SMTL ID : 6hu9.1

III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

PEF.1: 18 residues within 4Å: Chain A: S.424, S.427, M.429 Chain C: S.34, G.37, M.221, H.222, I.226, F.227, L.230 Chain D: K.230 Chain E: V.30, M.33, S.37 Ligands: UQ6.4, CDL.5, PEF.10, PCF.18 Ligand excluded by PLIP PEF.6: 15 residues within 4Å: Chain C: F.3, S.6, N.7, V.8, Y.9, L.10, V.13 Chain M: T.112, N.115, V.116, I.119, M.193, M.196, I.203 Ligands: UQ6.4 Ligand excluded by PLIP PEF.7: 10 residues within 4Å: Chain A: N.279, H.319, F.320, W.431 Chain C: A.2, F.3, V.13 Chain J: R.17 Ligands: UQ6.4, CDL.5 Ligand excluded by PLIP PEF.10: 20 residues within 4Å: Chain C: V.41, I.42, V.45, N.74, I.77, L.81, M.237, A.241, F.245 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47 Ligands: PEF.1 Ligand excluded by PLIP PEF.13: 12 residues within 4Å: Chain E: V.45, E.46, I.49, S.50, T.53 Chain J: F.44, G.47, W.48, P.49 Chain M: D.160, I.161, W.164 Ligand excluded by PLIP PEF.16: 8 residues within 4Å: Chain C: V.320, L.321, F.324 Chain G: K.40 Chain H: K.52, S.53, L.56, Y.57 Ligand excluded by PLIP PEF.22: 16 residues within 4Å: Chain K: S.424, S.427, M.429 Chain M: S.34, M.221, H.222, I.226, F.227, L.230, M.237 Chain N: K.230 Chain O: M.33, S.37 Ligands: CDL.19, PEF.28, PCF.35 Ligand excluded by PLIP PEF.23: 12 residues within 4Å: Chain C: T.112, N.115, I.119, I.189, M.193, M.196 Chain M: F.3, N.7, Y.9, L.10, V.13, I.195 Ligand excluded by PLIP PEF.24: 8 residues within 4Å: Chain K: H.319, F.320, W.431 Chain M: A.2, F.3, V.13 Chain T: R.17 Ligands: CDL.19 Ligand excluded by PLIP PEF.28: 14 residues within 4Å: Chain M: V.41, I.42, N.74, M.237 Chain N: L.208, K.211, T.212, I.215 Chain O: G.40, S.43, T.44, T.47, F.48 Ligands: PEF.22 Ligand excluded by PLIP PEF.31: 10 residues within 4Å: Chain C: D.160, I.161, W.164 Chain O: E.46, I.49, S.50, T.53 Chain T: F.44, W.48, P.49 Ligand excluded by PLIP PEF.33: 10 residues within 4Å: Chain M: V.320, L.321, I.370 Chain Q: L.35, K.40 Chain R: K.52, S.53, F.55, L.56, Y.57 Ligand excluded by PLIP PEF.41: 13 residues within 4Å: Chain 2: K.10, V.13, I.14, F.21 Chain U: F.268, F.321, L.324, A.325 Chain V: I.60, I.66, I.69, W.70, F.73 Ligand excluded by PLIP PEF.42: 12 residues within 4Å: Chain 5: A.56, V.57, F.60, S.61, K.62 Chain U: V.423, Y.452, V.453, I.456 Chain V: Y.6 Ligands: PEF.50, PCF.51 Ligand excluded by PLIP PEF.43: 17 residues within 4Å: Chain U: F.95, P.96, R.97, I.98, L.160 Chain W: