SMTL ID : 6adq.1

Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CU.1: 6 residues within 4Å: Chain A: H.232, C.273, C.277, H.281, M.284 Ligands: CU.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.273, A:C.277, A:H.281 CU.2: 6 residues within 4Å: Chain A: H.232, C.273, C.277, H.281, M.284 Ligands: CU.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.232, A:C.273, A:C.277 CU.5: 3 residues within 4Å: Chain B: H.264, H.313, H.314 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.264, B:H.313, B:H.314 CU.6: 4 residues within 4Å: Chain A: E.275 Chain B: Y.154, H.314, D.390 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.390 CU.39: 6 residues within 4Å: Chain M: H.232, C.273, C.277, H.281, M.284 Ligands: CU.40 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.273, M:C.277, M:H.281 CU.40: 6 residues within 4Å: Chain M: H.232, C.273, C.277, H.281, M.284 Ligands: CU.39 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:H.232, M:C.273, M:C.277 CU.43: 3 residues within 4Å: Chain N: H.264, H.313, H.314 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.264, N:H.313, N:H.314 CU.44: 4 residues within 4Å: Chain M: E.275 Chain N: Y.154, H.314, D.390 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.390

4 x HEA: HEME-A(Covalent)

HEA.3: 33 residues within 4Å: Chain A: V.60, P.102, I.105, I.106 Chain B: W.260, V.267, Y.268, I.270, A.271, H.313, H.314, T.330, A.334, T.337, G.338, F.341, F.342, L.370, G.373, G.376, V.377, L.379, A.380, D.385, T.389, D.390, V.394, H.397, F.398, V.401, L.402, T.405, R.459 30 PLIP interactions: 26 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:W.260, B:V.267, B:V.267, B:Y.268, B:I.270, B:A.271, B:T.330, B:T.337, B:F.341, B:F.342, B:F.342, B:V.377, B:V.377, B:A.380, B:F.398, B:F.398, B:V.401, B:L.402, B:L.402, B:L.402, A:V.60, A:P.102, A:I.105, A:I.106 Hydrogen bonds: B:Y.268, B:H.313, B:D.390 Salt bridges: B:R.459 pi-Stacking: B:H.313 Metal complexes: B:H.397 HEA.4: 32 residues within 4Å: Chain B: F.52, L.53, G.55, G.56, L.57, A.59, M.62, R.63, F.79, F.83, H.86, G.87, M.90, L.91, G.150, W.151, Y.392, I.395, F.398, H.399, L.402, F.403, I.406, F.446, R.459, R.460, Y.461, A.481, L.484, G.485, M.488 Ligands: PLM.17 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:F.52, B:L.53, B:L.57, B:A.59, B:M.90, B:L.91, B:L.91, B:W.151, B:I.395, B:F.398, B:F.398, B:L.402, B:L.402, B:F.403, B:I.406, B:F.446, B:A.481, B:L.484 Hydrogen bonds: B:W.151, B:R.460, B:Y.461 Salt bridges: B:R.459, B:R.460 Metal complexes: B:H.86 HEA.41: 33 residues within 4Å: Chain M: V.60, P.102, I.105, I.106 Chain N: W.260, V.267, Y.268, I.270, A.271, H.313, H.314, T.330, A.334, T.337, G.338, F.341, F.342, L.370, G.373, G.376, V.377, L.379, A.380, D.385, T.389, D.390, V.394, H.397, F.398, V.401, L.402, T.405, R.459 29 PLIP interactions: 25 interactions with chain N, 4 interactions with chain M, Hydrophobic interactions: N:W.260, N:V.267, N:V.267, N:Y.268, N:I.270, N:A.271, N:T.330, N:T.337, N:F.341, N:F.342, N:F.342, N:V.377, N:V.377, N:A.380, N:F.398, N:F.398, N:V.401, N:L.402, N:L.402, N:L.402, M:V.60, M:P.102, M:I.105, M:I.106 Hydrogen bonds: N:Y.268, N:D.390 Salt bridges: N:R.459 pi-Stacking: N:H.313 Metal complexes: N:H.397 HEA.42: 32 residues within 4Å: Chain N: F.52, L.53, G.55, G.56, L.57, A.59, M.62, R.63, F.79, F.83, H.86, G.87, M.90, L.91, G.150, W.151, Y.392, I.395, F.398, H.399, L.402, F.403, I.406, F.446, R.459, R.460, Y.461, A.481, L.484, G.485, M.488 Ligands: PLM.55 24 PLIP interactions: 24 interactions with chain N, Hydrophobic interactions: N:F.52, N:L.53, N:L.57, N:M.90, N:L.91, N:L.91, N:W.151, N:I.395, N:F.398, N:F.398, N:L.402, N:L.402, N:F.403, N:I.406, N:F.446, N:A.481, N:L.484 Hydrogen bonds: N:W.151, N:R.460, N:Y.461 Salt bridges: N:R.459, N:R.460 Metal complexes: N:H.86, N:H.399

18 x CDL: CARDIOLIPIN(Non-covalent)

