SMTL ID : 8iuj.1

Cryo-EM structure of Euglena gracilis super-complex III2+IV2, composite

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 26 residues within 4Å: Chain B: Q.33, I.34, G.37, Y.38, L.40, A.41, Y.44, I.55, R.70, H.73, I.74, C.77, L.80, I.116, A.117, G.120, Y.121, L.123, V.124, F.169, H.172, Y.173, P.176, L.177, N.246, Y.264 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:Q.33, B:Q.33, B:I.34, B:L.40, B:Y.44, B:I.74, B:L.80, B:I.116, B:L.123, B:F.169 Salt bridges: B:R.70, B:R.70 pi-Stacking: B:H.172 Metal complexes: B:H.73, B:H.172 HEM.2: 27 residues within 4Å: Chain B: Y.20, G.23, A.26, S.27, I.30, L.80, I.84, H.87, I.88, R.90, S.91, S.96, K.99, V.102, W.103, G.106, I.107, M.109, Y.110, I.113, L.179, I.183, H.186, L.187, L.190, S.195, T.196 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:A.26, B:I.84, B:I.88, B:V.102, B:W.103, B:I.107, B:Y.110, B:I.113, B:L.187, B:L.190, B:L.190 Hydrogen bonds: B:G.23, B:S.96, B:S.195, B:T.196, B:T.196 Salt bridges: B:H.87, B:R.90, B:K.99 pi-Stacking: B:H.87 Metal complexes: B:H.87, B:H.186 HEM.11: 27 residues within 4Å: Chain H: Q.33, I.34, G.37, Y.38, L.40, A.41, Y.44, I.55, R.70, H.73, I.74, C.77, L.80, F.81, I.113, I.116, A.117, G.120, Y.121, L.123, V.124, F.169, H.172, Y.173, P.176, L.177, Y.264 15 PLIP interactions: 15 interactions with chain H, Hydrophobic interactions: H:Q.33, H:I.34, H:L.40, H:A.41, H:I.74, H:L.80, H:I.116, H:L.123, H:F.169, H:Y.173, H:P.176 Salt bridges: H:R.70, H:R.70 Metal complexes: H:H.73, H:H.172 HEM.12: 28 residues within 4Å: Chain H: Y.20, L.22, G.23, A.26, S.27, I.30, L.80, I.84, H.87, I.88, R.90, S.91, S.96, K.99, V.102, W.103, G.106, I.107, M.109, Y.110, I.113, L.179, I.183, H.186, L.187, L.190, S.195, T.196 23 PLIP interactions: 23 interactions with chain H, Hydrophobic interactions: H:A.26, H:I.84, H:I.88, H:I.88, H:V.102, H:W.103, H:I.107, H:Y.110, H:I.113, H:L.187, H:L.190 Hydrogen bonds: H:G.23, H:S.96, H:S.195, H:T.196, H:T.196 Salt bridges: H:H.87, H:R.90, H:K.99 pi-Stacking: H:H.87, H:H.87 Metal complexes: H:H.87, H:H.186

