SMTL ID : 7q21.1

III2-IV2 respiratory supercomplex from Corynebacterium glutamicum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

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

Ligands

14 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 14 residues within 4Å: Chain B: L.106, I.109, S.113, L.164, M.165, H.168, K.169 Chain G: W.59, L.105, F.112, L.116, K.119 Chain J: W.278 Ligands: CDL.8 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:L.106, B:I.109, B:L.164, G:L.105, G:F.112 Salt bridges: B:H.168, B:H.168, B:K.169, B:K.169, G:K.120 CDL.8: 21 residues within 4Å: Chain B: V.157, M.158, V.161, M.165, K.169 Chain D: M.123, I.126, F.127, T.130, K.131, L.134, V.138 Chain G: L.108, F.112 Chain J: V.271, A.274, A.275, M.277, W.278 Ligands: CDL.1, CDL.43 17 PLIP interactions: 3 interactions with chain G, 2 interactions with chain J, 4 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: G:L.108, G:F.112, G:F.112, J:A.275, B:V.157, B:V.161, D:M.123, D:I.126, D:I.126, D:F.127, D:F.127, D:F.127, D:T.130 Hydrogen bonds: J:R.282 Salt bridges: B:K.169, B:K.169, D:K.131 CDL.18: 29 residues within 4Å: Chain B: V.25, T.29, F.32, H.152, A.159, V.162, R.166, A.179, V.182, V.183, Y.186 Chain D: S.90, M.99, V.103, L.122, L.125, I.129, L.132, N.133 Chain F: F.119, P.120, R.121, L.122, I.181, V.184, I.188, L.229 Chain W: A.45 Ligands: 7PH.2 26 PLIP interactions: 11 interactions with chain B, 9 interactions with chain F, 6 interactions with chain D Hydrophobic interactions: B:F.32, B:F.32, B:F.32, B:F.32, B:F.32, B:V.162, B:V.182, B:V.183, B:Y.186, F:L.122, F:I.181, F:V.184, F:I.188, F:L.229, D:V.103, D:L.122, D:I.129, D:I.129, D:L.132 Salt bridges: B:R.166, B:R.166, F:R.121 Hydrogen bonds: F:F.119, F:R.121, F:L.122, D:N.133 CDL.23: 25 residues within 4Å: Chain F: A.23, R.24, G.26, S.27, K.28, A.29, M.32, M.44, I.46, I.47, M.48, F.50, S.51, F.52, F.54, F.419, F.492, V.496, W.500, R.501 Chain I: F.417, I.418, R.421 Ligands: 9XX.5, 9YF.33 17 PLIP interactions: 2 interactions with chain I, 15 interactions with chain F Hydrophobic interactions: I:I.418, F:I.46, F:I.47, F:I.47, F:I.47, F:M.48, F:F.50, F:F.52, F:F.54, F:F.419, F:F.492 Salt bridges: I:R.421, F:R.501 Hydrogen bonds: F:A.23, F:G.26, F:K.28, F:A.29 CDL.39: 18 residues within 4Å: Chain I: H.31, W.32, F.123, R.359, P.360, R.361, V.371, L.374, I.378, G.411, T.419, C.423, L.426 Chain J: V.273, M.277, R.282 Ligands: 9YF.33, CDL.43 14 PLIP interactions: 11 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:W.32, I:F.123, I:V.371, I:V.371, I:T.419, J:V.273 Hydrogen bonds: I:R.359, I:R.359, I:R.361, J:R.282 Salt bridges: I:H.31, I:R.359, I:R.361, J:R.282 CDL.41: 19 residues within 4Å: Chain I: R.22, Q.23, K.26, A.218, A.221, L.222, W.224, Y.225 Chain S: L.10, Y.14, T.15, M.16, S.18, G.19, I.20, R.22 Ligands: MQ9.38, CDL.80, MQ9.84 14 PLIP interactions: 4 interactions with chain S, 10 interactions with chain I Hydrophobic interactions: S:L.10, S:I.20, I:A.218, I:A.221, I:L.222, I:W.224, I:W.224, I:Y.225 Hydrogen bonds: S:G.19, I:Q.23, I:Y.225 Salt bridges: S:R.22, I:R.22, I:K.26 CDL.43: 18 residues within 4Å: Chain D: I.94, W.95, A.97, A.98, F.105, L.124, F.127, K.131 Chain F: W.30, M.33 Chain I: R.361, L.426, K.479 Chain J: L.270, M.277, R.282 Ligands: CDL.8, CDL.39 9 PLIP interactions: 6 interactions with chain D, 2 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: D:I.94, D:W.95, D:F.105, D:L.124, D:L.124 Salt bridges: D:K.131, J:R.282, I:R.361 Hydrogen bonds: J:R.282 CDL.46: 14 residues within 4Å: Chain L: I.109, V.161, L.164, M.165, H.168, K.169 Chain Q: W.59, L.108, F.112, L.116, K.119, K.120 Chain T: W.278 Ligands: CDL.54 13 PLIP interactions: 8 interactions with chain L, 4 interactions with chain Q, 1 interactions with chain T Hydrophobic interactions: L:I.109, L:V.161, L:L.164, L:L.164, Q:L.108, Q:F.112, T:W.278 Salt bridges: L:H.168, L:H.168, L:K.169, L:K.169, Q:K.119, Q:K.120 CDL.54: 22 residues within 4Å: Chain L: V.157, M.158, V.161, M.165, K.169 Chain N: M.123, I.126, F.127, T.130, K.131, L.134, V.138 Chain Q: L.108, F.112 Chain S: F.264 Chain T: V.271, A.274, A.275, M.277, W.278 Ligands: CDL.46, CDL.87 16 PLIP interactions: 9 interactions with chain N, 4 interactions with chain L, 1 interactions with chain S, 1 interactions with chain T, 1 interactions with chain Q Hydrophobic interactions: N:M.123, N:I.126, N:I.126, N:F.127, N:F.127, N:F.127, L:V.157, L:V.161, S:F.264, T:A.275, Q:L.108 Hydrogen bonds: N:K.131, N:L.134 Salt bridges: N:K.131, L:K.169, L:K.169 CDL.63: 24 residues within 4Å: Chain L: V.25, T.29, F.32, E.36, A.159, V.162, R.166, A.179, V.182, V.183, Y.186 Chain N: V.103, L.122, L.125, I.129, L.132, N.133 Chain P: F.119, P.120, R.121, L.122, I.181, I.188 Chain X: A.45 19 PLIP interactions: 8 interactions with chain L, 4 interactions with chain P, 7 interactions with chain N Hydrophobic interactions: L:T.29, L:F.32, L:F.32, L:V.162, L:V.182, L:Y.186, P:I.181, N:V.103, N:L.122, N:L.125, N:I.129, N:I.129, N:L.132 Hydrogen bonds: L:A.175, P:R.121, P:L.122, N:N.133 Salt bridges: L:R.166, P:R.121 CDL.69: 24 residues within 4Å: Chain P: A.23, R.24, K.25, G.26, S.27, K.28, A.29, M.32, M.33, M.44, I.46, I.47, F.50, F.54, V.415, F.492, V.496, W.500, R.501 Chain S: F.417, I.418, R.421 Ligands: 9YF.79, CDL.87 16 PLIP interactions: 15 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:M.44, P:I.46, P:I.47, P:I.47, P:F.50, P:F.54, P:V.415, P:F.492, S:I.418 Hydrogen bonds: P:G.26, P:S.27, P:K.28, P:A.29, P:R.501 Salt bridges: P:K.28, P:K.28 CDL.80: 14 residues within 4Å: Chain I: Y.14, M.16, G.19, I.20, R.22 Chain S: R.22, Q.23, K.26, I.137, A.221, W.224, Y.225 Ligands: CDL.41, MQ9.84 12 PLIP interactions: 8 interactions with chain S, 4 interactions with chain I Hydrophobic interactions: S:I.137, S:W.224, S:W.224, S:Y.225, I:Y.14, I:Y.14, I:I.20 Hydrogen bonds: S:R.22, S:Q.23 Salt bridges: S:R.22, S:K.26, I:R.22 CDL.85: 18 residues within 4Å: Chain S: H.31, W.32, F.123, R.359, P.360, R.361, V.371, L.374, I.378, T.419, L.422, C.423, L.426 Chain T: L.270, M.277, R.282 Ligands: 9YF.79, CDL.87 15 PLIP interactions: 11 interactions with chain S, 4 interactions with chain T Hydrophobic interactions: S:F.123, S:V.371, S:L.374, S:T.419, S:L.422, T:L.270, T:L.270 Hydrogen bonds: S:R.359, S:R.359, S:R.361, T:R.282 Salt bridges: S:H.31, S:R.359, S:R.361, T:R.282 CDL.87: 19 residues within 4Å: Chain N: I.94, W.95, A.97, A.98, F.105, L.124, F.127, K.131 Chain P: W.30, M.33 Chain S: R.361, L.422, L.426 Chain T: L.270, M.277, R.282 Ligands: CDL.54, CDL.69, CDL.85 10 PLIP interactions: 1 interactions with chain S, 6 interactions with chain N, 3 interactions with chain T Hydrophobic interactions: S:L.422, N:I.94, N:W.95, N:F.105, N:L.124, N:F.127, T:L.270 Salt bridges: N:K.131, T:R.282 Hydrogen bonds: T:R.282