CDL.7: 33 residues within 4Å: Chain B: F.118, P.119, R.120, L.121, L.124, L.180 Chain C: R.15, V.25, G.28, T.29, W.32, E.36, F.146, L.149, I.152, G.153, A.157, L.160, L.161, R.164, A.177, V.180, V.181, Y.184 Chain D: A.86, I.95, F.99, V.118, V.121, I.122, V.125, L.128, V.129 Ligand excluded by PLIP CDL.8: 31 residues within 4Å: Chain B: M.21, G.22, P.23, K.24, G.25, N.26, L.27, I.28, L.31, I.42, M.43, C.45, V.46, F.49, F.126, W.127, I.414, F.418, F.491, V.492, V.495, F.496, W.499, R.500 Chain J: F.424, V.425, R.428 Ligands: CDL.11, 9XX.18, CDL.22, CDL.23 Ligand excluded by PLIP CDL.10: 26 residues within 4Å: Chain D: W.91, T.123, C.126, G.127, W.134, G.135, E.137 Chain J: L.274, M.275, L.278, L.279, R.487, K.490 Chain K: I.278, V.281, A.282, G.285, V.286, M.288, W.289, R.293 Chain L: L.141 Ligands: CDL.22, CDL.23, MQ9.34, CDL.36 Ligand excluded by PLIP CDL.11: 28 residues within 4Å: Chain B: M.21, V.46, V.47, A.50, F.496 Chain G: I.45, M.48, G.51, I.83, A.85, L.86, V.87, G.88, R.89, N.90, R.94, W.98 Chain J: M.379, L.383, M.415, P.419, A.420, I.421, Y.423, F.424, R.428 Ligands: CDL.8, 9XX.18 Ligand excluded by PLIP CDL.21: 22 residues within 4Å: Chain J: I.16, Y.20, A.25, V.26, R.28, Q.29, A.221, G.224, A.225, A.228, W.231, F.232, M.254 Chain V: H.21, P.22, A.25, A.139 Ligands: 9Y0.24, MQ9.25, CDL.29, 9Y0.30, CDL.60 Ligand excluded by PLIP CDL.22: 29 residues within 4Å: Chain J: H.37, W.38, L.42, F.129, T.130, R.366, P.367, R.368, T.374, S.378, I.381, A.382, F.389, I.421, V.422, V.425, A.426, W.429, A.430, L.433 Chain K: I.284, M.288, R.293, A.294 Ligands: CDL.8, CDL.10, 9YF.16, CDL.23, MQ9.34 Ligand excluded by PLIP CDL.23: 24 residues within 4Å: Chain B: Y.29, I.32, F.131 Chain D: W.90, W.91, I.93, L.94, S.98, F.120, T.123 Chain J: R.366, R.368, W.429, L.433, P.483, L.484, K.486, R.487, K.490 Chain K: R.293 Ligands: CDL.8, CDL.10, CDL.22, MQ9.26 Ligand excluded by PLIP CDL.29: 17 residues within 4Å: Chain J: Q.12, A.15, I.16, R.19 Chain V: E.138, A.139, V.142, I.143, L.146, A.342, I.345, A.346, F.349 Ligands: CDL.21, MQ9.27, 9Y0.30, MQ9.66 Ligand excluded by PLIP CDL.36: 26 residues within 4Å: Chain C: F.107, L.108, L.111, I.152, L.155, V.156, V.159, L.162, A.163, K.166, M.167 Chain D: I.122, C.126, F.130, W.134, K.138 Chain J: L.278, F.502, L.503 Chain K: W.289 Chain L: W.92, L.138, I.145, L.149, K.153 Ligands: CDL.10 Ligand excluded by PLIP CDL.45: 33 residues within 4Å: Chain N: F.118, P.119, R.120, L.121, L.124, L.180 Chain O: R.15, V.25, G.28, T.29, W.32, E.36, F.146, L.149, I.152, G.153, A.157, L.160, L.161, R.164, A.177, V.180, V.181, Y.184 Chain P: A.86, I.95, F.99, V.118, V.121, I.122, V.125, L.128, V.129 Ligand excluded by PLIP CDL.46: 30 residues within 4Å: Chain N: M.21, G.22, P.23, K.24, G.25, N.26, L.27, I.28, L.31, I.42, M.43, C.45, V.46, F.49, W.127, I.414, F.418, F.491, V.492, V.495, F.496, W.499, R.500 Chain V: F.424, V.425, R.428 Ligands: CDL.49, 9XX.56, CDL.61, CDL.62 Ligand excluded by PLIP CDL.48: 26 residues within 4Å: Chain P: W.91, T.123, C.126, G.127, W.134, G.135, E.137 Chain V: L.274, M.275, L.278, L.279, R.487, K.490 Chain W: I.278, V.281, A.282, G.285, V.286, M.288, W.289, R.293 Chain X: L.141 Ligands: CDL.61, CDL.62, MQ9.70, CDL.73 Ligand excluded by PLIP CDL.49: 28 residues within 4Å: Chain N: M.21, V.46, V.47, A.50, F.496 Chain S: I.45, M.48, G.51, I.83, A.85, L.86, V.87, G.88, R.89, N.90, R.94, W.98 Chain V: M.379, L.383, M.415, P.419, A.420, I.421, Y.423, F.424, R.428 Ligands: CDL.46, 9XX.56 Ligand excluded by PLIP CDL.57: 17 residues within 4Å: Chain J: E.138, A.139, V.142, I.143, L.146, A.342, I.345, A.346, F.349 Chain V: Q.12, A.15, I.16, R.19 Ligands: 9Y0.24, MQ9.28, CDL.60, MQ9.65 Ligand excluded by PLIP CDL.60: 21 residues within 4Å: Chain J: H.21, P.22, A.25 Chain V: I.16, Y.20, A.25, V.26, R.28, Q.29, A.221, G.224, A.225, A.228, W.231, F.232, M.254 Ligands: CDL.21, 9Y0.24, 9Y0.30, CDL.57, MQ9.63 Ligand excluded by PLIP CDL.61: 29 residues within 4Å: Chain V: H.37, W.38, L.42, F.129, T.130, R.366, P.367, R.368, T.374, S.378, I.381, A.382, F.389, I.421, V.422, V.425, A.426, W.429, A.430, L.433 Chain W: I.284, M.288, R.293, A.294 Ligands: CDL.46, CDL.48, 9YF.54, CDL.62, MQ9.70 Ligand excluded by PLIP CDL.62: 25 residues within 4Å: Chain N: Y.29, I.32, F.131 Chain P: W.90, W.91, I.93, L.94, L.97, S.98, F.120, T.123 Chain V: R.366, R.368, W.429, L.433, P.483, L.484, K.486, R.487, K.490 Chain W: R.293 Ligands: CDL.46, CDL.48, CDL.61, MQ9.64 Ligand excluded by PLIP CDL.73: 26 residues within 4Å: Chain O: F.107, L.108, L.111, I.152, L.155, V.156, V.159, L.162, A.163, K.166, M.167 Chain P: I.122, C.126, F.130, W.134, K.138 Chain V: L.278, F.502, L.503 Chain W: W.289 Chain X: W.92, L.138, I.145, L.149, K.153 Ligands: CDL.48 Ligand excluded by PLIP

