SMTL ID : 9bpb.1

Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae

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-mer

Ligands

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 11 residues within 4Å: Chain A: H.345, K.349, M.454, M.455, R.456 Chain C: R.4, I.17, H.222 Chain J: W.33 Ligands: 6PH.2, PCF.18 8 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 1 interactions with chain J Hydrogen bonds: A:R.456 Salt bridges: A:H.345, A:K.349, A:R.456, C:R.4, C:H.222 Hydrophobic interactions: C:I.17, J:W.33 CDL.12: 17 residues within 4Å: Chain C: Y.28, V.231, L.235 Chain D: S.279, Y.281, L.282, I.285, K.288, K.289 Chain G: H.85 Chain H: I.40, N.43, A.44, N.47, R.51 Ligands: CDL.14, CDL.15 9 PLIP interactions: 3 interactions with chain H, 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: H:I.40, D:L.282, D:I.285, C:Y.28, C:L.235 Hydrogen bonds: H:N.47, H:R.51 Salt bridges: D:K.288, D:K.289 CDL.14: 10 residues within 4Å: Chain D: W.286 Chain E: K.44, K.51, Y.55, M.59 Chain H: K.35, P.36, L.37 Ligands: CDL.12, CN3.25 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:Y.55 Hydrogen bonds: E:Y.55, H:P.36 Salt bridges: E:K.44, E:K.51 CDL.15: 13 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, M.91, F.236 Chain G: H.85 Chain H: S.48, R.51, F.52, Q.55 Ligands: 8PE.3, CDL.12 7 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C, 4 interactions with chain H Salt bridges: G:H.85, H:R.51, H:R.51, H:R.51, H:R.51 Hydrophobic interactions: C:F.236 Hydrogen bonds: C:Y.28 CDL.35: 11 residues within 4Å: Chain 4: W.33 Chain V: H.345, K.349, M.454, M.455, R.456 Chain X: R.4, I.17, H.222 Ligands: 6PH.36, PCF.51 8 PLIP interactions: 3 interactions with chain X, 4 interactions with chain V, 1 interactions with chain 4 Hydrophobic interactions: X:I.17, 4:W.33 Salt bridges: X:R.4, X:H.222, V:H.345, V:K.349, V:R.456 Hydrogen bonds: V:R.456 CDL.45: 17 residues within 4Å: Chain 1: H.85 Chain 2: I.40, N.43, A.44, N.47, R.51 Chain X: Y.28, V.231, L.235 Chain Y: S.279, Y.281, L.282, I.285, K.288, K.289 Ligands: CDL.47, CDL.48 9 PLIP interactions: 4 interactions with chain Y, 3 interactions with chain 2, 2 interactions with chain X Hydrophobic interactions: Y:L.282, Y:I.285, 2:I.40, X:Y.28, X:L.235 Salt bridges: Y:K.288, Y:K.289 Hydrogen bonds: 2:N.47, 2:R.51 CDL.47: 10 residues within 4Å: Chain 2: K.35, P.36, L.37 Chain Y: W.286 Chain Z: K.44, K.51, Y.55, M.59 Ligands: CDL.45, CN3.58 5 PLIP interactions: 4 interactions with chain Z, 1 interactions with chain 2 Hydrophobic interactions: Z:Y.55 Hydrogen bonds: Z:Y.55, 2:P.36 Salt bridges: Z:K.44, Z:K.51 CDL.48: 13 residues within 4Å: Chain 1: H.85 Chain 2: S.48, R.51, F.52, Q.55 Chain X: N.27, Y.28, W.29, M.32, M.91, F.236 Ligands: 8PE.37, CDL.45 7 PLIP interactions: 2 interactions with chain X, 1 interactions with chain 1, 4 interactions with chain 2 Hydrophobic interactions: X:F.236 Hydrogen bonds: X:Y.28 Salt bridges: 1:H.85, 2:R.51, 2:R.51, 2:R.51, 2:R.51

2 x 6PH: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate(Non-covalent)