16 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.2: 9 residues within 4Å: Chain B: Y.123, V.127, T.132, I.133, Q.134, F.143 Chain D: I.118 Chain F: L.241 Ligands: CDL.18 Ligand excluded by PLIP 7PH.4: 17 residues within 4Å: Chain C: W.28, L.31, K.32, T.35, A.39, I.42, F.46 Chain I: M.118, L.119, F.122, L.337, Y.340, F.347, L.369, A.373 Ligands: TWT.6, 9XX.42 Ligand excluded by PLIP 7PH.13: 17 residues within 4Å: Chain D: H.114, Y.115, W.116, V.120 Chain I: T.381, G.385, V.388, Q.392, F.393 Chain J: L.252, L.255, V.258, A.259, L.262, F.263, V.266, F.267 Ligand excluded by PLIP 7PH.16: 8 residues within 4Å: Chain E: A.56, N.59, F.60, W.63, A.67, I.71, V.123, F.127 Ligand excluded by PLIP 7PH.24: 12 residues within 4Å: Chain E: I.74, L.78, L.103, N.106, L.109, L.113 Chain F: F.343, V.346, G.347, W.350, T.561 Ligands: HAS.19 Ligand excluded by PLIP 7PH.25: 6 residues within 4Å: Chain A: X.15, X.20 Chain F: V.295, F.299, A.300, S.303 Ligand excluded by PLIP 7PH.26: 11 residues within 4Å: Chain E: W.76, L.80, I.83 Chain F: W.356, I.361, V.364, G.365, A.368, F.436, F.440 Chain Y: S.59 Ligand excluded by PLIP 7PH.27: 11 residues within 4Å: Chain C: I.77 Chain F: L.431, L.487, I.490, P.491, I.493, W.494, F.497 Chain Y: A.42, I.46, W.49 Ligand excluded by PLIP 7PH.47: 10 residues within 4Å: Chain L: Y.123, V.127, T.132, I.133, Q.134, F.143, F.148 Chain N: L.106 Chain P: Y.237, L.241 Ligand excluded by PLIP 7PH.49: 18 residues within 4Å: Chain M: W.28, L.31, K.32, T.35, L.38, A.39, I.42, F.46 Chain S: M.118, L.119, F.122, Y.340, F.347, A.373, I.409 Ligands: TWT.51, 9XX.52, TRD.86 Ligand excluded by PLIP 7PH.59: 18 residues within 4Å: Chain N: H.114, Y.115, W.116, V.120, M.123 Chain S: T.381, G.385, V.388, Q.392, F.393 Chain T: L.252, L.255, V.258, A.259, L.262, F.263, V.266, F.267 Ligand excluded by PLIP 7PH.62: 8 residues within 4Å: Chain O: A.56, N.59, F.60, W.63, A.67, I.71, V.123, F.127 Ligand excluded by PLIP 7PH.70: 11 residues within 4Å: Chain O: W.76, I.83 Chain P: W.356, I.361, V.364, A.368, F.436, W.437, F.440, H.444 Chain Z: S.59 Ligand excluded by PLIP 7PH.71: 5 residues within 4Å: Chain K: X.12, X.28 Chain P: V.295, F.299, S.303 Ligand excluded by PLIP 7PH.72: 8 residues within 4Å: Chain O: L.78, N.106, L.109, L.113 Chain P: F.292, F.343, G.347, W.350 Ligand excluded by PLIP 7PH.92: 12 residues within 4Å: Chain P: L.431, I.434, L.438, L.487, P.491, I.493, W.494, K.498 Chain Z: A.42, I.46, W.49 Ligands: HAS.66 Ligand excluded by PLIP