15 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 17 residues within 4Å: Chain A: Y.472, V.474 Chain B: N.2, K.3, L.6, Y.212, P.213, L.216, I.217, V.220 Chain C: Y.221 Chain E: L.121, I.122 Ligands: PC1.60 Chain c: K.91, W.95, L.98 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 2 interactions with chain c Hydrophobic interactions: B:L.6, c:L.98 Hydrogen bonds: B:Y.212, C:Y.221, C:Y.221 Salt bridges: B:K.3, c:K.91 CDL.5: 26 residues within 4Å: Chain B: S.17, P.18, A.19, L.22, M.86, R.218, F.221, I.222, N.225 Chain C: A.215, V.216, G.219, Y.220, N.222, R.223, S.226, R.230 Chain D: I.33, R.34, G.37, F.38, Q.40, I.41, L.44 Ligands: CDL.8, CDL.59 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.221, C:V.216 Salt bridges: B:R.218, B:R.218, C:R.223, C:R.223, C:R.223 Hydrogen bonds: C:N.222, C:S.226, C:R.230 CDL.8: 28 residues within 4Å: Chain B: S.17, P.18, A.19, L.22, I.82, Y.85, M.86, Y.89, R.90, Y.93, F.241, F.263, L.316, L.319, L.320 Chain D: I.41, L.44, G.45, K.48, I.49, F.52, I.55, G.56, C.59, L.60, A.63 Ligands: CDL.5 Chain f: R.186 17 PLIP interactions: 7 interactions with chain D, 8 interactions with chain B, 2 interactions with chain f Hydrophobic interactions: D:K.48, D:I.49, D:F.52, D:L.60, B:Y.85, B:Y.89, B:Y.89, B:F.241, B:F.263, B:L.316, B:L.319 Salt bridges: D:K.48, D:K.48, D:K.48, f:R.186, f:R.186 Hydrogen bonds: B:A.19 CDL.10: 15 residues within 4Å: Chain 7: M.1, I.2 Chain E: A.50, S.51, R.52, I.53, R.54, I.104, V.105, N.106, R.107 Chain j: H.25, I.26, F.27, L.29 19 PLIP interactions: 5 interactions with chain j, 12 interactions with chain E, 2 interactions with chain 7 Hydrophobic interactions: j:F.27, j:L.29, E:I.53, 7:M.1, 7:I.2 Hydrogen bonds: j:I.26, j:F.27, j:F.27, E:S.51, E:R.52, E:I.53, E:V.105, E:N.106, E:R.107 Salt bridges: E:R.52, E:R.52, E:R.54, E:R.54, E:R.107 CDL.14: 15 residues within 4Å: Chain G: Y.472, V.474 Chain H: K.3, L.6, Y.212, P.213, L.216, I.217, V.220 Chain I: Y.221 Chain K: I.122 Ligands: PC1.64 Chain d: K.91, W.95, L.98 8 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I, 3 interactions with chain H, 2 interactions with chain d Hydrophobic interactions: K:I.122, K:I.122, H:L.216, H:V.220, d:L.98 Hydrogen bonds: I:Y.221 Salt bridges: H:K.3, d:K.91 CDL.16: 35 residues within 4Å: Chain H: P.18, A.19, L.22, F.79, I.82, M.86, R.218, F.221, I.222, N.225, I.226, I.228, I.229 Chain I: A.212, A.215, V.216, G.219, Y.220, N.222, R.223, S.226, R.230 Chain J: I.33, R.34, G.37, F.38, Q.40, I.41, Y.42, L.44, G.45, M.46, I.49 Ligands: CDL.18, CDL.19 22 PLIP interactions: 7 interactions with chain J, 9 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: J:R.34, J:F.38, J:I.41, J:Y.42, J:Y.42, J:M.46, J:I.49, I:A.212, I:V.216, I:V.216, I:R.223, H:P.18, H:L.22, H:F.221, H:F.221 Hydrogen bonds: I:N.222, I:R.223, I:S.226 Salt bridges: I:R.223, I:R.223, H:R.218, H:R.218 CDL.18: 24 residues within 4Å: Chain H: S.17, P.18, A.19, L.22, I.82, Y.85, M.86, Y.89, R.90, Y.93, F.263, L.316, L.319 Chain J: I.41, L.44, G.45, K.48, F.52, I.55, G.56, C.59, L.60 Ligands: CDL.16 Chain j: R.186 15 PLIP interactions: 7 interactions with chain J, 6 interactions with chain H, 2 interactions with chain j Hydrophobic interactions: J:I.41, J:K.48, J:F.52, J:L.60, H:A.19, H:Y.89, H:Y.89, H:R.90, H:L.319, H:L.319 Salt bridges: J:K.48, J:K.48, J:K.48, j:R.186, j:R.186 CDL.19: 18 residues within 4Å: Chain I: V.216, Y.220 Chain J: D.32, I.33, R.34 Ligands: CDL.16 Chain d: K.71, R.82, S.83, A.85, F.86, A.89, A.90 Chain k: L.2, F.5, S.6, F.9, L.23 8 PLIP interactions: 3 interactions with chain d, 1 interactions with chain J, 2 interactions with chain k, 2 interactions with chain I Hydrophobic interactions: d:F.86, k:F.9, k:F.9, I:Y.220 Hydrogen bonds: d:K.71, I:Y.220 Salt bridges: d:K.71, J:R.34 CDL.21: 14 residues within 4Å: Chain B: S.364 Chain K: A.50, S.51, R.52, I.53, R.54, I.104, V.105, N.106, R.107 Chain f: H.25, I.26, F.27, L.29 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain f Hydrophobic interactions: K:I.53, K:R.54 Hydrogen bonds: K:A.50, K:S.51, K:R.52, K:I.53, K:N.106, f:I.26, f:F.27, f:F.27 Salt bridges: K:R.52, K:R.54, K:R.54, K:R.107 CDL.24: 25 residues within 4Å: Chain N: P.27, V.28, N.33, M.36, S.37, I.40 Chain R: Y.174, I.177, M.180, A.181, F.184 Chain V: F.330, N.334 Chain W: I.25, A.28, L.29, K.55, I.56, V.58, I.59, W.60, I.62, L.63, P.64 Chain t: V.1 18 PLIP interactions: 11 interactions with chain W, 1 interactions with chain t, 3 interactions with chain R, 3 interactions with chain N Hydrophobic interactions: W:A.28, W:I.56, W:V.58, W:I.59, W:I.59, W:W.60, W:I.62, W:L.63, t:V.1, R:I.177, R:A.181, R:F.184, N:M.36 Salt bridges: W:K.55, W:K.55, W:K.55 Hydrogen bonds: N:V.28, N:N.33 CDL.26: 18 residues within 4Å: Chain M: L.193, H.196, L.197, L.200 Chain O: P.2, W.7 Chain X: A.83, I.86, F.87, I.90, Q.153 Ligands: PC1.25, PC1.36 Chain r: L.5, L.6 Chain u: S.19, A.20, W.21 10 PLIP interactions: 3 interactions with chain M, 3 interactions with chain u, 2 interactions with chain O, 1 interactions with chain X, 1 interactions with chain r Hydrophobic interactions: M:L.193, M:H.196, M:L.197, O:W.7, X:F.87, r:L.5 Hydrogen bonds: u:S.19, u:A.20, u:W.21, O:W.7 CDL.27: 38 residues within 4Å: Chain U: F.62, P.63, K.64, Y.76, W.82, F.85, V.86, A.89, I.90, V.91, V.94, I.97 Chain V: M.8, I.9, K.11, Y.12, T.13, I.23, L.24, G.26, Y.27, M.28, Y.30, I.31, I.34, F.87, F.112, W.113, I.116, V.120, H.403, L.407, F.411, F.478, I.479, Y.482, L.486 Ligands: 3PE.70 22 PLIP interactions: 6 interactions with chain U, 16 interactions with chain V Hydrophobic interactions: U:A.89, U:I.90, U:V.94, V:Y.27, V:Y.27, V:Y.27, V:Y.27, V:Y.30, V:Y.30, V:I.34, V:F.87, V:I.116, V:F.411, V:F.478, V:Y.482, V:Y.482, V:Y.482, V:L.486 Hydrogen bonds: U:K.64, U:Y.76, U:W.82 Salt bridges: V:K.11 CDL.44: 19 residues within 4Å: Chain 1: P.2, W.7 Chain 9: A.83, I.86, F.87, I.90, Q.153 Chain Z: L.193, H.196, L.197, L.200 Ligands: PC1.43, PC1.53, PC1.56 Chain p: S.19, A.20, W.21 Chain x: L.5, L.6 14 PLIP interactions: 2 interactions with chain x, 3 interactions with chain 9, 4 interactions with chain p, 2 interactions with chain Z, 3 interactions with chain 1 Hydrophobic interactions: x:L.5, x:L.6, 9:F.87, 9:I.90, p:W.21, Z:H.196, Z:L.197, 1:W.7 Hydrogen bonds: 9:Q.153, p:S.19, p:S.19, p:A.20, 1:P.2, 1:W.7 CDL.50: 40 residues within 4Å: Chain 6: F.62, P.63, K.64, Y.76, W.82, F.85, V.86, A.89, I.90, V.91, V.94 Chain 7: M.8, I.9, K.11, Y.12, T.13, I.23, L.24, G.26, Y.27, M.28, Y.30, I.31, I.34, F.87, F.112, W.113, I.116, V.119, V.120, H.403, L.407, I.410, F.411, F.478, I.479, Y.482, L.486 Ligands: 3PE.75 Chain x: L.159 25 PLIP interactions: 18 interactions with chain 7, 6 interactions with chain 6, 1 interactions with chain x Hydrophobic interactions: 7:Y.12, 7:Y.12, 7:L.24, 7:Y.27, 7:Y.27, 7:Y.30, 7:Y.30, 7:I.34, 7:F.87, 7:I.116, 7:V.120, 7:F.411, 7:Y.482, 7:Y.482, 7:Y.482, 7:Y.482, 6:F.85, 6:I.90, x:L.159 Hydrogen bonds: 7:Y.12, 6:K.64, 6:Y.76, 6:W.82 Salt bridges: 7:K.11, 6:K.64 CDL.59: 17 residues within 4Å: Chain C: Y.220 Chain D: D.32, I.33, R.34 Ligands: CDL.5 Chain c: K.71, R.82, S.83, A.85, F.86, A.89 Chain g: M.1, L.2, F.5, S.6, F.9, L.23 10 PLIP interactions: 2 interactions with chain D, 5 interactions with chain g, 1 interactions with chain C, 2 interactions with chain c Hydrogen bonds: D:I.33, g:M.1, C:Y.220, c:K.71 Salt bridges: D:R.34, c:K.71 Hydrophobic interactions: g:L.2, g:F.9, g:F.9, g:F.9