H.15, V.17, V.26, S.62, W.65, F.66, I.69, I.87, G.90, F.91, F.94 Ligands: PEF.47 Ligand excluded by PLIP PEF.46: 16 residues within 4Å: Chain 2: W.31, F.35 Chain 5: L.51, P.54, G.55, Y.58 Chain U: T.354, H.429, F.430, I.433, W.450 Chain V: P.5, Y.6, C.8, M.29 Chain Y: S.128 Ligand excluded by PLIP PEF.47: 16 residues within 4Å: Chain W: F.66, I.69, V.70, A.73, T.74, I.87, M.222, V.225, R.229, H.234, T.236, H.239, H.240, V.241, G.242 Ligands: PEF.43 Ligand excluded by PLIP PEF.48: 18 residues within 4Å: Chain 4: T.105, L.106, F.107, N.113 Chain U: T.208, L.212, F.216 Chain W: I.101, Y.189, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.211, L.214 Ligand excluded by PLIP PEF.50: 14 residues within 4Å: Chain 5: W.53 Chain U: L.334, L.339, I.342, F.414, W.415, F.418, I.419, V.423 Chain V: S.40 Chain Y: S.72, I.75, V.79 Ligands: PEF.42 Ligand excluded by PLIP PEF.52: 13 residues within 4Å: Chain 1: F.13, K.14, R.18, K.19, T.20, Y.22, S.25, F.29 Chain U: F.19, M.20, Y.393, I.400, L.401 Ligand excluded by PLIP PEF.58: 15 residues within 4Å: Chain 6: F.268, F.321, A.325 Chain 7: M.42, I.60, I.66, I.69, W.70, F.73 Chain e: K.10, V.13, I.14, I.17, V.18, F.21 Ligand excluded by PLIP PEF.59: 17 residues within 4Å: Chain 6: F.95, P.96, R.97, I.98, L.160 Chain 8: H.15, V.17, V.26, S.62, W.65, F.66, I.69, H.79, G.90, F.91, F.94 Ligands: PEF.64 Ligand excluded by PLIP PEF.62: 18 residues within 4Å: Chain 6: T.354, H.429, F.430, I.433, W.450 Chain 7: T.4, P.5, Y.6, C.8, M.29 Chain a: S.128 Chain e: W.31, F.35 Chain h: L.51, P.54, G.55, Y.58, A.63 Ligand excluded by PLIP PEF.63: 11 residues within 4Å: Chain 6: V.423, V.453, I.456 Chain 7: Y.6 Ligands: PEF.67, PCF.68 Chain h: A.56, V.57, F.60, S.61, K.62 Ligand excluded by PLIP PEF.64: 18 residues within 4Å: Chain 8: F.66, I.69, V.70, A.73, T.74, I.87, F.91, M.218, M.222, R.229, H.234, T.236, H.239, H.240, V.241, G.242, T.245 Ligands: PEF.59 Ligand excluded by PLIP PEF.65: 18 residues within 4Å: Chain 6: T.208, L.212, F.216 Chain 8: I.101, Y.189, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.211, L.214 Chain g: T.105, L.106, F.107, N.113 Ligand excluded by PLIP PEF.67: 13 residues within 4Å: Chain 6: L.334, L.339, I.342, F.414, W.415, F.418, I.419 Ligands: PEF.63 Chain a: S.72, I.75, V.79 Chain h: V.46, W.53 Ligand excluded by PLIP PEF.69: 12 residues within 4Å: Chain 6: F.19, M.20, I.400, L.401 Chain d: F.13, K.14, R.18, K.19, Y.22, S.25, H.26, F.29 Ligand excluded by PLIP