18 x TRD: TRIDECANE(Non-covalent)(Non-functional Binders)

TRD.3: 5 residues within 4Å: Chain B: F.48, T.200, I.204 Ligands: TRD.7, TRD.9 Ligand excluded by PLIP TRD.7: 3 residues within 4Å: Chain D: V.47 Ligands: TRD.3, TRD.10 Ligand excluded by PLIP TRD.9: 7 residues within 4Å: Chain B: F.44 Chain D: I.23, M.27, W.40, V.44 Ligands: TRD.3, TRD.10 Ligand excluded by PLIP TRD.10: 6 residues within 4Å: Chain D: V.20, I.23, F.24, V.47 Ligands: TRD.7, TRD.9 Ligand excluded by PLIP TRD.11: 5 residues within 4Å: Chain A: X.41, X.63 Chain D: I.21, F.24 Ligands: TRD.12 Ligand excluded by PLIP TRD.12: 8 residues within 4Å: Chain A: X.41 Chain D: F.24, A.25, H.28, V.29 Chain F: P.325, F.326 Ligands: TRD.11 Ligand excluded by PLIP TRD.29: 3 residues within 4Å: Chain G: N.149, W.152 Chain S: L.3 Ligand excluded by PLIP TRD.30: 7 residues within 4Å: Chain G: S.151, L.157, A.167 Chain Q: Y.117 Chain S: M.247, P.248, V.252 Ligand excluded by PLIP TRD.32: 5 residues within 4Å: Chain G: R.141, I.144 Chain S: G.7, D.11, M.16 Ligand excluded by PLIP TRD.40: 4 residues within 4Å: Chain C: A.39 Chain I: L.369, A.413 Ligands: TWT.6 Ligand excluded by PLIP TRD.48: 5 residues within 4Å: Chain L: F.48, R.51, T.200 Ligands: TRD.53, TRD.55 Ligand excluded by PLIP TRD.53: 2 residues within 4Å: Ligands: TRD.48, TRD.56 Ligand excluded by PLIP TRD.55: 4 residues within 4Å: Chain N: I.23, W.40, V.44 Ligands: TRD.48 Ligand excluded by PLIP TRD.56: 3 residues within 4Å: Chain N: F.24, V.47 Ligands: TRD.53 Ligand excluded by PLIP TRD.57: 3 residues within 4Å: Chain N: I.21, F.24 Ligands: TRD.58 Ligand excluded by PLIP TRD.58: 7 residues within 4Å: Chain K: X.38, X.39 Chain N: A.25, H.28 Chain P: F.326, F.329 Ligands: TRD.57 Ligand excluded by PLIP TRD.78: 8 residues within 4Å: Chain G: Y.117 Chain I: P.248, V.252 Chain Q: L.148, W.152, S.155, L.157, A.167 Ligand excluded by PLIP TRD.86: 7 residues within 4Å: Chain M: L.31 Chain S: L.369, M.372, A.413, Y.416 Ligands: 7PH.49, TWT.51 Ligand excluded by PLIP

4 x 9XX: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate(Non-covalent)

9XX.5: 11 residues within 4Å: Chain C: V.59, I.62, W.63, V.66, L.70 Chain F: F.141, L.142 Chain H: C.32 Ligands: CDL.23, 9YF.33, PLM.34 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:I.62, C:W.63, C:W.63, C:W.63, C:V.66, C:L.70, F:F.141, F:L.142 9XX.42: 9 residues within 4Å: Chain C: F.46, F.52 Chain I: W.311, E.312, L.313, W.325, M.329 Chain U: C.1 Ligands: 7PH.4 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain C Hydrophobic interactions: I:W.311, I:L.313, I:W.325, I:W.325, C:F.46, C:F.52 9XX.50: 10 residues within 4Å: Chain M: V.59, I.62, W.63, V.66, L.70 Chain P: F.141, L.142 Chain R: C.32 Ligands: PLM.73, 9YF.79 6 PLIP interactions: 5 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:I.62, M:W.63, M:W.63, M:W.63, M:L.70, P:L.142 9XX.52: 13 residues within 4Å: Chain M: F.46, G.49, F.52 Chain S: M.308, W.311, L.313, W.325, V.328, M.329, I.332 Chain V: C.1 Ligands: 7PH.49, PLM.91 8 PLIP interactions: 8 interactions with chain S Hydrophobic interactions: S:W.311, S:W.311, S:W.325, S:W.325, S:W.325, S:V.328, S:M.329, S:I.332

2 x TWT: DOCOSANE(Non-covalent)

TWT.6: 13 residues within 4Å: Chain C: A.39, G.40, S.43, L.71 Chain I: L.333, M.372, A.373, F.376, I.409, P.412, A.413 Ligands: 7PH.4, TRD.40 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:A.373, I:F.376, I:P.412, I:A.413, C:A.39 TWT.51: 13 residues within 4Å: Chain M: A.39, G.40, S.43 Chain S: L.333, L.337, A.373, F.376, Y.377, I.409, P.412, A.413 Ligands: 7PH.49, TRD.86 7 PLIP interactions: 1 interactions with chain M, 6 interactions with chain S Hydrophobic interactions: M:A.39, S:L.333, S:A.373, S:F.376, S:Y.377, S:P.412, S:A.413

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

CU.14: 6 residues within 4Å: Chain E: C.285, E.287, C.289, H.293, M.296 Ligands: CU.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.285, E:E.287, E:C.289, E:H.293 CU.15: 5 residues within 4Å: Chain E: H.244, C.285, C.289, M.296 Ligands: CU.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.244, E:C.285, E:C.289 CU.21: 4 residues within 4Å: Chain F: H.265, H.314, H.315 Ligands: HAS.19 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.265, F:H.314, F:H.315 CU.60: 6 residues within 4Å: Chain O: C.285, E.287, C.289, H.293, M.296 Ligands: CU.61 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.285, O:E.287, O:C.289, O:H.293 CU.61: 5 residues within 4Å: Chain O: H.244, C.285, C.289, M.296 Ligands: CU.60 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:H.244, O:C.285, O:C.289 CU.67: 3 residues within 4Å: Chain P: H.265, H.314, H.315 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:H.265, P:H.314, P:H.315