6PH.2: 13 residues within 4Å: Chain A: S.450 Chain C: L.38, H.222, I.226, F.227, D.229, L.230 Chain D: K.291 Chain E: V.60, M.63 Ligands: CDL.1, PEF.10, PCF.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.226, C:D.229 Salt bridges: C:H.222, D:K.291 6PH.36: 13 residues within 4Å: Chain V: S.450 Chain X: L.38, H.222, I.226, F.227, D.229, L.230 Chain Y: K.291 Chain Z: V.60, M.63 Ligands: CDL.35, PEF.43, PCF.51 4 PLIP interactions: 1 interactions with chain Y, 3 interactions with chain X Salt bridges: Y:K.291, X:H.222 Hydrophobic interactions: X:I.226, X:D.229

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.3: 7 residues within 4Å: Chain C: W.29, K.99, Y.102, Y.103 Chain G: E.82 Chain H: Q.55 Ligands: CDL.15 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.29 Hydrogen bonds: C:Y.102, G:E.82 8PE.37: 7 residues within 4Å: Chain 1: E.82 Chain 2: Q.55 Chain X: W.29, K.99, Y.102, Y.103 Ligands: CDL.48 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain 1 Hydrophobic interactions: X:W.29 Hydrogen bonds: X:Y.102, 1:E.82

1 x CN5: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate(Non-covalent)

CN5.4: 7 residues within 4Å: Chain C: L.12, Y.16, M.199 Chain X: L.12, Y.16, I.195, M.199 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain X Hydrogen bonds: C:Y.16 Hydrophobic interactions: X:Y.16, X:Y.16

4 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL(Non-covalent)

UQ6.5: 14 residues within 4Å: Chain C: I.122, L.123, I.125, A.126, F.129, L.130, I.147, L.165, F.179, L.182, L.185, I.189, F.296 Ligands: UQ6.42 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.123, C:I.189 UQ6.9: 16 residues within 4Å: Chain C: Y.16, I.17, Q.22, S.34, G.37, L.40, V.41, I.44, F.49, L.198, L.201, M.221, D.229 Chain X: L.185 Ligands: HEM.6, UQ6.38 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain X Hydrophobic interactions: C:I.17, C:L.40, C:V.41, C:I.44, C:F.49, X:L.185 UQ6.38: 14 residues within 4Å: Chain X: I.122, L.123, I.125, A.126, F.129, L.130, I.147, L.165, F.179, L.182, L.185, I.189, F.296 Ligands: UQ6.9 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:L.123, X:I.189 UQ6.42: 16 residues within 4Å: Chain C: L.185 Chain X: Y.16, I.17, Q.22, S.34, G.37, L.40, V.41, I.44, F.49, L.198, L.201, M.221, D.229 Ligands: UQ6.5, HEM.39 6 PLIP interactions: 5 interactions with chain X, 1 interactions with chain C Hydrophobic interactions: X:I.17, X:L.40, X:V.41, X:I.44, X:F.49, C:L.185

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

HEM.6: 24 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.9 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:F.89, C:L.113, C:W.114, C:L.198, C:L.201 Hydrogen bonds: C:W.30, C:G.33, C:S.105, C:S.105, C:S.207 Salt bridges: C:H.96, C:K.99, C:K.99 Metal complexes: C:H.96, C:H.197 HEM.8: 23 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, C.134, V.135, F.180, H.183, Y.184, P.187 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.48, C:A.86, C:F.180, C:Y.184 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.183 Metal complexes: C:H.82, C:H.183 HEM.39: 24 residues within 4Å: Chain X: W.30, G.33, S.34, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.42 17 PLIP interactions: 17 interactions with chain X, Hydrophobic interactions: X:L.36, X:L.36, X:F.89, X:L.113, X:W.114, X:L.198, X:L.201 Hydrogen bonds: X:W.30, X:G.33, X:S.105, X:S.105, X:S.207 Salt bridges: X:H.96, X:K.99, X:K.99 Metal complexes: X:H.96, X:H.197 HEM.41: 23 residues within 4Å: Chain X: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, C.134, V.135, F.180, H.183, Y.184, P.187 12 PLIP interactions: 12 interactions with chain X, Hydrophobic interactions: X:L.40, X:Q.43, X:I.48, X:A.86, X:F.180, X:Y.184 Salt bridges: X:R.79, X:R.79 pi-Stacking: X:H.82, X:H.183 Metal complexes: X:H.82, X:H.183

2 x 9PE: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(Non-covalent)