8 x 9Y0: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate(Non-covalent)

9Y0.9: 14 residues within 4Å: Chain B: M.173, F.232, A.236, L.240 Chain C: V.125, T.130, I.131, P.132, Y.141, L.142, G.145, L.149 Chain D: A.106, I.114 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:A.236, D:A.106, C:L.142, C:L.149 9Y0.12: 12 residues within 4Å: Chain G: M.43, P.44, V.47 Chain J: L.343, Y.347, I.350, K.353, V.354, I.376, M.379, L.383 Ligands: MQ9.34 8 PLIP interactions: 7 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: J:L.343, J:Y.347, J:I.350, J:K.353, J:V.354, J:M.379, J:L.383, G:V.47 9Y0.15: 11 residues within 4Å: Chain A: L.335 Chain B: F.61, F.73 Chain G: V.68, H.70, V.71, W.74 Chain I: Q.28, I.29 Ligands: 9YF.16, 9XX.18 7 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: G:H.70, G:V.71, G:V.71, I:Q.28, B:F.61, B:F.73, A:L.335 9Y0.24: 18 residues within 4Å: Chain J: L.213, G.217, I.218, A.221, L.222, A.225, A.228, L.229, F.232 Chain V: Y.20, L.54, V.58, L.220 Ligands: CDL.21, 9Y0.30, CDL.57, CDL.60, MQ9.65 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain V Hydrophobic interactions: J:L.222, J:A.225, J:A.228, J:F.232, J:F.232, V:Y.20, V:Y.20, V:L.220 Hydrogen bonds: J:L.213 9Y0.30: 18 residues within 4Å: Chain J: Y.20, L.54, V.58, L.220 Chain V: L.213, G.217, I.218, A.221, L.222, A.225, A.228, L.229, F.232 Ligands: CDL.21, 9Y0.24, MQ9.27, CDL.29, CDL.60 9 PLIP interactions: 3 interactions with chain J, 6 interactions with chain V Hydrophobic interactions: J:Y.20, J:Y.20, J:L.220, V:L.222, V:A.225, V:A.228, V:F.232, V:F.232 Hydrogen bonds: V:L.213 9Y0.47: 14 residues within 4Å: Chain N: M.173, F.232, A.236, L.240 Chain O: V.125, T.130, I.131, P.132, Y.141, L.142, G.145, L.149 Chain P: A.106, I.114 4 PLIP interactions: 2 interactions with chain O, 1 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: O:L.142, O:L.149, N:A.236, P:A.106 9Y0.50: 12 residues within 4Å: Chain S: M.43, P.44, V.47 Chain V: L.343, Y.347, I.350, K.353, V.354, I.376, M.379, L.383 Ligands: MQ9.70 8 PLIP interactions: 7 interactions with chain V, 1 interactions with chain S Hydrophobic interactions: V:L.343, V:Y.347, V:I.350, V:K.353, V:V.354, V:M.379, V:L.383, S:V.47 9Y0.53: 11 residues within 4Å: Chain M: L.335 Chain N: F.61, F.73 Chain S: V.68, H.70, V.71, W.74 Chain U: Q.28, I.29 Ligands: 9YF.54, 9XX.56 6 PLIP interactions: 2 interactions with chain S, 1 interactions with chain U, 2 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: S:H.70, S:V.71, U:Q.28, N:F.61, N:F.73, M:L.335