2 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 2 residues within 4Å: Chain E: E.287 Chain F: D.391 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.287 MG.64: 4 residues within 4Å: Chain O: D.256, E.287 Chain P: Y.155, D.391 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain O Metal complexes: P:D.391, O:E.287

4 x HAS: HEME-AS(Non-covalent)

HAS.19: 34 residues within 4Å: Chain E: V.64, A.68, I.71, I.120, L.124 Chain F: W.152, W.261, V.268, Y.269, A.272, H.314, H.315, S.335, T.338, G.339, F.370, L.371, G.374, G.377, I.378, L.380, A.381, D.386, A.390, L.395, H.398, F.399, T.402, L.403, T.406, R.460 Ligands: HAS.20, CU.21, 7PH.24 23 PLIP interactions: 20 interactions with chain F, 3 interactions with chain E, Hydrophobic interactions: F:V.268, F:A.272, F:T.338, F:F.370, F:L.371, F:I.378, F:I.378, F:I.378, F:L.380, F:F.399, F:F.399, F:L.403, F:L.403, F:L.403, E:V.64, E:I.71, E:I.71 Hydrogen bonds: F:Y.269, F:H.315, F:H.315 Salt bridges: F:R.460 pi-Stacking: F:H.314 Metal complexes: F:H.398 HAS.20: 27 residues within 4Å: Chain F: F.53, F.54, G.57, L.58, A.60, L.61, R.64, F.84, H.87, G.88, M.91, G.151, W.152, Y.393, I.396, F.399, H.400, L.403, F.447, Q.450, R.460, R.461, S.482, L.485, G.486, V.489 Ligands: HAS.19 21 PLIP interactions: 21 interactions with chain F, Hydrophobic interactions: F:F.53, F:F.53, F:F.54, F:A.60, F:L.61, F:F.84, F:M.91, F:F.399, F:F.399, F:L.485, F:L.485, F:V.489 Hydrogen bonds: F:R.64, F:F.84, F:W.152, F:Q.450, F:R.461 Salt bridges: F:R.460, F:R.461 Metal complexes: F:H.87, F:H.400 HAS.65: 34 residues within 4Å: Chain O: A.67, A.68, I.71, M.75, P.117, I.120, L.124 Chain P: W.152, W.261, H.265, Y.269, A.272, H.314, H.315, S.335, T.338, G.339, F.370, L.371, G.374, L.375, G.377, I.378, L.380, A.381, D.386, A.390, L.395, H.398, F.399, T.402, L.403, T.406, R.460 23 PLIP interactions: 18 interactions with chain P, 5 interactions with chain O, Hydrophobic interactions: P:W.261, P:A.272, P:T.338, P:F.370, P:F.370, P:I.378, P:L.380, P:L.395, P:F.399, P:F.399, P:L.403, P:L.403, P:L.403, O:A.68, O:I.71, O:I.71, O:P.117, O:L.124 Hydrogen bonds: P:Y.269, P:Y.269, P:D.386 Salt bridges: P:R.460 pi-Stacking: P:H.314 HAS.66: 29 residues within 4Å: Chain P: F.53, F.54, G.57, L.58, A.60, L.61, I.63, R.64, F.80, F.84, H.87, G.88, M.91, L.92, G.151, W.152, I.396, F.399, H.400, F.404, V.408, F.447, R.460, R.461, S.482, L.485, G.486, V.489 Ligands: 7PH.92 23 PLIP interactions: 23 interactions with chain P, Hydrophobic interactions: P:F.53, P:F.53, P:A.60, P:L.61, P:F.84, P:M.91, P:L.92, P:I.396, P:F.399, P:F.399, P:F.404, P:V.408, P:F.447, P:V.489, P:V.489 Hydrogen bonds: P:F.84, P:W.152 Salt bridges: P:R.460, P:R.461 pi-Stacking: P:F.399, P:F.447 Metal complexes: P:H.87, P:H.400

2 x CA: CALCIUM ION(Non-covalent)

CA.22: 4 residues within 4Å: Chain F: E.66, T.69, G.71, Q.73 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.66, F:E.66, F:T.69, F:G.71 CA.68: 4 residues within 4Å: Chain P: E.66, T.69, G.71, Q.73 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.66, P:T.69, P:G.71

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

FES.28: 8 residues within 4Å: Chain G: C.333, H.335, I.336, C.338, C.352, C.354, H.355, S.357 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.333, G:H.335, G:C.352, G:H.355 FES.76: 9 residues within 4Å: Chain Q: C.333, H.335, I.336, C.338, C.352, C.354, H.355, Q.356, S.357 4 PLIP interactions: 4 interactions with chain Q, Metal complexes: Q:C.333, Q:H.335, Q:C.352, Q:H.355