9PE.7: 8 residues within 4Å: Chain C: F.3, S.6, N.7, Y.9 Chain X: T.112, N.115, I.119, M.196 6 PLIP interactions: 4 interactions with chain X, 2 interactions with chain C Hydrophobic interactions: X:I.119 Hydrogen bonds: X:T.112, X:T.112, X:N.115, C:S.6, C:N.7 9PE.40: 8 residues within 4Å: Chain C: T.112, N.115, I.119, M.196 Chain X: F.3, S.6, N.7, Y.9 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain X Hydrophobic interactions: C:I.119 Hydrogen bonds: C:T.112, C:T.112, C:N.115, X:S.6, X:N.7

6 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.10: 11 residues within 4Å: Chain C: I.42, N.74, L.81, M.237 Chain D: L.269, K.272, T.273, I.276 Chain E: S.73, T.77 Ligands: 6PH.2 8 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: C:I.42, C:I.42, C:L.81, D:T.273 Hydrogen bonds: C:N.74, E:S.73, E:T.77 Salt bridges: D:K.272 PEF.19: 8 residues within 4Å: Chain E: E.76, I.79 Chain J: F.44, G.47, W.48, P.49 Chain X: D.160, W.164 6 PLIP interactions: 3 interactions with chain X, 1 interactions with chain E, 2 interactions with chain J Hydrophobic interactions: X:W.164, X:W.164, E:I.79, J:W.48, J:W.48 Hydrogen bonds: X:D.160 PEF.26: 9 residues within 4Å: Chain K: L.334, L.339, I.342, F.414, W.415 Chain L: L.58 Chain O: N.88, S.92 Chain U: W.43 10 PLIP interactions: 7 interactions with chain K, 1 interactions with chain L, 1 interactions with chain U, 1 interactions with chain O Hydrophobic interactions: K:L.334, K:I.342, K:F.414, K:W.415, K:W.415, K:W.415, K:W.415, L:L.58, U:W.43 Hydrogen bonds: O:N.88 PEF.43: 11 residues within 4Å: Chain X: I.42, N.74, L.81, M.237 Chain Y: L.269, K.272, T.273, I.276 Chain Z: S.73, T.77 Ligands: 6PH.36 8 PLIP interactions: 4 interactions with chain X, 2 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: X:I.42, X:I.42, X:L.81, Y:T.273 Hydrogen bonds: X:N.74, Z:S.73, Z:T.77 Salt bridges: Y:K.272 PEF.52: 8 residues within 4Å: Chain 4: F.44, G.47, W.48, P.49 Chain C: D.160, W.164 Chain Z: E.76, I.79 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain Z, 2 interactions with chain 4 Hydrophobic interactions: C:W.164, C:W.164, Z:I.79, 4:W.48, 4:W.48 Hydrogen bonds: C:D.160 PEF.59: 9 residues within 4Å: Chain 5: L.334, L.339, I.342, F.414, W.415 Chain 6: L.58 Chain 9: N.88, S.92 Chain f: W.43 10 PLIP interactions: 7 interactions with chain 5, 1 interactions with chain 9, 1 interactions with chain f, 1 interactions with chain 6 Hydrophobic interactions: 5:L.334, 5:I.342, 5:F.414, 5:W.415, 5:W.415, 5:W.415, 5:W.415, f:W.43, 6:L.58 Hydrogen bonds: 9:N.88

2 x HEC: HEME C(Non-covalent)

HEC.11: 23 residues within 4Å: Chain D: V.100, C.101, C.104, H.105, N.169, A.172, L.173, P.174, P.175, L.177, I.180, R.184, Y.190, I.191, L.194, L.195, F.218, I.223, A.224, M.225, V.228, V.251, L.255 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:P.175, D:I.180, D:I.191, D:V.251, D:L.255 Hydrogen bonds: D:Y.190, D:A.224 Salt bridges: D:R.184 pi-Cation interactions: D:H.105, D:H.105 Metal complexes: D:H.105 HEC.44: 23 residues within 4Å: Chain Y: V.100, C.101, C.104, H.105, N.169, A.172, L.173, P.174, P.175, L.177, I.180, R.184, Y.190, I.191, L.194, L.195, F.218, I.223, A.224, M.225, V.228, V.251, L.255 11 PLIP interactions: 11 interactions with chain Y, Hydrophobic interactions: Y:P.175, Y:I.180, Y:I.191, Y:V.251, Y:L.255 Hydrogen bonds: Y:Y.190, Y:A.224 Salt bridges: Y:R.184 pi-Cation interactions: Y:H.105, Y:H.105 Metal complexes: Y:H.105