2 x HEC: HEME C(Non-covalent)

HEC.4: 25 residues within 4Å: Chain C: V.35, F.36, C.39, H.40, N.103, A.106, P.108, P.109, L.111, I.114, R.118, Y.124, I.125, L.128, L.129, F.152, I.157, G.158, M.159, P.160, P.162, L.163, V.185, L.189 Chain d: H.212 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain d, Hydrophobic interactions: C:V.35, C:F.36, C:N.103, C:A.106, C:P.108, C:L.111, C:I.114, C:L.128, C:L.129, C:I.157, C:M.159, C:P.160, C:L.163 Hydrogen bonds: C:Y.124, C:Y.124, C:G.158 Salt bridges: C:R.118, d:H.212 Metal complexes: C:H.40 HEC.15: 25 residues within 4Å: Chain I: V.35, F.36, C.39, H.40, N.103, A.106, P.108, P.109, L.111, I.114, R.118, Y.124, I.125, L.128, L.129, F.152, I.157, G.158, M.159, P.160, P.162, L.163, V.185, L.189 Chain c: H.212 22 PLIP interactions: 21 interactions with chain I, 1 interactions with chain c, Hydrophobic interactions: I:V.35, I:F.36, I:N.103, I:A.106, I:P.108, I:P.109, I:L.111, I:L.111, I:I.114, I:L.128, I:L.129, I:M.159, I:P.160, I:P.162, I:L.163, I:V.185 Hydrogen bonds: I:Y.124, I:Y.124, I:G.158 Salt bridges: I:R.118, c:H.212 Metal complexes: I:H.40