6 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.31: 20 residues within 4Å: Chain G: T.177, I.178, P.181, M.182 Chain I: M.151, M.168, R.199 Chain Q: S.103, I.107 Chain S: L.49, T.50, V.52, Y.53, L.56, F.98, I.99, M.102, F.262, A.266 Ligands: MQ9.37 9 PLIP interactions: 6 interactions with chain S, 2 interactions with chain G, 1 interactions with chain Q Hydrophobic interactions: S:L.49, S:L.49, S:T.50, S:Y.53, S:F.98, S:A.266, G:T.177, G:I.178, Q:I.107 MQ9.37: 12 residues within 4Å: Chain I: F.150, I.167, M.168, I.171, T.301, D.302, A.327, L.330, I.332, V.335, T.339 Ligands: MQ9.31 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:F.150, I:I.167, I:I.171, I:D.302, I:A.327, I:L.330, I:I.332 MQ9.38: 13 residues within 4Å: Chain I: E.38, Y.42, L.48, L.49, L.213, A.217, L.220, F.250, A.254, F.262 Ligands: HEM.36, CDL.41, MQ9.84 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:E.38, I:Y.42, I:Y.42, I:L.48, I:L.49, I:L.49, I:A.217, I:L.220, I:F.250, I:F.262 Hydrogen bonds: I:Y.42 MQ9.75: 19 residues within 4Å: Chain G: S.103, I.107 Chain I: L.49, T.50, V.52, Y.53, L.56, F.98, I.99, M.102, F.262, A.266 Chain Q: T.177, I.178, P.181, M.182 Chain S: F.200, A.203, I.207 12 PLIP interactions: 3 interactions with chain S, 2 interactions with chain Q, 1 interactions with chain G, 6 interactions with chain I Hydrophobic interactions: S:F.200, S:A.203, S:I.207, Q:T.177, Q:I.178, G:I.107, I:L.49, I:T.50, I:Y.53, I:L.56, I:F.98, I:A.266 MQ9.83: 6 residues within 4Å: Chain S: F.150, I.167, M.168, I.171, T.301, V.335 5 PLIP interactions: 5 interactions with chain S Hydrophobic interactions: S:F.150, S:I.167, S:I.171, S:I.171, S:V.335 MQ9.84: 17 residues within 4Å: Chain I: A.210, I.211, G.214, A.218, A.221 Chain S: L.41, Y.42, I.45, A.217, L.220, A.221, W.224, A.254 Ligands: MQ9.38, CDL.41, CDL.80, HEM.82 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain S Hydrophobic interactions: I:A.210, I:I.211, I:A.218, I:A.221, S:L.41, S:L.41, S:I.45, S:A.217, S:L.220, S:A.254

4 x 9YF: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate(Non-covalent)

9YF.33: 21 residues within 4Å: Chain C: V.59, E.60, W.63 Chain F: L.142 Chain H: C.32, S.33, I.37, Q.39 Chain I: S.396, N.398, A.399, W.402, I.403, I.406, V.410, I.414, I.418 Chain J: S.192 Ligands: 9XX.5, CDL.23, CDL.39 17 PLIP interactions: 2 interactions with chain J, 11 interactions with chain I, 1 interactions with chain C, 2 interactions with chain H, 1 interactions with chain F Hydrogen bonds: J:S.192, J:S.192, I:S.396, I:N.398, H:I.37, H:Q.39 Hydrophobic interactions: I:W.402, I:I.403, I:I.403, I:I.406, I:I.406, I:V.410, I:I.414, I:I.414, I:I.418, C:W.63, F:L.142 9YF.74: 13 residues within 4Å: Chain G: L.176, A.180, G.183, G.184, I.186, K.187, N.188 Chain I: W.181 Chain Q: Y.74, I.75, W.79 Chain S: E.92, R.94 11 PLIP interactions: 4 interactions with chain S, 2 interactions with chain Q, 1 interactions with chain I, 4 interactions with chain G Hydrogen bonds: S:E.92, S:R.94, S:R.94, G:N.188 Salt bridges: S:R.94 Hydrophobic interactions: Q:Y.74, Q:I.75, I:W.181, G:L.176, G:A.180, G:I.186 9YF.77: 13 residues within 4Å: Chain G: W.79 Chain I: E.92, V.93, R.94 Chain Q: I.179, M.182, G.183, G.184, I.186, K.187, N.188, N.191 Chain S: L.185 10 PLIP interactions: 4 interactions with chain Q, 5 interactions with chain I, 1 interactions with chain S Hydrophobic interactions: Q:I.179, S:L.185 Hydrogen bonds: Q:G.184, Q:K.187, Q:N.188, I:E.92, I:R.94, I:R.94, I:R.94 Salt bridges: I:R.94 9YF.79: 21 residues within 4Å: Chain M: V.59, E.60, W.63 Chain P: L.142 Chain R: C.32, S.33, I.37, Q.39 Chain S: S.396, N.398, A.399, W.402, I.403, I.406, V.410, I.414, I.418 Chain T: S.192 Ligands: 9XX.50, CDL.69, CDL.85 16 PLIP interactions: 8 interactions with chain S, 1 interactions with chain P, 2 interactions with chain R, 3 interactions with chain M, 2 interactions with chain T Hydrophobic interactions: S:W.402, S:I.403, S:I.406, S:I.414, S:I.414, S:I.418, P:L.142, M:W.63, M:W.63, M:W.63 Hydrogen bonds: S:S.396, S:N.398, R:I.37, R:Q.39, T:S.192, T:S.192