4 x PLM: PALMITIC ACID(Covalent)

PLM.13: 8 residues within 4Å: Chain G: V.61, R.64 Chain H: C.21, S.22 Chain J: W.318, E.319, F.320 Ligands: 9XX.14 8 PLIP interactions: 5 interactions with chain J, 3 interactions with chain G Hydrophobic interactions: J:W.318, J:W.318, J:W.318, J:W.318, J:F.320, G:V.61, G:R.64 Hydrogen bonds: G:R.64 PLM.17: 15 residues within 4Å: Chain B: V.54, L.57, M.58, F.61, Q.78, Q.81, L.82, F.140, T.142, P.143 Chain I: C.24, S.25, A.26 Ligands: HEA.4, 9XX.18 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain I Hydrophobic interactions: B:V.54, B:F.61, B:F.61, B:Q.78, B:F.140, B:F.140, I:A.26 Hydrogen bonds: I:S.25, I:A.26 PLM.51: 8 residues within 4Å: Chain S: V.61, R.64 Chain T: C.21, S.22 Chain V: W.318, E.319, F.320 Ligands: 9XX.52 8 PLIP interactions: 5 interactions with chain V, 3 interactions with chain S Hydrophobic interactions: V:W.318, V:W.318, V:W.318, V:W.318, V:F.320, S:V.61, S:R.64 Hydrogen bonds: S:R.64 PLM.55: 15 residues within 4Å: Chain N: V.54, L.57, M.58, F.61, Q.78, Q.81, L.82, F.140, T.142, P.143 Chain U: C.24, S.25, A.26 Ligands: HEA.42, 9XX.56 9 PLIP interactions: 6 interactions with chain N, 3 interactions with chain U Hydrophobic interactions: N:V.54, N:F.61, N:F.61, N:Q.78, N:F.140, N:F.140, U:A.26 Hydrogen bonds: U:S.25, U:A.26

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

9XX.14: 6 residues within 4Å: Chain H: C.21 Chain J: F.320, Y.321, V.331, W.332 Ligands: PLM.13 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:F.320, J:F.320, J:F.320, J:V.331, J:W.332 9XX.18: 17 residues within 4Å: Chain B: L.134, I.137, A.138, F.140, I.141 Chain G: V.71, W.74, F.75, F.79, V.82 Chain I: C.24 Ligands: CDL.8, CDL.11, 9Y0.15, 9YF.16, PLM.17, MQ9.26 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain B Hydrophobic interactions: G:W.74, G:F.75, G:F.75, G:F.79, G:V.82, B:L.134, B:A.138, B:F.140 9XX.52: 6 residues within 4Å: Chain T: C.21 Chain V: F.320, Y.321, V.331, W.332 Ligands: PLM.51 5 PLIP interactions: 5 interactions with chain V Hydrophobic interactions: V:F.320, V:F.320, V:F.320, V:V.331, V:W.332 9XX.56: 16 residues within 4Å: Chain N: L.134, I.137, A.138, F.140, I.141 Chain S: V.71, W.74, F.75, F.79, V.82 Chain U: C.24 Ligands: CDL.46, CDL.49, 9Y0.53, 9YF.54, PLM.55 9 PLIP interactions: 4 interactions with chain S, 5 interactions with chain N Hydrophobic interactions: S:W.74, S:F.75, S:F.75, S:V.82, N:L.134, N:L.134, N:I.137, N:A.138, N:F.140

