W.42, N:W.42, N:V.66, N:F.70, N:V.82, N:F.109 Hydrogen bonds: N:N.73, N:V.76, L:S.112, L:S.112 Salt bridges: N:K.32 ZMP.45: 17 residues within 4Å: Chain Z: D.111, S.112, L.113 Chain g: H.12, Q.13, V.16, H.26, M.44, R.47, F.48, H.51, K.52, L.63, A.67, E.70, F.71, N.74 13 PLIP interactions: 10 interactions with chain g, 3 interactions with chain Z Hydrophobic interactions: g:V.16, g:V.16, g:H.26, g:F.48, g:F.71 Hydrogen bonds: g:H.12, g:Q.13, g:K.52, g:K.52, Z:S.112, Z:S.112, Z:L.113 Salt bridges: g:K.52

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 15 residues within 4Å: Chain 3: W.2, F.3, L.6, A.10 Chain O: L.3, V.6, L.7, R.9, G.10, Q.13 Chain P: S.3, A.4, T.5, I.8 Chain S: Y.43 11 PLIP interactions: 3 interactions with chain O, 5 interactions with chain 3, 1 interactions with chain S, 2 interactions with chain P Hydrophobic interactions: O:V.6, O:L.7, 3:W.2, 3:W.2, 3:F.3, 3:F.3, 3:A.10, S:Y.43 Salt bridges: O:R.9 Hydrogen bonds: P:S.3, P:T.5 CDL.24: 27 residues within 4Å: Chain 9: L.97 Chain V: L.16, I.19, M.23, M.78, R.116, K.119, Y.120, L.123, I.130, I.142, M.150, L.153 Chain W: P.353, L.354, T.357, M.361, P.371, I.442, L.446 Ligands: 3PE.28, CDL.40, 3PE.42 Chain a: L.68, M.71, K.72, G.79 17 PLIP interactions: 6 interactions with chain W, 9 interactions with chain V, 2 interactions with chain a Hydrophobic interactions: W:L.354, W:P.371, W:I.442, W:L.446, V:L.16, V:I.19, V:M.23, V:I.130, V:I.142, a:K.72 Hydrogen bonds: W:P.353, W:T.357, V:Y.120 Salt bridges: V:R.116, V:K.119, V:K.119, a:K.72 CDL.25: 12 residues within 4Å: Chain V: I.290, L.293, T.294, M.421, R.425, L.504, T.508, N.514, K.515, N.517, Y.519, S.520 6 PLIP interactions: 6 interactions with chain V Hydrophobic interactions: V:I.290, V:Y.519 Hydrogen bonds: V:N.514, V:N.517, V:S.520, V:S.520 CDL.30: 30 residues within 4Å: Chain 6: V.32, G.35, L.36, Y.39, L.43, M.47, V.53, M.54 Chain W: L.12, W.16, L.17, V.90, L.91, L.94, M.98, S.101, I.127, P.128, I.131 Chain X: P.238, A.239, L.241, T.242, S.245, L.246, P.256, L.257, S.301, M.335 Ligands: CDL.38 18 PLIP interactions: 4 interactions with chain X, 11 interactions with chain W, 3 interactions with chain 6 Hydrophobic interactions: X:L.241, X:T.242, X:L.246, X:L.257, W:L.12, W:W.16, W:W.16, W:W.16, W:L.17, W:L.17, W:L.94, W:L.94, W:I.127, W:P.128, W:P.128, 6:Y.39, 6:L.43, 6:L.43 CDL.33: 29 residues within 4Å: Chain 1: L.28, C.32, I.35, G.36, Y.39, S.40, L.43, N.44, R.55, R.58, Y.59, F.70, T.105, A.121, F.125 Chain V: M.573, L.576, N.579, Q.580, N.594, L.597, I.598 Chain X: P.110, F.113, M.156, L.157, T.160, M.164 Ligands: 3PE.26 22 PLIP interactions: 12 interactions with chain 1, 4 interactions with chain X, 6 interactions with chain V Hydrophobic interactions: 1:L.28, 1:I.35, 1:Y.39, 1:Y.39, 1:Y.39, 1:Y.39, 1:F.70, 1:A.121, 1:F.125, X:P.110, X:P.110, X:F.113, X:L.157, V:L.576, V:L.576, V:N.594, V:L.597, V:I.598 Hydrogen bonds: 1:N.44, 1:R.58, 1:Y.59, V:N.579 CDL.35: 6 residues within 4Å: Chain 1: M.69, T.100, A.103, R.104, H.106 Ligands: 3PE.34 4 PLIP interactions: 4 interactions with chain 1 Hydrophobic interactions: 1:T.100, 1:A.103 Salt bridges: 1:R.104, 1:H.106 CDL.38: 20 residues within 4Å: Chain 0: F.169, W.170, T.171, V.172 Chain 6: K.25, N.27, P.29, R.30, V.32, Y.33 Chain 8: F.22, L.26, K.29, K.33 Chain W: M.55, L.105 Chain X: P.256, M.335, P.338 Ligands: CDL.30 17 PLIP interactions: 7 interactions with chain 6, 4 interactions with chain X, 1 interactions with chain W, 4 interactions with chain 8, 1 interactions with chain 0 Hydrophobic interactions: 6:P.29, 6:P.29, 6:V.32, 6:V.32, 6:Y.33, 6:Y.33, X:P.256, X:P.256, X:M.335, X:P.338, W:L.105, 8:F.22, 0:F.169 Salt bridges: 6:K.25, 8:K.29, 8:K.33, 8:K.33 CDL.40: 27 residues within 4Å: Chain 9: V.98, A.105, Y.106 Chain V: W.66, W.68, L.76, K.77, M.78, F.138, I.142 Chain W: T.449 Ligands: CDL.24, 3PE.28, 3PE.42 Chain a: I.83, I.86, T.87, N.90, I.91, E.95, H.115 Chain b: W.80, Y.84, H.89 Chain i: V.48, R.49, I.52 19 PLIP interactions: 5 interactions with chain V, 3 interactions with chain i, 4 interactions with chain b, 4 interactions with chain a, 3 interactions with chain 9 Hydrophobic interactions: V:W.66, V:W.68, V:W.68, V:L.76, V:F.138, i:V.48, i:V.48, b:W.80, b:Y.84, b:Y.84, a:I.83, 9:V.98, 9:A.105 Salt bridges: i:R.49, b:H.89, a:H.115 Hydrogen bonds: a:N.90, a:E.95, 9:Y.106 CDL.43: 17 residues within 4Å: Chain 1: L.99, Y.108, G.109, A.112, C.115 Chain V: W.557, L.558, T.561 Ligands: 3PE.26, 3PE.34, 3PE.44 Chain f: P.82, T.83, P.84, S.87, G.90, A.91 11 PLIP interactions: 4 interactions with chain 1, 5 interactions with chain V, 2 interactions with chain f Hydrophobic interactions: 1:L.99, 1:Y.108, 1:A.112, V:W.557, V:W.557, V:W.557, V:L.558, V:T.561, f:P.84 Hydrogen bonds: 1:Y.108, f:S.87