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

HEM.2: 22 residues within 4Å: Chain C: L.40, Q.43, G.47, I.48, M.50, Y.54, V.65, R.79, H.82, A.83, A.86, F.89, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, I.190, Y.274 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.48, C:Y.54, C:Y.54, C:V.65, C:A.83, C:F.89, C:F.89, C:T.127, C:F.180, C:Y.184, C:Y.184, C:I.190 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.183 Metal complexes: C:H.82, C:H.183 HEM.3: 23 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 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:F.89, C:L.113, C:W.114, C:V.118, C:I.120, C:F.121, C:L.198, C:L.201 Hydrogen bonds: C:G.33, 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.20: 22 residues within 4Å: Chain M: L.40, Q.43, I.44, G.47, I.48, M.50, V.65, R.79, H.82, A.83, A.86, F.89, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, I.190, Y.274 16 PLIP interactions: 16 interactions with chain M, Hydrophobic interactions: M:L.40, M:Q.43, M:I.44, M:I.48, M:V.65, M:A.83, M:F.89, M:F.89, M:T.127, M:F.180, M:Y.184, M:Y.184, M:I.190 Salt bridges: M:R.79 Metal complexes: M:H.82, M:H.183 HEM.21: 21 residues within 4Å: Chain M: W.30, G.33, S.34, L.36, G.37, F.89, 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.201, S.206, S.207 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:L.36, M:L.36, M:F.89, M:L.113, M:V.118, M:I.120, M:F.121, M:L.201, M:L.201 Hydrogen bonds: M:W.30, M:G.33, M:S.105, M:S.207 Salt bridges: M:H.96, M:K.99, M:K.99 Metal complexes: M:H.96, M:H.197

1 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)

UQ6.4: 17 residues within 4Å: Chain C: L.12, Y.16, I.17, L.40, V.41, I.44, V.45, I.48, V.194, I.195, L.198, M.199 Chain M: L.12, Y.16 Ligands: PEF.1, PEF.6, PEF.7 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain M Hydrophobic interactions: C:Y.16, C:I.17, C:L.40, C:V.41, C:I.44, C:V.45, C:I.48, C:V.194, C:I.195, C:L.198 Hydrogen bonds: C:Y.16, M:Y.16, M:Y.16