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

PC1.6: 11 residues within 4Å: Chain B: I.232, Y.236, Y.237 Chain C: F.14, Q.15, W.16, F.17, K.201, Y.205, I.208, A.209 Ligand excluded by PLIP PC1.13: 18 residues within 4Å: Chain B: I.35, Y.38, I.39 Chain H: F.118, T.119, C.137, L.153, I.154, W.155, T.164, R.167, I.168, I.171, L.175 Ligands: PX2.9 Chain c: L.109, M.110, F.113 Ligand excluded by PLIP PC1.17: 11 residues within 4Å: Chain H: I.232, Y.236, Y.237 Chain I: F.14, Q.15, W.16, F.17, K.201, Y.205, I.208, A.209 Ligand excluded by PLIP PC1.20: 19 residues within 4Å: Chain B: I.146, K.149, L.150, L.153 Chain K: W.144, A.145, W.146, R.147, W.148 Ligands: PC1.61, PC1.64 Chain d: L.98, L.99, T.102, R.103, V.106, V.107, M.110, M.114 Ligand excluded by PLIP PC1.22: 29 residues within 4Å: Chain M: I.163, F.164, I.167, M.168, L.171, W.175, S.180, V.181, G.182, S.185, H.186, A.187, F.190 Chain X: L.48, I.51, I.52, N.55, I.56, W.58, P.59, I.62, I.63, Y.66, L.78, I.82, F.85, E.89 Ligands: 3PE.23, PC1.33 Ligand excluded by PLIP PC1.25: 14 residues within 4Å: Chain M: H.196, L.200, I.203 Chain O: P.2, S.3, S.4, W.7, W.11 Chain S: R.36 Chain X: T.149, Q.153, R.157 Ligands: CDL.26 Chain r: H.22 Ligand excluded by PLIP PC1.28: 17 residues within 4Å: Chain R: Y.194 Chain U: Y.135, G.136, G.137, G.138, K.144 Chain V: V.429, L.433, Y.436, L.440, V.463, H.466 Chain Y: M.89, G.90, Y.93, P.165, N.168 Ligand excluded by PLIP PC1.33: 33 residues within 4Å: Chain V: M.104, P.105, R.106, M.107, V.162, H.163, G.166, I.167, T.170, I.171, V.174, L.211, P.212, L.214, G.215 Chain X: Y.9, I.20, M.23, I.27, I.51, N.55, W.58, I.62, E.65, I.74, L.78, N.81, I.82, T.84, F.85, L.88, L.92 Ligands: PC1.22 Ligand excluded by PLIP PC1.36: 22 residues within 4Å: Chain V: I.177, K.181, Y.182, I.205, I.208 Chain X: N.76, Y.80, A.83, T.84, F.87 Ligands: CDL.26 Chain r: L.6, H.7, Y.17 Chain s: C.29, Q.30, G.31, P.32 Chain u: W.21, F.23, Q.24, E.25 Ligand excluded by PLIP PC1.39: 27 residues within 4Å: Chain M: L.154, V.201, I.204, L.205, L.207 Chain T: Y.48 Chain V: G.236, D.237 Chain W: R.160 Chain X: F.93, I.94, Y.97, W.98, I.101, N.102, N.103, I.105, H.106 Ligands: 3PE.35 Chain s: I.65, C.68, L.69, L.75, L.77, V.80, I.81, P.82 Ligand excluded by PLIP PC1.40: 26 residues within 4Å: Chain 9: L.48, I.51, I.52, N.55, I.56, W.58, P.59, I.62, I.63, Y.66, L.78, I.82, F.85 Chain Z: I.163, F.164, I.167, M.168, L.171, W.175, S.180, V.181, S.185, H.186, A.187, F.190 Ligands: PC1.49 Ligand excluded by PLIP PC1.41: 29 residues within 4Å: Chain 7: H.163, G.215, V.216, T.219, L.223, I.227 Chain 9: I.27, F.28, L.31, L.92, F.96 Chain Z: F.135, A.136, L.139, S.140, F.141, D.142, I.143, Y.152, M.153, G.156, L.157, S.160 Ligands: PC1.49 Chain b: W.84, A.89, F.90, L.91, D.92 Ligand excluded by PLIP PC1.43: 16 residues within 4Å: Chain 1: P.2, S.3, S.4, W.7, W.11 Chain 9: T.149, L.150, Q.153, R.157 Chain Z: H.196, L.200, I.203 Ligands: CDL.44 Chain b: D.33, R.36 Chain x: H.22 Ligand excluded by PLIP PC1.49: 33 residues within 4Å: Chain 7: M.104, P.105, R.106, M.107, I.110, H.163, G.166, I.167, T.170, I.171, V.174, L.211, P.212, G.215 Chain 9: Y.9, I.20, V.24, N.55, W.58, I.62, E.65, L.69, I.74, L.78, N.81, I.82, F.85, L.88, E.89, L.92 Chain Z: F.164 Ligands: PC1.40, PC1.41 Ligand excluded by PLIP PC1.53: 22 residues within 4Å: Chain 7: I.177, K.181, Y.182, I.205, I.208 Chain 9: Y.80, A.83, T.84, F.87 Ligands: CDL.44 Chain n: C.29, Q.30, G.31, P.32 Chain p: W.21, F.23, Q.24, E.25 Chain x: L.6, H.7, G.8, Y.17 Ligand excluded by PLIP PC1.56: 27 residues within 4Å: Chain 5: Y.48 Chain 7: D.237 Chain 8: R.160 Chain 9: I.90, F.93, I.94, Y.97, W.98, I.101, N.102, N.103, I.105, H.106 Chain Z: L.197, L.200, V.201, I.204 Ligands: CDL.44, 3PE.52 Chain n: I.65, C.68, L.69, E.74, L.75, L.77, V.80, I.81 Ligand excluded by PLIP PC1.57: 20 residues within 4Å: Chain 7: W.349, F.352, S.353, I.356, F.421, T.424, F.425, L.428 Chain 8: I.37, R.38, W.40, Y.41, N.42 Chain a: K.47, Y.59, F.78, P.79, F.81, L.82 Chain q: A.274 Ligand excluded by PLIP PC1.60: 22 residues within 4Å: Chain A: Y.446, D.447, Y.472, V.474 Chain E: G.141, G.142, W.144, A.145 Ligands: CDL.3 Chain c: Y.88, K.91, W.95, L.99 Chain g: Y.10, L.14, Q.15, S.16, N.17, L.20, I.21, T.24, L.25 Ligand excluded by PLIP PC1.61: 29 residues within 4Å: Chain B: I.108, L.112, F.118, T.119, S.122, I.133, I.136, C.137, L.153, I.154, W.155, T.164, R.167, I.168, I.171, L.174, L.175, L.178, F.182 Chain H: I.34, I.35, Y.38, I.39, L.177, I.180 Ligands: PC1.20 Chain d: L.109, M.110, F.113 Ligand excluded by PLIP PC1.62: 29 residues within 4Å: Chain H: I.32, I.35, S.36, T.65, L.68, I.69, N.72, L.227, Y.230, N.231, Y.235 Chain I: L.203, K.206, T.207, T.210, L.211, I.214 Chain K: A.149, S.150, A.151 Chain d: G.97, L.98, G.101, T.102, V.104, T.105, V.106, Y.108, L.109 Ligand excluded by PLIP PC1.64: 24 residues within 4Å: Chain G: Y.446, D.447, Y.472, V.474, L.476 Chain K: G.141, G.142, W.144, A.145 Ligands: CDL.14, PC1.20 Chain d: Y.88, K.91, W.95, L.99 Chain k: Y.10, L.14, Q.15, S.16, N.17, L.20, I.21, T.24, L.25 Ligand excluded by PLIP PC1.65: 9 residues within 4Å: Chain E: R.43 Chain L: K.63, L.67 Chain j: R.22, R.23, R.45, T.116, P.117, Y.118 Ligand excluded by PLIP