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

DGT.31: 23 residues within 4Å: Chain Y: N.65, I.66, C.67, S.68, G.69, K.70, N.71, E.88, L.114, F.117, Y.118, L.131, Q.132, L.135, R.139, R.161, D.166, F.169, M.173, K.221, E.226, Y.233 Ligands: MG.32 17 PLIP interactions: 17 interactions with chain Y Hydrophobic interactions: Y:I.66 Hydrogen bonds: Y:S.68, Y:S.68, Y:K.70, Y:N.71, Y:Q.132, Y:Q.132, Y:Q.132, Y:R.139, Y:R.161, Y:E.226 Salt bridges: Y:K.70, Y:K.70, Y:R.161, Y:K.221 pi-Stacking: Y:F.169, Y:F.169

1 x MG: MAGNESIUM ION(Non-covalent)

MG.32: 5 residues within 4Å: Chain Y: K.70, N.71, E.88, E.160 Ligands: DGT.31 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vercellino, I. et al., SCAF1 drives the compositional diversity of mammalian respirasomes. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-04-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
6

B
C

C
D

D
2

E
1

F
3

G
9

H
P

I
Q

J
7

K
S

L
T

Z
U

M
V

N
W

O
q

P
r

Q
s

R
A

S
H

T
J

U
K

V
L

W
M

X
N

Y
O

0
X

1
Y

2
Z

3
a

4
b

5
c

6
d

7
e

8
f

9
g

a
h

b
i

c
j

d
k

e
l

f
m

g
n

h
o

i
p

Membrane

We predict this structure to be a membrane protein.
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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 dehydrogenase [ubiquinone] iron-sulfur protein 8, 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 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

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 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

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