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.34: 7 residues within 4Å: Chain F: L.55, M.59, Q.82, L.83, F.141 Chain H: C.32 Ligands: 9XX.5 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain F Hydrogen bonds: H:C.32, F:Q.82 Hydrophobic interactions: F:L.55, F:L.83, F:F.141, F:F.141 PLM.73: 6 residues within 4Å: Chain P: L.55, M.59, Q.82, L.83, F.141 Ligands: 9XX.50 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:L.55, P:L.83, P:F.141, P:F.141, P:F.141 Hydrogen bonds: P:Q.82 PLM.90: 3 residues within 4Å: Chain I: L.313, Y.314 Chain U: C.1 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain U Hydrogen bonds: I:Y.314, U:C.1 PLM.91: 4 residues within 4Å: Chain S: L.313, Y.314 Chain V: C.1 Ligands: 9XX.52 2 PLIP interactions: 1 interactions with chain S, 1 interactions with chain V Hydrophobic interactions: S:L.313 Hydrogen bonds: V:C.1

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

HEM.35: 25 residues within 4Å: Chain I: L.47, L.48, G.51, V.52, L.54, T.55, F.58, R.100, H.103, H.104, A.107, F.110, E.148, G.149, G.152, Y.153, L.155, P.156, H.204, V.205, P.209, L.212, N.275, Y.297 Chain S: L.206 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain S, Hydrophobic interactions: I:L.47, I:L.47, I:L.48, I:V.52, I:F.58, I:F.110, I:E.148, I:Y.153, I:L.155, I:V.205, I:V.205, I:P.209, I:L.212, S:L.206 Hydrogen bonds: I:N.275 Salt bridges: I:R.100, I:R.100, I:H.104 pi-Stacking: I:H.204 Metal complexes: I:H.103, I:H.204 HEM.36: 24 residues within 4Å: Chain I: F.34, G.37, A.40, L.41, M.114, H.117, M.118, R.120, I.121, A.126, R.131, N.134, W.135, G.138, V.139, L.141, I.142, I.216, H.219, L.220, V.223, H.228, T.229 Ligands: MQ9.38 22 PLIP interactions: 22 interactions with chain I, Hydrophobic interactions: I:A.40, I:L.41, I:I.121, I:I.121, I:I.121, I:W.135, I:V.139, I:L.141, I:I.142, I:I.216, I:V.223, I:V.223 Hydrogen bonds: I:G.37, I:T.229 Salt bridges: I:H.117, I:R.120, I:R.120, I:R.131, I:H.228, I:H.228 Metal complexes: I:H.117, I:H.219 HEM.81: 24 residues within 4Å: Chain I: L.206 Chain S: F.44, L.47, L.48, G.51, V.52, L.54, T.55, I.89, R.100, H.103, H.104, A.107, E.148, G.149, G.152, Y.153, P.156, H.204, V.205, P.209, L.212, N.275, Y.297 19 PLIP interactions: 18 interactions with chain S, 1 interactions with chain I, Hydrophobic interactions: S:F.44, S:L.47, S:L.47, S:V.52, S:L.54, S:E.148, S:Y.153, S:V.205, S:V.205, S:P.209, S:L.212, I:L.206 Hydrogen bonds: S:N.275 Salt bridges: S:R.100, S:R.100, S:H.104 pi-Stacking: S:H.204 Metal complexes: S:H.103, S:H.204 HEM.82: 23 residues within 4Å: Chain S: F.34, G.37, A.40, L.41, M.114, H.117, M.118, R.120, I.121, A.126, R.131, N.134, W.135, G.138, V.139, L.141, I.216, H.219, L.220, V.223, H.228, T.229 Ligands: MQ9.84 22 PLIP interactions: 22 interactions with chain S, Hydrophobic interactions: S:A.40, S:L.41, S:I.121, S:I.121, S:I.121, S:W.135, S:V.139, S:L.141, S:I.216, S:L.220, S:V.223, S:V.223 Hydrogen bonds: S:G.37, S:T.229 Salt bridges: S:H.117, S:R.120, S:R.120, S:R.131, S:H.228, S:H.228 Metal complexes: S:H.117, S:H.219