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 14 residues within 4Å: Chain A: H.319, K.323, M.428, M.429, W.431 Chain C: R.4, I.17, I.18, H.222 Chain I: F.22 Chain J: W.33 Ligands: PEF.1, PEF.7, PCF.18 9 PLIP interactions: 1 interactions with chain J, 3 interactions with chain C, 4 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: J:W.33, C:I.17, I:F.22 Salt bridges: C:R.4, C:H.222, A:H.319, A:K.323 Hydrogen bonds: A:M.429, A:W.431 CDL.12: 19 residues within 4Å: Chain D: W.225 Chain E: K.14, K.21, G.22, S.24, Y.25, F.28, M.29 Chain H: Q.33, K.34, P.35 Chain I: F.3, L.6, F.11 Chain Y: K.77, A.80, L.84 Ligands: CDL.15, PCF.17 14 PLIP interactions: 6 interactions with chain E, 4 interactions with chain Y, 2 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: E:F.28, E:F.28, Y:K.77, Y:A.80, Y:L.84, I:L.6, I:F.11 Hydrogen bonds: E:Y.25, H:Q.33, H:P.35 Salt bridges: E:K.14, E:K.21, E:K.21, Y:K.77 CDL.14: 18 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, L.35, F.88, M.91, V.92, M.95, L.235 Chain G: H.85 Chain H: A.43, S.47, R.50, F.51, Q.54 Ligands: PCF.8, CDL.15 12 PLIP interactions: 4 interactions with chain H, 7 interactions with chain C, 1 interactions with chain G Hydrogen bonds: H:R.50, C:Y.28, C:W.29 Salt bridges: H:R.50, H:R.50, H:R.50, G:H.85 Hydrophobic interactions: C:L.35, C:F.88, C:F.88, C:V.92, C:L.235 CDL.15: 15 residues within 4Å: Chain C: Y.28, L.235 Chain D: Y.220, L.221, I.224, K.227, K.228 Chain G: H.85 Chain H: I.39, N.42, A.43, N.46, R.50 Ligands: CDL.12, CDL.14 12 PLIP interactions: 4 interactions with chain H, 5 interactions with chain D, 1 interactions with chain G, 2 interactions with chain C Hydrogen bonds: H:N.46, H:R.50, H:R.50, G:H.85, C:Y.28 Salt bridges: H:R.50, D:K.227, D:K.228, D:K.228 Hydrophobic interactions: D:I.224, D:I.224, C:L.235 CDL.19: 13 residues within 4Å: Chain K: H.319, K.323, D.425, M.428, M.429, W.431 Chain M: R.4, I.18, H.222 Chain T: W.33 Ligands: PEF.22, PEF.24, PCF.35 9 PLIP interactions: 5 interactions with chain K, 3 interactions with chain M, 1 interactions with chain T Hydrogen bonds: K:M.429, K:W.431, K:W.431 Salt bridges: K:H.319, K:K.323, M:R.4, M:H.222 Hydrophobic interactions: M:I.18, T:W.33 CDL.27: 20 residues within 4Å: Chain M: Y.28, V.231, L.235 Chain N: S.218, Y.220, L.221, L.222, I.224, W.225, K.227, K.228 Chain Q: H.85 Chain R: I.39, N.42, A.43, N.46, S.47, R.50 Ligands: CDL.30, CDL.32 14 PLIP interactions: 8 interactions with chain N, 5 interactions with chain R, 1 interactions with chain M Hydrophobic interactions: N:L.222, N:L.222, N:I.224, N:W.225, R:I.39, M:L.235 Hydrogen bonds: N:Y.220, R:N.46, R:R.50, R:R.50 Salt bridges: N:K.227, N:K.228, N:K.228, R:R.50 CDL.30: 15 residues within 4Å: Chain N: W.225 Chain O: K.14, K.21, G.22, Y.25, F.28, M.29 Chain R: K.34, P.35, L.36, F.40 Chain S: F.3, L.6, F.11 Ligands: CDL.27 12 PLIP interactions: 7 interactions with chain O, 2 interactions with chain S, 2 interactions with chain R, 1 interactions with chain a Hydrophobic interactions: O:Y.25, O:F.28, S:L.6, S:F.11, R:F.40 Hydrogen bonds: O:Y.25, R:P.35 Salt bridges: O:K.14, O:K.21, O:K.21, O:K.21, a:K.77 CDL.32: 15 residues within 4Å: Chain M: N.27, Y.28, W.29, F.88, M.91, M.95, F.236, I.239 Chain Q: H.85 Chain R: S.47, R.50, F.51, Q.54 Ligands: PCF.25, CDL.27 9 PLIP interactions: 5 interactions with chain M, 3 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: M:F.88, M:F.88 Hydrogen bonds: M:N.27, M:Y.28, M:W.29 Salt bridges: R:R.50, R:R.50, R:R.50, Q:H.85