8 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.16: 25 residues within 4Å: Chain B: I.141 Chain G: G.69, V.71, E.72, F.75, F.79 Chain I: C.24, S.25, I.29, Q.31 Chain J: L.386, F.389, S.403, N.405, A.406, W.409, I.410, I.413, V.417, L.418 Chain K: S.203 Ligands: 9Y0.15, 9XX.18, CDL.22, MQ9.26 21 PLIP interactions: 10 interactions with chain J, 3 interactions with chain G, 4 interactions with chain I, 3 interactions with chain K, 1 interactions with chain B Hydrophobic interactions: J:L.386, J:F.389, J:A.406, J:I.410, J:I.410, J:I.413, J:V.417, J:L.418, G:F.75, G:F.75, G:F.79, B:I.141 Hydrogen bonds: J:S.403, J:N.405, I:C.24, I:S.25, I:I.29, I:Q.31, K:S.203, K:S.203, K:S.203 9YF.33: 21 residues within 4Å: Chain D: P.111, W.112, L.113, A.115, A.116, F.120 Chain J: L.278 Chain K: K.197, D.209, A.253, S.257, G.260, Y.261, G.262, M.273, I.277, I.278 Chain L: P.130, L.131, L.134 Ligands: MQ9.26 16 PLIP interactions: 8 interactions with chain K, 3 interactions with chain L, 1 interactions with chain J, 4 interactions with chain D Hydrophobic interactions: K:Y.261, K:Y.261, K:I.277, K:I.278, L:P.130, L:L.131, L:L.134, J:L.278, D:P.111, D:W.112, D:L.113, D:F.120 Hydrogen bonds: K:K.197, K:K.197, K:D.209, K:G.262 9YF.37: 10 residues within 4Å: Chain J: V.184, I.185, W.188, P.322, H.325 Chain L: W.224, W.239, W.417, E.418 Ligands: 9YF.38 10 PLIP interactions: 5 interactions with chain J, 5 interactions with chain L Hydrophobic interactions: J:I.185, J:I.185, J:W.188, J:P.322, J:P.322, L:W.417, L:W.417 Hydrogen bonds: L:W.224, L:W.239, L:E.418 9YF.38: 16 residues within 4Å: Chain J: I.185, W.188, M.189 Chain L: V.213, G.217, G.218, L.219, I.220, K.221, N.222, K.225 Chain V: E.98, V.99, R.100 Chain X: L.108 Ligands: 9YF.37 14 PLIP interactions: 7 interactions with chain L, 1 interactions with chain X, 3 interactions with chain J, 3 interactions with chain V Hydrophobic interactions: L:V.213, L:L.219, L:I.220, L:I.220, X:L.108, J:I.185, J:W.188, J:M.189 Hydrogen bonds: L:G.217, L:G.218, L:N.222, V:R.100, V:R.100 Salt bridges: V:R.100 9YF.54: 25 residues within 4Å: Chain N: I.141 Chain S: G.69, V.71, E.72, F.75, F.79 Chain U: C.24, S.25, I.29, Q.31 Chain V: L.386, F.389, S.403, N.405, A.406, W.409, I.410, I.413, V.417, L.418 Chain W: S.203 Ligands: 9Y0.53, 9XX.56, CDL.61, MQ9.64 21 PLIP interactions: 10 interactions with chain V, 3 interactions with chain S, 4 interactions with chain U, 3 interactions with chain W, 1 interactions with chain N Hydrophobic interactions: V:L.386, V:F.389, V:A.406, V:I.410, V:I.410, V:I.413, V:V.417, V:L.418, S:F.75, S:F.75, S:F.79, N:I.141 Hydrogen bonds: V:S.403, V:N.405, U:C.24, U:S.25, U:I.29, U:Q.31, W:S.203, W:S.203, W:S.203 9YF.69: 20 residues within 4Å: Chain P: P.111, W.112, L.113, A.115, A.116, F.120 Chain V: L.278 Chain W: K.197, D.209, A.253, S.257, G.260, Y.261, G.262, M.273, I.277, I.278 Chain X: P.130, L.134 Ligands: MQ9.64 14 PLIP interactions: 7 interactions with chain W, 2 interactions with chain X, 1 interactions with chain V, 4 interactions with chain P Hydrophobic interactions: W:Y.261, W:I.277, W:I.278, X:P.130, X:L.134, V:L.278, P:P.111, P:W.112, P:L.113, P:F.120 Hydrogen bonds: W:K.197, W:K.197, W:D.209, W:G.262 9YF.71: 16 residues within 4Å: Chain J: E.98, V.99, R.100 Chain L: L.108 Chain V: I.185, W.188, M.189 Chain X: V.213, G.217, G.218, L.219, I.220, K.221, N.222, K.225 Ligands: 9YF.74 14 PLIP interactions: 1 interactions with chain L, 3 interactions with chain V, 7 interactions with chain X, 3 interactions with chain J Hydrophobic interactions: L:L.108, V:I.185, V:W.188, V:M.189, X:V.213, X:L.219, X:I.220, X:I.220 Hydrogen bonds: X:G.217, X:G.218, X:N.222, J:R.100, J:R.100 Salt bridges: J:R.100 9YF.74: 11 residues within 4Å: Chain V: P.183, V.184, I.185, W.188, P.322, H.325 Chain X: W.224, W.239, W.417, E.418 Ligands: 9YF.71 9 PLIP interactions: 4 interactions with chain X, 5 interactions with chain V Hydrophobic interactions: X:W.417, X:W.417, V:P.183, V:I.185, V:I.185, V:W.188, V:P.322 Hydrogen bonds: X:W.224, X:W.239