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.44: 23 residues within 4Å: Chain H: T.40, Q.43, V.44, A.45, A.46 Chain J: A.66, C.67, C.70, H.71, R.81, P.83, L.85, V.88, A.92, V.93, Q.96, V.97, M.102, P.103, I.104, A.111, I.126, Q.216 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain H, Hydrophobic interactions: J:A.66, J:L.85, J:L.85, J:V.88, J:Q.96, J:V.97, J:P.103, J:I.104, J:I.104, J:I.104, J:I.104, J:I.126, H:Q.43 Metal complexes: J:H.71 HEC.45: 26 residues within 4Å: Chain G: Y.343 Chain J: F.95, R.101, Q.110, R.113, N.176, C.177, C.180, H.181, L.190, Y.195, A.196, P.197, N.198, A.202, I.207, A.210, M.211, P.215, Q.216, N.217, M.218, P.219, F.221, I.234, I.238 16 PLIP interactions: 16 interactions with chain J, Hydrophobic interactions: J:F.95, J:L.190, J:A.196, J:I.207, J:I.207, J:A.210, J:P.215, J:M.218, J:F.221, J:I.234, J:I.234, J:I.238 Salt bridges: J:R.101, J:R.101, J:R.113 Metal complexes: J:H.181 HEC.88: 23 residues within 4Å: Chain R: T.40, Q.43, V.44, A.45, A.46 Chain T: A.66, C.67, C.70, H.71, R.81, P.83, L.85, V.88, A.92, V.93, Q.96, V.97, M.102, P.103, I.104, A.111, I.126, Q.216 15 PLIP interactions: 13 interactions with chain T, 2 interactions with chain R, Hydrophobic interactions: T:A.66, T:P.83, T:L.85, T:L.85, T:V.88, T:Q.96, T:V.97, T:P.103, T:I.104, T:I.104, T:I.126, R:Q.43 Hydrogen bonds: T:Q.216, R:V.44 Metal complexes: T:H.71 HEC.89: 27 residues within 4Å: Chain Q: Y.343 Chain T: F.95, Q.96, R.101, Q.110, R.113, F.173, N.176, C.177, C.180, H.181, L.190, Y.195, A.196, P.197, N.198, L.199, A.202, A.210, M.211, P.215, Q.216, M.218, P.219, F.221, I.234, I.238 22 PLIP interactions: 22 interactions with chain T, Hydrophobic interactions: T:F.95, T:F.173, T:F.173, T:L.190, T:A.196, T:P.197, T:L.199, T:L.199, T:A.202, T:A.210, T:P.215, T:Q.216, T:M.218, T:P.219, T:F.221, T:I.238 Hydrogen bonds: T:Q.96, T:Q.216 Salt bridges: T:R.101, T:R.101, T:R.113 Metal complexes: T:H.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moe, A. et al., The respiratory supercomplex from C. glutamicum. Structure (2022)

Release Date

2022-02-02

Peptides

Co-purified unknown transmembrane helices built as polyALA (AscD): AK
Cytochrome c oxidase subunit 3: BL
Uncharacterized membrane protein Cgl2017/cg2211: CM
Cytochrome c oxidase polypeptide 4: DN
Cytochrome c oxidase subunit 2: EO
Cytochrome c oxidase subunit 1: FP
Cytochrome bc1 complex Rieske iron-sulfur subunit: GQ
Uncharacterized protein Cgl2664/cg2949: HR
Cytochrome bc1 complex cytochrome b subunit: IS
Cytochrome bc1 complex cytochrome c subunit: JT
Co-purified unknown peptide built as polyALA (AscE): U
Co-purified unknown peptide built as polyALA (AscE): V
Actinobacterial supercomplex, subunit C (AscC): WX
Hypothetical membrane protein: YZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

K
y

B
E

L
e

C
H

M
h

D
F

N
f

E
G

O
g

F
D

P
d

G
A

Q
a

H
L

R
l

I
B

S
b

J
C

T
c

U
X

V
x

W
V

X
v

Y
K

Z
k

Membrane

We predict this structure to be a membrane protein.
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Co-purified unknown transmembrane helices built as polyALA (AscD)

Cytochrome c oxidase subunit 3

Uncharacterized membrane protein Cgl2017/cg2211

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 1

Cytochrome bc1 complex Rieske iron-sulfur subunit

Uncharacterized protein Cgl2664/cg2949

Cytochrome bc1 complex cytochrome b subunit

Cytochrome bc1 complex cytochrome c subunit

Co-purified unknown peptide built as polyALA (AscE)

Co-purified unknown peptide built as polyALA (AscE)

Actinobacterial supercomplex, subunit C (AscC)

Hypothetical membrane protein

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