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

PCF.8: 14 residues within 4Å: Chain C: W.29, F.94, M.97, A.98, Y.102, Y.103, T.317, F.326, F.327, V.330 Chain G: L.41, E.82 Chain H: Q.54 Ligands: CDL.14 9 PLIP interactions: 7 interactions with chain C, 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:W.29, C:W.29, C:F.94, C:F.94, C:Y.102, C:F.326 Hydrogen bonds: C:Y.103, H:Q.54 Salt bridges: G:E.82 PCF.17: 9 residues within 4Å: Chain H: G.38, F.40, H.41, V.44 Chain Y: G.70, S.73, A.76, K.77 Ligands: CDL.12 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain Y Hydrophobic interactions: H:V.44, Y:A.76 Hydrogen bonds: H:G.38, H:F.40, H:H.41, Y:S.73 PCF.18: 16 residues within 4Å: Chain A: W.401, D.402, S.427, M.429 Chain E: Y.27, V.30, G.34, S.38, A.41 Chain I: F.11, K.12, N.14, F.17, V.18 Ligands: PEF.1, CDL.5 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I, 2 interactions with chain E Salt bridges: A:D.402 Hydrogen bonds: I:N.14 Hydrophobic interactions: E:A.41 pi-Cation interactions: E:Y.27 PCF.25: 20 residues within 4Å: Chain M: W.29, F.94, M.95, M.97, A.98, Y.102, Y.103, T.317, F.326, F.327, V.330, F.331, F.333, V.334, Y.359 Chain Q: L.41, E.82 Chain R: Q.54, V.58 Ligands: CDL.32 13 PLIP interactions: 12 interactions with chain M, 1 interactions with chain R Hydrophobic interactions: M:F.94, M:A.98, M:A.98, M:Y.102, M:F.326, M:F.327, M:F.331, M:F.333, M:V.334, M:V.334, R:V.58 Hydrogen bonds: M:Y.103, M:Y.103 PCF.34: 8 residues within 4Å: Chain R: Q.37, G.38, I.39, F.40, H.41, V.44 Chain a: S.73, K.77 8 PLIP interactions: 6 interactions with chain R, 2 interactions with chain a Hydrophobic interactions: R:F.40, R:F.40, R:V.44, a:K.77 Hydrogen bonds: R:G.38, R:F.40, R:H.41 Salt bridges: a:K.77 PCF.35: 15 residues within 4Å: Chain K: D.402, S.427, M.429 Chain O: Y.27, V.30, G.34, S.38, A.41 Chain S: F.11, K.12, N.14, F.17, V.18 Ligands: CDL.19, PEF.22 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain S, 2 interactions with chain O Salt bridges: K:D.402 Hydrogen bonds: S:N.14 Hydrophobic interactions: O:A.41 pi-Cation interactions: O:Y.27 PCF.51: 12 residues within 4Å: Chain U: Q.46, Y.452, I.456 Chain Y: G.88, A.91, V.92, R.94, M.95, G.97, G.98, D.100 Ligands: PEF.42 6 PLIP interactions: 3 interactions with chain Y, 3 interactions with chain U Hydrophobic interactions: Y:V.92, U:Y.452, U:I.456 Salt bridges: Y:R.94, Y:D.100 Hydrogen bonds: U:Y.452 PCF.68: 9 residues within 4Å: Chain 6: Y.452, I.456 Ligands: PEF.63 Chain a: F.90, A.91, R.94, M.95, G.98, D.100 4 PLIP interactions: 1 interactions with chain a, 3 interactions with chain 6 Salt bridges: a:D.100 Hydrophobic interactions: 6:I.456 Hydrogen bonds: 6:Y.452, 6:Y.452

2 x HEC: HEME C(Covalent)

HEC.9: 23 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, A.111, L.112, P.113, P.114, L.116, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, V.190, L.194 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:N.108, D:P.113, D:P.114, D:L.116, D:I.119, D:I.130, D:L.133, D:L.134, D:L.134, D:I.162, D:A.163, D:V.167, D:V.167, D:V.190, D:L.194 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEC.26: 22 residues within 4Å: Chain N: V.35, V.39, C.40, C.43, H.44, N.108, L.112, P.113, P.114, L.116, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.194 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:N.108, N:P.113, N:P.113, N:P.114, N:L.116, N:I.130, N:L.133, N:L.134, N:L.134, N:A.163, N:M.164, N:V.167, N:V.167, N:L.194 Hydrogen bonds: N:Y.129, N:Y.129, N:A.163 Salt bridges: N:R.123 Metal complexes: N:H.44

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

FES.11: 8 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, H.151, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151 FES.29: 8 residues within 4Å: Chain O: C.129, H.131, L.132, G.133, C.134, C.148, H.151, S.153 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.129, O:H.131, O:C.148, O:H.151

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

CU.36: 3 residues within 4Å: Chain U: H.241, H.290, H.291 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:H.241, U:H.290, U:H.291 CU.53: 3 residues within 4Å: Chain 6: H.241, H.290, H.291 3 PLIP interactions: 3 interactions with chain 6 Metal complexes: 6:H.241, 6:H.290, 6:H.291