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

HEM.19: 26 residues within 4Å: Chain J: S.39, F.40, G.43, E.44, A.46, L.47, F.116, I.120, H.123, L.124, R.126, I.127, A.132, R.137, N.140, W.141, G.144, S.145, L.147, I.223, H.226, L.227, V.230, H.235, T.236 Ligands: MQ9.27 28 PLIP interactions: 28 interactions with chain J, Hydrophobic interactions: J:E.44, J:A.46, J:F.116, J:I.120, J:I.120, J:I.120, J:L.124, J:I.127, J:I.127, J:A.132, J:N.140, J:W.141, J:L.147, J:L.147, J:I.223, J:I.223, J:L.227, J:V.230, J:V.230 Hydrogen bonds: J:G.43, J:T.236 Salt bridges: J:H.123, J:R.126, J:R.126, J:H.235, J:H.235 pi-Stacking: J:H.226 Metal complexes: J:H.226 HEM.20: 26 residues within 4Å: Chain J: F.50, L.53, L.54, G.57, V.58, L.60, T.61, F.64, I.95, R.106, H.109, H.110, A.113, F.116, E.154, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, I.219, N.282 Chain V: L.213 20 PLIP interactions: 19 interactions with chain J, 1 interactions with chain V, Hydrophobic interactions: J:F.50, J:L.53, J:L.54, J:V.58, J:L.60, J:F.64, J:F.116, J:F.116, J:L.161, J:Y.208, J:I.212, J:P.216, J:I.219, V:L.213 Salt bridges: J:R.106, J:R.106, J:H.110 pi-Stacking: J:H.211, J:H.211 Metal complexes: J:H.109 HEM.58: 25 residues within 4Å: Chain V: S.39, F.40, G.43, E.44, A.46, L.47, F.116, I.120, H.123, L.124, R.126, I.127, A.132, N.140, W.141, G.144, S.145, L.147, I.223, H.226, L.227, V.230, H.235, T.236 Ligands: MQ9.65 28 PLIP interactions: 28 interactions with chain V, Hydrophobic interactions: V:E.44, V:A.46, V:F.116, V:I.120, V:I.120, V:I.120, V:L.124, V:I.127, V:I.127, V:A.132, V:N.140, V:W.141, V:L.147, V:L.147, V:I.223, V:I.223, V:L.227, V:V.230, V:V.230 Hydrogen bonds: V:G.43, V:T.236 Salt bridges: V:H.123, V:R.126, V:R.126, V:H.235, V:H.235 pi-Stacking: V:H.226 Metal complexes: V:H.226 HEM.59: 26 residues within 4Å: Chain J: L.213 Chain V: F.50, L.53, L.54, G.57, V.58, L.60, T.61, F.64, I.95, R.106, H.109, H.110, A.113, F.116, E.154, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, I.219, N.282 20 PLIP interactions: 19 interactions with chain V, 1 interactions with chain J, Hydrophobic interactions: V:F.50, V:L.53, V:L.54, V:V.58, V:L.60, V:F.64, V:F.116, V:F.116, V:L.161, V:Y.208, V:I.212, V:P.216, V:I.219, J:L.213 Salt bridges: V:R.106, V:R.106, V:H.110 pi-Stacking: V:H.211, V:H.211 Metal complexes: V:H.109