3 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.7: 17 residues within 4Å: Chain B: L.68, L.227, N.231, Y.235 Chain C: L.203, K.206, T.207, T.210, L.211 Chain E: A.149, S.150, A.151 Chain c: L.98, G.101, T.102, V.104, Y.108 7 PLIP interactions: 2 interactions with chain c, 4 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: c:V.104, c:Y.108, C:L.203, C:T.207 Salt bridges: C:K.206, C:K.206 Hydrogen bonds: E:S.150 PX2.9: 16 residues within 4Å: Chain E: W.144, A.145, W.146, R.147, W.148 Chain H: I.146, K.149, L.150, L.153 Ligands: PC1.13 Chain c: T.102, R.103, V.106, V.107, M.110, M.114 9 PLIP interactions: 2 interactions with chain c, 4 interactions with chain H, 3 interactions with chain E Hydrophobic interactions: c:V.106, c:V.107, H:K.149, E:A.145, E:W.146, E:W.148 Salt bridges: H:K.149, H:K.149, H:K.149 PX2.42: 20 residues within 4Å: Chain 0: H.25, P.27, V.28, N.33, M.36, S.37, I.40 Chain 4: Y.174, I.177, M.180, A.181, F.184 Chain 7: N.334 Chain 8: A.28, H.53, K.55, I.56, I.59, W.60, L.63 10 PLIP interactions: 2 interactions with chain 4, 4 interactions with chain 0, 4 interactions with chain 8 Hydrophobic interactions: 4:A.181, 0:M.36, 0:I.40, 8:I.59, 8:W.60, 8:L.63 Hydrogen bonds: 4:Y.174, 0:V.28 Salt bridges: 0:H.25, 8:K.55