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

FES.13: 9 residues within 4Å: Chain E: C.159, H.161, L.162, G.163, C.164, C.178, C.180, H.181, S.183 1 PLIP interactions: 1 interactions with chain E, Metal complexes: E:H.181 FES.46: 9 residues within 4Å: Chain Z: C.159, H.161, L.162, G.163, C.164, C.178, C.180, H.181, S.183 1 PLIP interactions: 1 interactions with chain Z, Metal complexes: Z:H.181

8 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.16: 8 residues within 4Å: Chain H: Q.38, G.39, F.41, H.42, V.45 Chain O: S.93, K.97, A.100 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain O Hydrophobic interactions: H:F.41, H:V.45, O:K.97, O:A.100 Hydrogen bonds: H:F.41, H:F.41 Salt bridges: O:K.97 PCF.18: 13 residues within 4Å: Chain A: D.428, S.453, M.455 Chain E: Y.57, G.64, S.68, A.71 Chain I: F.11, N.14, F.17, V.18 Ligands: CDL.1, 6PH.2 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I, 1 interactions with chain E Salt bridges: A:D.428 Hydrogen bonds: I:N.14 Hydrophobic interactions: E:A.71 PCF.33: 20 residues within 4Å: Chain K: S.204, T.208, L.212, F.216 Chain M: Y.189, T.190, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.214 Chain T: W.108, T.114, L.115, F.116, N.118, N.122 7 PLIP interactions: 2 interactions with chain M, 3 interactions with chain T, 2 interactions with chain K Hydrophobic interactions: M:L.214, K:F.216, K:F.216 Hydrogen bonds: M:I.196, T:T.114, T:T.114, T:F.116 PCF.34: 11 residues within 4Å: Chain K: V.423, Y.452, V.453, I.456 Chain L: Y.21 Chain U: A.56, V.57, F.60, S.61, K.62, A.63 10 PLIP interactions: 3 interactions with chain K, 5 interactions with chain U, 2 interactions with chain L Hydrophobic interactions: K:V.423, K:I.456, U:A.56, U:V.57, U:F.60, U:F.60 pi-Cation interactions: K:Y.452 Hydrogen bonds: U:S.61, L:Y.21, L:Y.21 PCF.49: 8 residues within 4Å: Chain 2: Q.38, G.39, F.41, H.42, V.45 Chain 9: S.93, K.97, A.100 7 PLIP interactions: 4 interactions with chain 2, 3 interactions with chain 9 Hydrophobic interactions: 2:F.41, 2:V.45, 9:K.97, 9:A.100 Hydrogen bonds: 2:F.41, 2:F.41 Salt bridges: 9:K.97 PCF.51: 13 residues within 4Å: Chain 3: F.11, N.14, F.17, V.18 Chain V: D.428, S.453, M.455 Chain Z: Y.57, G.64, S.68, A.71 Ligands: CDL.35, 6PH.36 3 PLIP interactions: 1 interactions with chain 3, 1 interactions with chain V, 1 interactions with chain Z Hydrogen bonds: 3:N.14 Salt bridges: V:D.428 Hydrophobic interactions: Z:A.71 PCF.66: 20 residues within 4Å: Chain 5: S.204, T.208, L.212, F.216 Chain 7: Y.189, T.190, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.214 Chain e: W.108, T.114, L.115, F.116, N.118, N.122 7 PLIP interactions: 2 interactions with chain 7, 2 interactions with chain 5, 3 interactions with chain e Hydrophobic interactions: 7:L.214, 5:F.216, 5:F.216 Hydrogen bonds: 7:I.196, e:T.114, e:T.114, e:F.116 PCF.67: 11 residues within 4Å: Chain 5: V.423, Y.452, V.453, I.456 Chain 6: Y.21 Chain f: A.56, V.57, F.60, S.61, K.62, A.63 10 PLIP interactions: 5 interactions with chain f, 3 interactions with chain 5, 2 interactions with chain 6 Hydrophobic interactions: f:A.56, f:V.57, f:F.60, f:F.60, 5:V.423, 5:I.456 Hydrogen bonds: f:S.61, 6:Y.21, 6:Y.21 pi-Cation interactions: 5:Y.452