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

MQ9.25: 20 residues within 4Å: Chain J: L.55, T.56, F.104, V.105, A.258, S.261, G.262, F.265, A.266, T.269 Chain L: F.136, I.140, A.147 Chain X: L.204, F.207, T.211, A.214, F.215 Ligands: CDL.21, MQ9.27 15 PLIP interactions: 6 interactions with chain X, 7 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: X:L.204, X:F.207, X:T.211, X:A.214, X:F.215, X:F.215, J:L.55, J:T.56, J:F.104, J:V.105, J:F.265, J:F.265, J:T.269, L:I.140, L:A.147 MQ9.26: 24 residues within 4Å: Chain B: F.131, L.134, I.135, A.138 Chain D: T.101, V.104, W.112 Chain J: F.389, M.392, I.395, I.396, F.400, I.402, T.407, I.410 Chain K: L.263, G.264, F.266, P.270, M.273 Ligands: 9YF.16, 9XX.18, CDL.23, 9YF.33 20 PLIP interactions: 3 interactions with chain B, 3 interactions with chain K, 7 interactions with chain J, 7 interactions with chain D Hydrophobic interactions: B:F.131, B:L.134, B:A.138, K:F.266, K:P.270, K:P.270, J:I.395, J:I.396, J:I.396, J:F.400, J:I.402, J:I.410, J:I.410, D:T.101, D:V.104, D:V.104, D:W.112 pi-Stacking: D:W.112, D:W.112, D:W.112 MQ9.27: 21 residues within 4Å: Chain J: F.34, E.44, L.47, Y.48, I.51, L.54, L.55, V.58, L.220, L.227, W.231, F.257 Chain V: I.149, L.150, F.153, L.214, I.215 Ligands: HEM.19, MQ9.25, CDL.29, 9Y0.30 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain V Hydrophobic interactions: J:F.34, J:E.44, J:L.47, J:I.51, J:L.55, J:V.58, J:L.220, J:L.227, J:F.257, V:I.149, V:F.153, V:F.153, V:L.214, V:L.214 Hydrogen bonds: J:Y.48 MQ9.28: 12 residues within 4Å: Chain J: A.174, L.175, I.178, I.182, A.334, M.337, G.338, A.342, A.346, I.350, K.353 Ligands: CDL.57 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:A.174, J:L.175, J:I.178, J:I.178, J:I.182, J:A.342, J:A.346, J:I.350 MQ9.34: 29 residues within 4Å: Chain J: M.121, V.122, L.124, A.125, F.128, F.129, F.303, V.340, L.343, L.344, G.377, A.380, I.381, L.383, Y.384, L.385, T.388, F.389, M.392 Chain K: A.269, G.272, M.273, W.276, I.277, V.281, I.284 Ligands: CDL.10, 9Y0.12, CDL.22 29 PLIP interactions: 7 interactions with chain K, 22 interactions with chain J Hydrophobic interactions: K:M.273, K:W.276, K:W.276, K:W.276, K:I.277, K:I.284, J:M.121, J:V.122, J:A.125, J:F.128, J:F.128, J:F.129, J:F.303, J:L.343, J:A.380, J:A.380, J:I.381, J:I.381, J:L.383, J:Y.384, J:Y.384, J:Y.384, J:Y.384, J:L.385, J:L.385, J:T.388, J:F.389 pi-Stacking: K:W.276 Hydrogen bonds: J:Y.384 MQ9.63: 20 residues within 4Å: Chain L: L.204, F.207, T.211, A.214, F.215 Chain V: L.55, T.56, F.104, V.105, A.258, S.261, G.262, F.265, A.266, T.269 Chain X: F.136, I.140, A.147 Ligands: CDL.60, MQ9.65 15 PLIP interactions: 2 interactions with chain X, 6 interactions with chain L, 7 interactions with chain V Hydrophobic interactions: X:I.140, X:A.147, L:L.204, L:F.207, L:T.211, L:A.214, L:F.215, L:F.215, V:L.55, V:T.56, V:F.104, V:V.105, V:F.265, V:F.265, V:T.269 MQ9.64: 23 residues within 4Å: Chain N: F.131, L.134, I.135, A.138 Chain P: T.101, V.104, W.112 Chain V: F.389, M.392, I.395, I.396, F.400, I.402, T.407, I.410 Chain W: L.263, G.264, F.266, P.270, M.273 Ligands: 9YF.54, CDL.62, 9YF.69 20 PLIP interactions: 3 interactions with chain N, 7 interactions with chain V, 3 interactions with chain W, 7 interactions with chain P Hydrophobic interactions: N:F.131, N:L.134, N:A.138, V:I.395, V:I.396, V:I.396, V:F.400, V:I.402, V:I.410, V:I.410, W:F.266, W:P.270, W:P.270, P:T.101, P:V.104, P:V.104, P:W.112 pi-Stacking: P:W.112, P:W.112, P:W.112 MQ9.65: 21 residues within 4Å: Chain J: I.149, L.150, F.153, L.214, I.215 Chain V: F.34, E.44, L.47, Y.48, I.51, L.54, L.55, V.58, L.220, L.227, W.231, F.257 Ligands: 9Y0.24, CDL.57, HEM.58, MQ9.63 15 PLIP interactions: 5 interactions with chain J, 10 interactions with chain V Hydrophobic interactions: J:I.149, J:F.153, J:F.153, J:L.214, J:L.214, V:F.34, V:E.44, V:L.47, V:I.51, V:L.55, V:V.58, V:L.220, V:L.227, V:F.257 Hydrogen bonds: V:Y.48 MQ9.66: 12 residues within 4Å: Chain V: A.174, L.175, I.178, I.182, A.334, M.337, G.338, A.342, A.346, I.350, K.353 Ligands: CDL.29 8 PLIP interactions: 8 interactions with chain V Hydrophobic interactions: V:A.174, V:L.175, V:I.178, V:I.178, V:I.182, V:A.342, V:A.346, V:I.350 MQ9.70: 29 residues within 4Å: Chain V: M.121, V.122, L.124, A.125, F.128, F.129, F.303, V.340, L.343, L.344, G.377, A.380, I.381, L.383, Y.384, L.385, T.388, F.389, M.392 Chain W: A.269, G.272, M.273, W.276, I.277, V.281, I.284 Ligands: CDL.48, 9Y0.50, CDL.61 28 PLIP interactions: 7 interactions with chain W, 21 interactions with chain V Hydrophobic interactions: W:M.273, W:W.276, W:W.276, W:W.276, W:I.277, W:I.284, V:M.121, V:V.122, V:A.125, V:F.128, V:F.128, V:F.129, V:F.303, V:L.343, V:A.380, V:A.380, V:I.381, V:I.381, V:L.383, V:Y.384, V:Y.384, V:Y.384, V:L.385, V:L.385, V:T.388, V:F.389 pi-Stacking: W:W.276 Hydrogen bonds: V:Y.384

4 x HEC: HEME C(Non-covalent)