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

3PE.23: 27 residues within 4Å: Chain M: F.135, A.136, H.137, E.138, L.139, S.140, F.141, D.142, I.143, Y.152, M.153, G.156, L.157, S.160, I.163 Chain S: M.82, W.84, A.89, F.90, L.91 Chain V: L.223, I.227 Chain X: Y.30, L.31, L.34, I.44 Ligands: PC1.22 10 PLIP interactions: 1 interactions with chain X, 4 interactions with chain M, 5 interactions with chain S Hydrophobic interactions: X:L.31, M:F.135, M:I.143, S:W.84, S:W.84, S:F.90 Hydrogen bonds: M:A.136, M:Y.152, S:F.90, S:L.91 3PE.34: 18 residues within 4Å: Chain V: F.419, Y.422, F.473, L.476, T.477, R.480 Chain Y: F.66, F.67, T.84, I.88 Chain v: W.31, G.35, W.36, G.37, L.38, K.39, D.40, F.47 7 PLIP interactions: 3 interactions with chain v, 4 interactions with chain V Hydrophobic interactions: v:K.39, V:F.473, V:L.476 Hydrogen bonds: v:G.35 Salt bridges: v:K.39, V:R.480, V:R.480 3PE.35: 25 residues within 4Å: Chain V: G.209, I.213, H.243, F.247, Y.294, F.295, W.297, A.298, L.306, D.307, S.310, Y.313, F.314 Chain X: F.87, L.91, I.94, W.98, H.106 Ligands: PC1.39 Chain s: G.61, H.64, I.65, N.72, E.74, L.75 18 PLIP interactions: 12 interactions with chain V, 2 interactions with chain X, 4 interactions with chain s Hydrophobic interactions: V:F.247, V:F.247, V:Y.294, V:F.295, V:F.295, V:F.295, V:W.297, V:W.297, V:Y.313, X:I.94, X:W.98, s:I.65, s:I.65 Hydrogen bonds: V:D.307, V:D.307, s:E.74 Salt bridges: V:H.243, s:H.64 3PE.51: 19 residues within 4Å: Chain 7: F.419, Y.422, F.473, L.476, T.477, R.480 Chain a: F.66, F.67, T.84, I.88 Chain q: W.31, G.35, W.36, G.37, L.38, K.39, I.42, F.43, F.47 7 PLIP interactions: 4 interactions with chain 7, 3 interactions with chain q Hydrophobic interactions: 7:F.473, 7:L.476, q:K.39 Hydrogen bonds: 7:T.477, q:G.35 Salt bridges: 7:R.480, q:K.39 3PE.52: 25 residues within 4Å: Chain 7: G.209, I.213, H.243, F.247, Y.294, F.295, W.297, L.306, D.307, S.310, Y.313, F.314 Chain 9: F.87, L.91, I.94, W.98, H.106 Ligands: PC1.56 Chain n: G.61, H.64, I.65, C.68, N.72, E.74, L.75 17 PLIP interactions: 11 interactions with chain 7, 4 interactions with chain n, 2 interactions with chain 9 Hydrophobic interactions: 7:F.247, 7:F.295, 7:F.295, 7:F.295, 7:W.297, 7:W.297, 7:Y.313, n:I.65, 9:I.94, 9:W.98 Hydrogen bonds: 7:D.307, 7:S.310, n:E.74, n:E.74 Salt bridges: 7:H.243, 7:H.243, n:H.64 3PE.67: 15 residues within 4Å: Chain n: I.66, C.68, L.69, V.70, V.71, N.72, P.73, L.75, S.76, L.77, I.81, L.85, F.88, T.89, N.90 7 PLIP interactions: 7 interactions with chain n Hydrophobic interactions: n:V.70, n:L.77, n:I.81 Hydrogen bonds: n:N.72, n:S.76, n:L.77, n:N.90 3PE.68: 35 residues within 4Å: Chain 0: T.48, Y.49, S.51, L.52, W.53, R.55, Y.58, R.60 Chain 7: D.309, S.312, Y.313, I.316 Chain 8: L.73, H.74, V.76, T.77, Y.80 Ligands: S12.69 Chain n: L.60, F.63, H.64, R.67, G.113, M.114, W.115, H.118, Y.121 Chain o: F.40, F.43, K.44, Y.46, A.47, Y.50, L.54, Y.58 19 PLIP interactions: 6 interactions with chain o, 5 interactions with chain n, 2 interactions with chain 7, 5 interactions with chain 0, 1 interactions with chain 8 Hydrophobic interactions: o:F.40, o:F.43, o:F.43, o:A.47, n:L.60, n:F.63, n:H.64, 7:D.309, 7:Y.313, 0:L.52, 0:L.52, 0:R.55, 0:Y.58, 8:L.73 Hydrogen bonds: o:Y.50, o:Y.50, n:Y.121 Salt bridges: n:H.118, 0:R.60 3PE.70: 28 residues within 4Å: Chain U: N.43, T.44, D.45, D.49 Chain V: M.6, I.9, N.10, T.13, L.14, W.113, I.116, V.117, V.120, I.124 Chain X: R.15, Y.18, P.21, L.22, H.25 Ligands: CDL.27 Chain r: R.139, F.142, R.152, I.156, L.159, G.162, A.163, Y.166 14 PLIP interactions: 3 interactions with chain V, 8 interactions with chain r, 3 interactions with chain X Hydrophobic interactions: V:I.116, V:V.117, V:V.120, r:R.152, r:L.159, r:L.159, r:A.163, r:Y.166, X:Y.18, X:Y.18 Hydrogen bonds: r:R.152 Salt bridges: r:R.139, r:R.152, X:R.15 3PE.71: 15 residues within 4Å: Chain s: I.66, L.69, V.70, V.71, N.72, P.73, L.75, S.76, L.77, I.81, L.85, F.88, T.89, N.90, P.91 5 PLIP interactions: 5 interactions with chain s Hydrophobic interactions: s:V.70 Hydrogen bonds: s:N.72, s:S.76, s:L.77, s:N.90 3PE.72: 32 residues within 4Å: Chain N: L.52, W.53, R.55, Y.58, R.60 Chain V: D.309, S.312, Y.313, I.316 Chain W: L.73, H.74, V.76, T.77, Y.80 Ligands: S12.73 Chain s: L.60, F.63, H.64, R.67, G.113, M.114, W.115, H.118, Y.121 Chain t: F.40, F.43, K.44, Y.46, A.47, Y.50, L.54, Y.58 14 PLIP interactions: 4 interactions with chain N, 1 interactions with chain V, 5 interactions with chain s, 2 interactions with chain t, 2 interactions with chain W Hydrophobic interactions: N:L.52, N:R.55, N:Y.58, V:Y.313, s:L.60, s:F.63, t:Y.46, W:V.76, W:T.77 Salt bridges: N:R.60, s:H.118 Hydrogen bonds: s:W.115, s:Y.121, t:Y.50 3PE.75: 27 residues within 4Å: Chain 6: N.43, D.45, D.49 Chain 7: M.6, I.9, N.10, T.13, L.14, W.113, I.116, V.117, V.120, I.124 Chain 9: R.15, Y.18, P.21, L.22, H.25 Ligands: CDL.50 Chain x: R.139, F.142, R.152, I.156, L.159, G.162, A.163, Y.166 8 PLIP interactions: 4 interactions with chain x, 1 interactions with chain 9, 3 interactions with chain 7 Hydrophobic interactions: x:L.159, x:Y.166, 7:W.113, 7:V.120, 7:I.124 Salt bridges: x:R.139, x:R.152, 9:R.15

4 x HEA: HEME-A(Non-covalent)