10 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.17: 6 residues within 4Å: Chain D: F.82 Chain I: A.35, I.36, W.39 Chain O: A.111, M.115 6 PLIP interactions: 1 interactions with chain O, 4 interactions with chain I, 1 interactions with chain D Hydrophobic interactions: O:A.111, I:A.35, I:I.36, I:W.39, I:W.39, D:F.82 PTY.23: 11 residues within 4Å: Chain K: F.95, R.97, I.98 Chain M: H.15, V.26, W.65, F.66, I.69, H.79, F.94 Ligands: PTY.31 10 PLIP interactions: 6 interactions with chain M, 4 interactions with chain K Hydrophobic interactions: M:V.26, M:W.65, M:F.66, M:F.66, M:F.94 Hydrogen bonds: M:E.72, K:F.95, K:R.97, K:I.98 Salt bridges: K:R.97 PTY.28: 11 residues within 4Å: Chain K: F.268, F.321, L.324, A.325 Chain L: L.53, G.78, I.81, W.85 Chain R: K.11, V.14, I.15 7 PLIP interactions: 4 interactions with chain L, 1 interactions with chain K, 2 interactions with chain R Hydrophobic interactions: L:L.53, L:I.81, L:I.81, L:W.85, K:F.321, R:V.14, R:V.14 PTY.30: 11 residues within 4Å: Chain K: H.429, W.450 Chain L: T.19, P.20, Y.21, A.22, C.23 Chain R: F.36 Chain U: P.54, G.55, Y.58 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain U, 1 interactions with chain K, 1 interactions with chain R Hydrogen bonds: L:C.23 Hydrophobic interactions: U:P.54, K:H.429, R:F.36 PTY.31: 20 residues within 4Å: Chain M: S.62, F.66, I.69, V.70, A.73, T.74, H.79, I.87, F.91, M.218, M.222, V.225, R.229, H.234, L.235, H.239, H.240, V.241, G.242 Ligands: PTY.23 12 PLIP interactions: 12 interactions with chain M Hydrophobic interactions: M:F.66, M:F.66, M:F.66, M:I.87, M:F.91, M:V.225 Hydrogen bonds: M:H.234, M:V.241, M:G.242 Salt bridges: M:H.79, M:R.229, M:H.239 PTY.50: 6 residues within 4Å: Chain 3: A.35, I.36, W.39 Chain 9: A.111, M.115 Chain Y: F.82 6 PLIP interactions: 4 interactions with chain 3, 1 interactions with chain Y, 1 interactions with chain 9 Hydrophobic interactions: 3:A.35, 3:I.36, 3:W.39, 3:W.39, Y:F.82, 9:A.111 PTY.56: 11 residues within 4Å: Chain 5: F.95, R.97, I.98 Chain 7: H.15, V.26, W.65, F.66, I.69, H.79, F.94 Ligands: PTY.64 10 PLIP interactions: 4 interactions with chain 5, 6 interactions with chain 7 Hydrogen bonds: 5:F.95, 5:R.97, 5:I.98, 7:E.72 Salt bridges: 5:R.97 Hydrophobic interactions: 7:V.26, 7:W.65, 7:F.66, 7:F.66, 7:F.94 PTY.61: 11 residues within 4Å: Chain 5: F.268, F.321, L.324, A.325 Chain 6: L.53, G.78, I.81, W.85 Chain c: K.11, V.14, I.15 7 PLIP interactions: 4 interactions with chain 6, 1 interactions with chain 5, 2 interactions with chain c Hydrophobic interactions: 6:L.53, 6:I.81, 6:I.81, 6:W.85, 5:F.321, c:V.14, c:V.14 PTY.63: 11 residues within 4Å: Chain 5: H.429, W.450 Chain 6: T.19, P.20, Y.21, A.22, C.23 Chain c: F.36 Chain f: P.54, G.55, Y.58 4 PLIP interactions: 1 interactions with chain 5, 1 interactions with chain c, 1 interactions with chain f, 1 interactions with chain 6 Hydrophobic interactions: 5:H.429, c:F.36, f:P.54 Hydrogen bonds: 6:C.23 PTY.64: 20 residues within 4Å: Chain 7: S.62, F.66, I.69, V.70, A.73, T.74, H.79, I.87, F.91, M.218, M.222, V.225, R.229, H.234, L.235, H.239, H.240, V.241, G.242 Ligands: PTY.56 12 PLIP interactions: 12 interactions with chain 7 Hydrophobic interactions: 7:F.66, 7:F.66, 7:F.66, 7:I.87, 7:F.91, 7:V.225 Hydrogen bonds: 7:H.234, 7:V.241, 7:G.242 Salt bridges: 7:H.79, 7:R.229, 7:H.239