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

HEA.37: 33 residues within 4Å: Chain U: F.19, 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, F.377, H.378, L.381, S.382, I.386, L.389, F.390, Y.393, I.424, F.425, M.428, R.438, R.439, I.440, A.461, L.465 36 PLIP interactions: 36 interactions with chain U, Hydrophobic interactions: U:F.19, U:F.19, U:T.30, U:V.59, U:A.63, U:M.66, U:I.67, U:I.67, U:L.70, U:V.71, U:F.377, U:F.377, U:L.381, U:I.386, U:I.386, U:L.389, U:L.389, U:F.390, U:F.390, U:F.390, U:Y.393, U:I.424, U:A.461, U:L.465, U:L.465 Hydrogen bonds: U:R.37, U:W.127, U:S.382, U:R.439, U:I.440 Salt bridges: U:R.438, U:R.439 pi-Stacking: U:F.377, U:H.378, U:F.425 Metal complexes: U:H.378 HEA.38: 29 residues within 4Å: Chain U: W.127, T.128, W.237, V.244, Y.245, I.248, H.290, T.309, A.313, T.316, G.317, I.320, G.352, 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 V: I.35, P.74, I.77, L.78 27 PLIP interactions: 23 interactions with chain U, 4 interactions with chain V, Hydrophobic interactions: U:W.237, U:V.244, U:I.248, U:T.309, U:T.316, U:I.320, U:V.356, U:V.356, U:L.358, U:A.359, U:V.373, U:F.377, U:F.377, U:F.377, U:V.380, U:L.381, V:I.35, V:P.74, V:I.77, V:L.78 Hydrogen bonds: U:W.127, U:Y.245, U:R.438 Salt bridges: U:H.368, U:R.438, U:R.439 Metal complexes: U:H.376 HEA.54: 33 residues within 4Å: Chain 6: F.19, I.23, G.26, T.30, S.33, R.37, V.59, H.62, A.63, M.66, I.67, L.70, V.71, G.126, W.127, Y.371, F.377, H.378, L.381, S.382, I.386, L.389, F.390, Y.393, I.424, F.425, M.428, R.438, R.439, I.440, A.461, L.465, F.468 32 PLIP interactions: 32 interactions with chain 6, Hydrophobic interactions: 6:I.23, 6:V.59, 6:A.63, 6:I.67, 6:I.67, 6:L.70, 6:V.71, 6:F.377, 6:L.381, 6:I.386, 6:I.386, 6:L.389, 6:F.390, 6:F.390, 6:Y.393, 6:I.424, 6:A.461, 6:L.465, 6:L.465, 6:F.468 Hydrogen bonds: 6:R.37, 6:W.127, 6:Y.371, 6:R.439, 6:I.440 Salt bridges: 6:R.438, 6:R.439 pi-Stacking: 6:F.377, 6:H.378, 6:H.378, 6:F.425 Metal complexes: 6:H.378 HEA.55: 33 residues within 4Å: Chain 6: W.127, T.128, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, 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, H.376, F.377, V.380, L.381, R.438 Chain 7: I.35, P.74, I.77, L.78 28 PLIP interactions: 4 interactions with chain 7, 24 interactions with chain 6, Hydrophobic interactions: 7:I.35, 7:P.74, 7:I.77, 7:L.78, 6:W.237, 6:V.244, 6:V.244, 6:I.248, 6:I.248, 6:T.309, 6:T.316, 6:I.320, 6:F.321, 6:F.348, 6:T.349, 6:L.353, 6:F.377, 6:F.377, 6:V.380, 6:L.381, 6:L.381 Hydrogen bonds: 6:W.127, 6:Y.245, 6:Y.245 Salt bridges: 6:H.368, 6:R.438, 6:R.439 Metal complexes: 6:H.376

2 x CA: CALCIUM ION(Non-covalent)