HEA.29: 37 residues within 4Å: Chain V: W.137, W.246, V.253, Y.254, I.257, H.299, H.300, F.302, T.318, I.321, S.322, I.323, T.325, S.326, M.329, F.330, F.358, C.359, G.362, F.363, G.365, L.366, L.368, S.369, D.374, H.378, V.383, H.386, F.387, V.390, L.391, R.448 Chain W: Y.22, I.25, L.29, P.64, L.68 24 PLIP interactions: 22 interactions with chain V, 2 interactions with chain W, Hydrophobic interactions: V:W.246, V:V.253, V:F.358, V:F.363, V:L.368, V:V.383, V:F.387, V:F.387, V:V.390, V:L.391, V:L.391, W:I.25, W:L.68 Hydrogen bonds: V:W.137, V:Y.254, V:Y.254, V:D.374 Salt bridges: V:H.378, V:R.448 pi-Cation interactions: V:H.250, V:H.299, V:H.300, V:H.386 Metal complexes: V:H.386 HEA.30: 39 residues within 4Å: Chain V: Y.30, G.33, Y.37, S.40, M.41, I.43, R.44, L.47, Y.64, I.68, T.69, H.71, G.72, M.75, L.76, F.79, I.80, V.83, G.136, W.137, Y.381, V.384, F.387, H.388, L.391, S.392, T.396, L.399, L.400, L.427, V.434, F.435, M.438, R.448, R.449, V.450, L.471, T.475, F.478 33 PLIP interactions: 33 interactions with chain V, Hydrophobic interactions: V:Y.30, V:Y.37, V:I.43, V:R.44, V:M.75, V:L.76, V:F.79, V:I.80, V:F.387, V:F.387, V:L.391, V:L.391, V:L.399, V:L.400, V:L.427, V:F.435, V:L.471, V:T.475, V:F.478, V:F.478 Hydrogen bonds: V:S.40, V:R.44, V:W.137, V:Y.381, V:Y.381, V:R.449, V:V.450 Salt bridges: V:R.448, V:R.449 pi-Stacking: V:F.387, V:F.435 Metal complexes: V:H.71, V:H.388 HEA.45: 41 residues within 4Å: Chain 7: W.137, T.138, W.246, H.250, V.253, Y.254, I.256, I.257, H.299, H.300, F.302, T.318, I.321, S.322, I.323, T.325, S.326, M.329, F.330, F.358, C.359, G.362, F.363, G.365, L.366, L.368, S.369, D.374, H.378, V.383, H.386, F.387, V.390, L.391, R.448 Chain 8: L.21, Y.22, I.25, L.29, P.64, L.68 29 PLIP interactions: 26 interactions with chain 7, 3 interactions with chain 8, Hydrophobic interactions: 7:W.137, 7:W.246, 7:V.253, 7:T.325, 7:F.363, 7:L.368, 7:L.368, 7:V.383, 7:F.387, 7:F.387, 7:V.390, 7:L.391, 7:L.391, 8:I.25, 8:P.64, 8:L.68 Hydrogen bonds: 7:W.137, 7:Y.254, 7:Y.254, 7:D.374 Salt bridges: 7:H.378, 7:R.448 pi-Stacking: 7:H.386, 7:H.386 pi-Cation interactions: 7:H.250, 7:H.250, 7:H.299, 7:H.386 Metal complexes: 7:H.386 HEA.46: 39 residues within 4Å: Chain 7: Y.30, G.33, I.34, Y.37, S.40, M.41, I.43, R.44, L.47, Y.64, I.68, T.69, H.71, G.72, M.75, L.76, F.79, I.80, G.136, W.137, Y.381, V.384, F.387, H.388, L.391, S.392, T.396, L.399, L.400, L.427, V.434, F.435, M.438, R.448, R.449, V.450, L.471, T.475, F.478 30 PLIP interactions: 30 interactions with chain 7, Hydrophobic interactions: 7:Y.30, 7:Y.30, 7:R.44, 7:M.75, 7:L.76, 7:L.76, 7:F.79, 7:I.80, 7:F.387, 7:F.387, 7:L.391, 7:L.399, 7:L.400, 7:L.427, 7:F.435, 7:L.471, 7:T.475, 7:F.478 Hydrogen bonds: 7:S.40, 7:R.44, 7:Y.64, 7:Y.64, 7:W.137, 7:R.449 Salt bridges: 7:R.448, 7:R.449 pi-Stacking: 7:F.387, 7:F.435 Metal complexes: 7:H.71, 7:H.388

6 x CU: COPPER (II) ION(Non-covalent)

CU.31: 3 residues within 4Å: Chain V: H.250, H.299, H.300 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:H.250, V:H.299, V:H.300 CU.37: 6 residues within 4Å: Chain W: H.143, C.178, C.182, H.186, M.189 Ligands: CU.38 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:H.143, W:C.178, W:C.182 CU.38: 6 residues within 4Å: Chain W: C.178, E.180, L.181, C.182, H.186 Ligands: CU.37 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.178, W:E.180, W:C.182, W:H.186 CU.47: 3 residues within 4Å: Chain 7: H.250, H.299, H.300 3 PLIP interactions: 3 interactions with chain 7 Metal complexes: 7:H.250, 7:H.299, 7:H.300 CU.54: 5 residues within 4Å: Chain 8: H.143, C.178, C.182, M.189 Ligands: CU.55 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:H.143, 8:C.178, 8:C.182 CU.55: 6 residues within 4Å: Chain 8: C.178, E.180, L.181, C.182, H.186 Ligands: CU.54 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.178, 8:E.180, 8:C.182, 8:H.186