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

HEA.20: 32 residues within 4Å: Chain K: I.23, G.26, T.30, S.33, I.36, R.37, V.59, H.62, A.63, M.66, I.67, L.70, V.71, G.126, W.127, Y.371, V.374, F.377, H.378, L.381, S.382, I.386, L.389, F.390, I.417, I.424, F.425, R.438, R.439, A.461, L.465, F.468 27 PLIP interactions: 27 interactions with chain K, Hydrophobic interactions: K:V.59, K:A.63, K:M.66, K:I.67, K:L.70, K:V.71, K:I.386, K:I.386, K:L.389, K:L.389, K:F.390, K:F.390, K:F.390, K:F.425, K:L.465 Hydrogen bonds: K:S.33, K:R.37, K:W.127, K:R.439, K:I.440 Salt bridges: K:R.438, K:R.439 pi-Stacking: K:H.62, K:H.62, K:F.377, K:H.378 Metal complexes: K:H.62 HEA.22: 35 residues within 4Å: Chain K: W.127, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, I.312, A.313, T.316, G.317, I.320, F.321, F.348, T.349, G.352, L.353, G.355, V.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain L: I.50, V.54, P.89, I.92, L.93 21 PLIP interactions: 18 interactions with chain K, 3 interactions with chain L, Hydrophobic interactions: K:W.127, K:V.244, K:V.244, K:I.248, K:I.248, K:T.316, K:I.320, K:T.349, K:L.353, K:V.356, K:F.377, K:F.377, K:V.380, L:P.89, L:I.92, L:L.93 Hydrogen bonds: K:W.127, K:H.291 Salt bridges: K:H.291, K:H.368, K:R.438 HEA.53: 32 residues within 4Å: Chain 5: I.23, G.26, T.30, S.33, I.36, R.37, V.59, H.62, A.63, M.66, I.67, L.70, V.71, G.126, W.127, Y.371, V.374, F.377, H.378, L.381, S.382, I.386, L.389, F.390, I.417, I.424, F.425, R.438, R.439, A.461, L.465, F.468 27 PLIP interactions: 27 interactions with chain 5, Hydrophobic interactions: 5:V.59, 5:A.63, 5:M.66, 5:I.67, 5:L.70, 5:V.71, 5:I.386, 5:I.386, 5:L.389, 5:L.389, 5:F.390, 5:F.390, 5:F.390, 5:F.425, 5:L.465 Hydrogen bonds: 5:S.33, 5:R.37, 5:W.127, 5:R.439, 5:I.440 Salt bridges: 5:R.438, 5:R.439 pi-Stacking: 5:H.62, 5:H.62, 5:F.377, 5:H.378 Metal complexes: 5:H.62 HEA.55: 35 residues within 4Å: Chain 5: W.127, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, I.312, A.313, T.316, G.317, I.320, F.321, F.348, T.349, G.352, L.353, G.355, V.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain 6: I.50, V.54, P.89, I.92, L.93 21 PLIP interactions: 18 interactions with chain 5, 3 interactions with chain 6, Hydrophobic interactions: 5:W.127, 5:V.244, 5:V.244, 5:I.248, 5:I.248, 5:T.316, 5:I.320, 5:T.349, 5:L.353, 5:V.356, 5:F.377, 5:F.377, 5:V.380, 6:P.89, 6:I.92, 6:L.93 Hydrogen bonds: 5:W.127, 5:H.291 Salt bridges: 5:H.291, 5:H.368, 5:R.438

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

CU.21: 4 residues within 4Å: Chain K: H.241, V.244, H.290, H.291 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:H.241, K:H.290, K:H.291 CU.54: 4 residues within 4Å: Chain 5: H.241, V.244, H.290, H.291 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:H.241, 5:H.290, 5:H.291

2 x CA: CALCIUM ION(Non-covalent)

CA.24: 5 residues within 4Å: Chain K: E.39, A.42, G.44, S.45, Q.46 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.39, K:A.42, K:G.44 CA.57: 5 residues within 4Å: Chain 5: E.39, A.42, G.44, S.45, Q.46 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:E.39, 5:A.42, 5:G.44