HEC.31: 27 residues within 4Å: Chain A: W.138 Chain I: T.32, T.33, Q.35, P.37, A.38 Chain K: S.86, C.87, C.90, H.91, R.101, P.103, L.105, T.108, A.112, V.113, Q.116, V.117, M.122, P.123, A.124, M.125, L.146, G.225, P.226, Q.227 Chain L: Q.359 14 PLIP interactions: 1 interactions with chain A, 10 interactions with chain K, 1 interactions with chain L, 2 interactions with chain I, Hydrophobic interactions: A:W.138, K:P.103, K:L.105, K:T.108, K:A.112, K:Q.116, K:V.117, K:A.124, K:L.146, K:Q.227, I:T.33 Metal complexes: K:H.91 Hydrogen bonds: L:Q.359, I:A.38 HEC.32: 26 residues within 4Å: Chain K: F.115, Q.116, T.119, R.121, Q.130, A.131, C.188, C.191, H.192, L.201, Y.206, P.208, D.209, L.210, D.212, A.213, I.218, M.222, P.226, Q.227, N.228, M.229, P.230, F.232, I.245 Chain L: Y.356 19 PLIP interactions: 19 interactions with chain K, Hydrophobic interactions: K:F.115, K:L.210, K:L.210, K:A.213, K:I.218, K:I.218, K:P.226, K:Q.227, K:M.229, K:P.230, K:F.232, K:I.245 Hydrogen bonds: K:Q.116, K:Q.116, K:T.119, K:D.209 Salt bridges: K:R.121, K:R.121 Metal complexes: K:H.192 HEC.67: 26 residues within 4Å: Chain M: W.138 Chain U: T.32, T.33, Q.35, P.37, A.38 Chain W: S.86, C.87, C.90, H.91, P.103, L.105, T.108, A.112, V.113, Q.116, V.117, M.122, P.123, A.124, M.125, L.146, G.225, P.226, Q.227 Chain X: Q.359 14 PLIP interactions: 10 interactions with chain W, 2 interactions with chain U, 1 interactions with chain M, 1 interactions with chain X, Hydrophobic interactions: W:P.103, W:L.105, W:T.108, W:A.112, W:Q.116, W:V.117, W:A.124, W:L.146, W:Q.227, U:T.33, M:W.138 Metal complexes: W:H.91 Hydrogen bonds: U:A.38, X:Q.359 HEC.68: 26 residues within 4Å: Chain W: F.115, Q.116, T.119, R.121, Q.130, A.131, C.188, C.191, H.192, L.201, Y.206, P.208, D.209, L.210, D.212, A.213, I.218, M.222, P.226, Q.227, N.228, M.229, P.230, F.232, I.245 Chain X: Y.356 19 PLIP interactions: 19 interactions with chain W, Hydrophobic interactions: W:F.115, W:L.210, W:L.210, W:A.213, W:I.218, W:I.218, W:P.226, W:Q.227, W:M.229, W:P.230, W:F.232, W:I.245 Hydrogen bonds: W:Q.116, W:Q.116, W:T.119, W:D.209 Salt bridges: W:R.121, W:R.121 Metal complexes: W:H.192

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

FES.35: 8 residues within 4Å: Chain L: C.346, H.348, L.349, C.351, C.365, C.367, H.368, S.370 2 PLIP interactions: 2 interactions with chain L, Metal complexes: L:H.348, L:H.368 FES.72: 7 residues within 4Å: Chain X: C.346, H.348, C.351, C.365, C.367, H.368, S.370 3 PLIP interactions: 3 interactions with chain X, Metal complexes: X:H.348, X:H.348, X:H.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, H. et al., An electron transfer path connects subunits of a mycobacterial respiratory supercomplex. Science (2018)

Release Date

2018-11-14

Peptides

Cytochrome c oxidase subunit 2: AM
Cytochrome c oxidase subunit 1: BN
Cytochrome c oxidase subunit 3: CO
Cytochrome c oxidase polypeptide 4: DP
Cytochrome c oxidase subunit CtaJ: EQ
Uncharacterized protein MSMEG_4692/MSMEI_4575: FR
Prokaryotic respiratory supercomplex associate factor 1 PRSAF1: GS
Superoxide dismutase [Cu-Zn]: HT
LpqE protein: IU
Ubiquinol-cytochrome c reductase cytochrome b subunit: JV
Cytochrome bc1 complex cytochrome c subunit: KW
Rieske iron-sulfur protein QcrA: LX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

M
Q

B
F

N
R

C
G

O
S

D
H

P
T

E
I

Q
U

F
J

R
V

G
D

S
P

H
Y

T
Z

I
K

U
W

J
B

V
N

K
C

W
O

L
A

X
M

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 3

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit CtaJ

Uncharacterized protein MSMEG_4692/MSMEI_4575

Prokaryotic respiratory supercomplex associate factor 1 PRSAF1

Superoxide dismutase [Cu-Zn]

LpqE protein

Ubiquinol-cytochrome c reductase cytochrome b subunit

Cytochrome bc1 complex cytochrome c subunit

Rieske iron-sulfur protein QcrA

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