CA.39: 4 residues within 4Å: Chain U: E.39, A.42, G.44, P.441 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.39, U:A.42, U:G.44 CA.56: 5 residues within 4Å: Chain 6: E.39, A.42, P.43, G.44, P.441 2 PLIP interactions: 2 interactions with chain 6 Metal complexes: 6:E.39, 6:A.42

2 x MG: MAGNESIUM ION(Non-covalent)

MG.40: 3 residues within 4Å: Chain U: H.368, D.369 Chain V: E.208 4 PLIP interactions: 2 interactions with chain U, 2 interactions with chain V Metal complexes: U:H.368, U:D.369, V:E.208, V:E.208 MG.57: 3 residues within 4Å: Chain 6: H.368, D.369 Chain 7: E.208 4 PLIP interactions: 2 interactions with chain 7, 2 interactions with chain 6 Metal complexes: 7:E.208, 7:E.208, 6:H.368, 6:D.369

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

CUA.44: 5 residues within 4Å: Chain V: H.171, C.206, C.210, M.217 Ligands: CUA.45 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:H.171, V:C.206, V:C.210 CUA.45: 5 residues within 4Å: Chain V: C.206, E.208, C.210, H.214 Ligands: CUA.44 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.206, V:E.208, V:C.210, V:H.214 CUA.60: 5 residues within 4Å: Chain 7: H.171, C.206, C.210, M.217 Ligands: CUA.61 3 PLIP interactions: 3 interactions with chain 7 Metal complexes: 7:H.171, 7:C.206, 7:C.210 CUA.61: 7 residues within 4Å: Chain 7: C.206, E.208, L.209, C.210, H.214, M.217 Ligands: CUA.60 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.206, 7:E.208, 7:C.210, 7:H.214

2 x ZN: ZINC ION(Non-covalent)

ZN.49: 4 residues within 4Å: Chain X: C.86, H.94, C.109, C.112 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.86, X:H.94, X:C.109, X:C.112 ZN.66: 4 residues within 4Å: Chain 9: C.86, H.94, C.109, C.112 3 PLIP interactions: 3 interactions with chain 9 Metal complexes: 9:C.86, 9:C.109, 9:C.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hartley, A.M. et al., Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1. Nat. Struct. Mol. Biol. (2019)

Release Date

2018-12-26

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 6: FP
Cytochrome b-c1 complex subunit 7: GQ
Cytochrome b-c1 complex subunit 8: HR
Cytochrome b-c1 complex subunit 9: IS
Cytochrome b-c1 complex subunit 10: JT
Cytochrome c oxidase subunit 1: U6
Cytochrome c oxidase subunit 2: V7
Cytochrome c oxidase subunit 3: W8
Cytochrome c oxidase subunit 4, mitochondrial: X9
Cytochrome c oxidase polypeptide 5A, mitochondrial: Ya
Cytochrome c oxidase subunit 6, mitochondrial: Zb
Cytochrome c oxidase subunit 7: 0c
Cytochrome c oxidase polypeptide VIII, mitochondrial: 1d
Cytochrome c oxidase subunit 7A: 2e
Cytochrome c oxidase subunit 6B: 3f
Cytochrome c oxidase subunit 6A, mitochondrial: 4g
Cox26: 5h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
L

B
B

L
M

C
C

M
N

D
D

N
O

E
E

O
P

F
F

P
Q

G
G

Q
R

H
H

R
S

I
I

S
T

J
J

T
U

U
a

6
m

V
b

7
n

W
c

8
o

X
d

9
p

Y
e

a
q

Z
f

b
r

0
g

c
s

1
h

d
t

2
i

e
u

3
j

f
v

4
k

g
w

5
l

h
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

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase polypeptide 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7

Cytochrome c oxidase polypeptide VIII, mitochondrial

Cytochrome c oxidase subunit 7A

Cytochrome c oxidase subunit 6B

Cytochrome c oxidase subunit 6A, mitochondrial

Cox26

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