2 x MG: MAGNESIUM ION(Non-covalent)

MG.32: 4 residues within 4Å: Chain V: Y.140, H.378, D.379 Chain W: E.180 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain W Metal complexes: V:H.378, V:D.379, W:E.180 MG.48: 4 residues within 4Å: Chain 7: H.378, D.379 Chain 8: D.155, E.180 3 PLIP interactions: 2 interactions with chain 7, 1 interactions with chain 8 Metal complexes: 7:H.378, 7:D.379, 8:E.180

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

FES.58: 10 residues within 4Å: Chain c: C.190, H.192, L.193, C.195, C.209, C.211, H.212, G.213, S.214, P.226 4 PLIP interactions: 4 interactions with chain c, Metal complexes: c:C.190, c:H.192, c:C.209, c:H.212 FES.63: 10 residues within 4Å: Chain d: C.190, H.192, L.193, C.195, C.209, C.211, H.212, G.213, S.214, P.226 4 PLIP interactions: 4 interactions with chain d, Metal complexes: d:C.190, d:H.192, d:C.209, d:H.212

2 x ZN: ZINC ION(Non-covalent)

ZN.66: 3 residues within 4Å: Chain m: C.99, C.103, C.128 3 PLIP interactions: 3 interactions with chain m Metal complexes: m:C.99, m:C.103, m:C.128 ZN.74: 5 residues within 4Å: Chain v: R.127 Chain w: C.99, C.103, C.125, C.128 3 PLIP interactions: 3 interactions with chain w Metal complexes: w:C.99, w:C.125, w:C.128

2 x S12: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine(Non-covalent)

S12.69: 26 residues within 4Å: Chain 7: I.316, S.319, I.320, I.323 Chain 8: I.65, L.68, I.69, V.72 Ligands: 3PE.68 Chain n: L.49, A.52, C.53, V.56, L.60, F.63, R.67, V.71, G.113 Chain o: L.32, T.33, P.36, F.37, F.40, I.41, K.44, Y.45 17 PLIP interactions: 8 interactions with chain o, 2 interactions with chain 8, 4 interactions with chain n, 3 interactions with chain 7 Hydrophobic interactions: o:P.36, o:P.36, o:F.40, o:F.40, o:F.40, 8:I.65, 8:I.65, n:A.52, n:V.56, n:L.60, 7:I.320, 7:I.320, 7:I.323 Hydrogen bonds: o:K.44, o:Y.45 Salt bridges: o:K.44, n:R.67 S12.73: 25 residues within 4Å: Chain V: I.316, S.319, I.320, I.323 Chain W: I.65, L.68, I.69, V.72 Ligands: 3PE.72 Chain s: L.49, A.52, C.53, V.56, L.60, F.63, R.67, V.71, G.113 Chain t: L.32, P.36, F.37, F.40, I.41, K.44, Y.45 14 PLIP interactions: 7 interactions with chain t, 4 interactions with chain s, 2 interactions with chain V, 1 interactions with chain W Hydrophobic interactions: t:P.36, t:P.36, t:F.40, t:F.40, t:F.40, s:A.52, s:L.60, s:L.60, V:I.316, V:I.320, W:I.65 Hydrogen bonds: t:Y.45 Salt bridges: t:K.44, s:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Z. et al., Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun (2024)

Release Date

2024-02-28

Peptides

MPP-beta: AG
Cytochrome b: BH
Cytochrome c1, heme protein: CI
UQCRQ: DJ
UQCR10: EK
Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial: FL
COXEG1: MZ
COXEG3: N0
COXEG5: O1
COXEG8: P2
COXEG10: Q3
COX5c: R4
COX6a: Sb
COX6b-1: T5
COX7c: U6
Cytochrome c oxidase subunit 1: V7
Cytochrome c oxidase subunit 2: W8
Putative NADH dehydrogenase subunit 6: X9
COX4: Ya
UQCRFS1: cd
UQCRH: ei
UQCRB: fj
UQCR9: gk
Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial: hl
COX5b-2: mw
COXEG4: ns
COXEG6: ot
COXEG7: pu
COXEG9: qv
COX7a: rx

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
QA

G
Qa

B
QC

H
Qc

C
QD

I
Qd

D
QH

J
Qh

E
QJ

K
Qj

F
QK

L
Qk

M
4a

Z
4A

N
4c

0
4C

O
4e

1
4E

P
4h

2
4H

Q
4j

3
4J

R
5c

4
5C

S
6a

b
6A

T
6b

5
6B

U
7c

6
7C

V
c1

7
C1

W
c2

8
C2

X
c3

9
C3

Y
dc

a
DC

c
QE

d
Qe

e
QF

i
Qf

f
QG

j
Qg

g
QI

k
Qi

h
Qb

l
QB

m
5B

w
5b

n
4D

s
4d

o
4F

t
4f

p
4G

u
4g

q
4I

v
4i

r
7a

x
7A

Membrane

We predict this structure to be a membrane protein.
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MPP-beta

Cytochrome b

Cytochrome c1, heme protein

UQCRQ

UQCR10

Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial

COXEG1

COXEG3

COXEG5

COXEG8

COXEG10

COX5c

COX6a

COX6b-1

COX7c

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Putative NADH dehydrogenase subunit 6

COX4

UQCRFS1

UQCRH

UQCRB

UQCR9

Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial

COX5b-2

COXEG4

COXEG6

COXEG7

COXEG9

COX7a

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