2 x CN3: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate(Non-covalent)

CN3.25: 8 residues within 4Å: Chain H: K.35 Chain K: N.406, K.408, L.467, Y.470, K.487 Chain O: F.94 Ligands: CDL.14 8 PLIP interactions: 7 interactions with chain K, 1 interactions with chain H Hydrophobic interactions: K:L.467, K:Y.470 Hydrogen bonds: K:N.406, K:K.408, K:K.408 Salt bridges: K:K.408, K:K.487, H:K.35 CN3.58: 8 residues within 4Å: Chain 2: K.35 Chain 5: N.406, K.408, L.467, Y.470, K.487 Chain 9: F.94 Ligands: CDL.47 8 PLIP interactions: 7 interactions with chain 5, 1 interactions with chain 2 Hydrophobic interactions: 5:L.467, 5:Y.470 Hydrogen bonds: 5:N.406, 5:K.408, 5:K.408 Salt bridges: 5:K.408, 5:K.487, 2:K.35

2 x MG: MAGNESIUM ION(Non-covalent)

MG.27: 4 residues within 4Å: Chain K: H.368 Chain L: D.187, D.198, E.223 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.223 MG.60: 4 residues within 4Å: Chain 5: H.368 Chain 6: D.187, D.198, E.223 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:E.223

2 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.29: 6 residues within 4Å: Chain L: H.186, C.221, E.223, C.225, H.229, M.232 6 PLIP interactions: 6 interactions with chain L Metal complexes: L:C.221, L:C.221, L:E.223, L:C.225, L:C.225, L:H.229 CUA.62: 6 residues within 4Å: Chain 6: H.186, C.221, E.223, C.225, H.229, M.232 6 PLIP interactions: 6 interactions with chain 6 Metal complexes: 6:C.221, 6:C.221, 6:E.223, 6:C.225, 6:C.225, 6:H.229

2 x ZN: ZINC ION(Non-covalent)

ZN.32: 4 residues within 4Å: Chain N: C.111, H.119, C.134, C.137 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.111, N:H.119, N:C.134 ZN.65: 4 residues within 4Å: Chain 8: C.111, H.119, C.134, C.137 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:C.111, 8:H.119, 8:C.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eldeeb, M.H. et al., Differential substrate utilization by yeast respiratory supercomplexes. To Be Published

Release Date

2025-05-21

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AV
Cytochrome b-c1 complex subunit 2, mitochondrial: BW
Cytochrome b: CX
Cytochrome c1, heme protein, mitochondrial: DY
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EZ
Cytochrome b-c1 complex subunit 6, mitochondrial: F0
Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial: G1
Cytochrome b-c1 complex subunit 8, mitochondrial: H2
Cytochrome b-c1 complex subunit 9, mitochondrial: I3
Cytochrome b-c1 complex subunit 10, mitochondrial: J4
Cytochrome c oxidase subunit 1: K5
Cytochrome c oxidase subunit 2: L6
Cytochrome c oxidase subunit 3: M7
Cytochrome c oxidase subunit 4, mitochondrial: N8
Cytochrome c oxidase subunit 5A, mitochondrial: O9
Cytochrome c oxidase subunit 6, mitochondrial: Pa
Cytochrome c oxidase subunit 7, mitochondrial: Qb
Cytochrome c oxidase subunit 9, mitochondrial: Rc
Cytochrome c oxidase subunit 12, mitochondrial: Sd
Cytochrome c oxidase subunit 13, mitochondrial: Te
Cytochrome c oxidase subunit 26, mitochondrial: Uf

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

V
K

B
B

W
L

C
C

X
M

D
D

Y
N

E
E

Z
O

F
F

0
P

G
G

1
Q

H
H

2
R

I
I

3
S

J
J

4
T

K
a

5
m

L
b

6
n

M
c

7
o

N
d

8
p

O
e

9
q

P
f

a
r

Q
g

b
s

R
i

c
u

S
j

d
v

T
k

e
w

U
l

f
x

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial

Cytochrome b-c1 complex subunit 8, mitochondrial

Cytochrome b-c1 complex subunit 9, mitochondrial

Cytochrome b-c1 complex subunit 10, mitochondrial

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

Cytochrome c oxidase subunit 12, mitochondrial

Cytochrome c oxidase subunit 13, mitochondrial

Cytochrome c oxidase subunit 26, mitochondrial

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