SMTL ID : 7rh6.1

Mycobacterial CIII2CIV2 supercomplex, inhibitor free, -Lpqe cyt cc open

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x HEC: HEME C(Non-covalent)

HEC.1: 22 residues within 4Å: Chain A: F.12, S.15, C.16, C.19, H.20, R.30, G.31, P.32, L.34, T.37, A.41, V.42, Q.45, V.46, P.52, A.53, M.54, F.67, L.75, V.79, P.155, Q.156 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:P.32, A:L.34, A:L.34, A:V.42, A:Q.45, A:P.52, A:F.67, A:L.75, A:L.75 Hydrogen bonds: A:Q.45 HEC.2: 35 residues within 4Å: Chain A: F.44, Q.45, T.48, G.49, R.50, Q.59, S.62, F.113, N.116, C.117, C.120, H.121, L.130, K.134, Y.135, A.136, P.137, D.138, L.139, D.141, A.142, Q.146, I.147, A.150, M.151, P.155, Q.156, N.157, M.158, P.159, F.161, L.166, I.174, V.178 Chain K: R.167 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.44, A:T.48, A:L.130, A:P.137, A:L.139, A:L.139, A:A.142, A:I.147, A:A.150, A:Q.156, A:P.159, A:F.161, A:F.161, A:V.178 Hydrogen bonds: A:S.62, A:D.141, A:Q.156, A:Q.156 Salt bridges: A:R.50 Metal complexes: A:H.121 HEC.54: 34 residues within 4Å: Chain P: W.112, F.254 Chain U: T.9, T.10, Q.12, P.14, A.15, V.16 Chain V: F.12, S.15, C.16, C.19, H.20, R.30, G.31, P.32, L.34, T.37, A.41, V.42, Q.45, V.46, M.51, P.52, A.53, M.54, A.60, F.67, L.75, V.79, T.153, G.154, P.155, Q.156 12 PLIP interactions: 1 interactions with chain P, 10 interactions with chain V, 1 interactions with chain U, Hydrophobic interactions: P:W.112, V:P.32, V:L.34, V:T.37, V:A.41, V:V.42, V:V.46, V:F.67 Hydrogen bonds: V:Q.45, V:Q.156, U:A.15 Metal complexes: V:H.20 HEC.55: 38 residues within 4Å: Chain V: F.44, Q.45, T.48, R.50, Q.59, A.60, S.62, F.113, N.116, C.117, S.119, C.120, H.121, L.130, Y.135, A.136, P.137, D.138, L.139, D.141, A.142, Q.146, I.147, A.150, M.151, P.155, Q.156, N.157, M.158, P.159, F.161, L.166, I.174, V.178 Chain W: M.240, L.316, Y.317, E.318 18 PLIP interactions: 18 interactions with chain V, Hydrophobic interactions: V:F.44, V:N.116, V:L.130, V:A.142, V:I.147, V:I.147, V:A.150, V:P.155, V:Q.156, V:M.158, V:P.159, V:F.161 Hydrogen bonds: V:Q.45, V:D.138, V:Q.156 Salt bridges: V:R.50, V:R.50 Metal complexes: V:H.121

5 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.3: 18 residues within 4Å: Chain A: M.202, A.203, I.206, I.207 Chain F: V.268, L.271, M.272, L.275, L.276 Chain L: P.111, W.112, L.113, A.115, A.116, F.120 Ligands: CDL.40, CDL.41, MQ9.42 9 PLIP interactions: 4 interactions with chain F, 3 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: F:L.271, F:L.275, F:L.276, F:L.276, L:P.111, L:W.112, L:F.120, A:I.207, A:I.207 9YF.16: 29 residues within 4Å: Chain E: L.382, L.383, F.386, S.400, N.402, A.403, W.406, I.407, I.410, G.411, V.414, L.415 Chain G: I.132 Chain H: V.71, E.72, F.75, F.79 Chain U: C.1, S.2, I.6, S.7, Q.8 Chain V: S.132 Ligands: CDL.18, 9Y0.31, MQ9.49, CDL.50, 9XX.53, MQ9.56 16 PLIP interactions: 8 interactions with chain E, 4 interactions with chain H, 3 interactions with chain U, 1 interactions with chain V Hydrophobic interactions: E:F.386, E:F.386, E:W.406, E:I.407, E:I.410, E:I.410, H:F.75, H:F.75, H:F.79, H:F.79 Hydrogen bonds: E:S.400, E:N.402, U:S.2, U:I.6, U:Q.8, V:S.132 9YF.57: 28 residues within 4Å: Chain E: L.271, M.272, L.275, L.276 Chain R: P.111, W.112, L.113, A.115, A.116, F.120 Chain V: K.126, D.138, G.140, A.182, E.183, P.185, S.186, G.189, Y.190, G.191, L.192, M.202, A.203, I.206, I.207 Ligands: CDL.47, MQ9.49, CDL.51 19 PLIP interactions: 4 interactions with chain R, 12 interactions with chain V, 3 interactions with chain E Hydrophobic interactions: R:P.111, R:W.112, R:A.116, R:F.120, V:Y.190, V:Y.190, V:Y.190, V:Y.190, V:A.203, V:I.207, V:I.207, E:L.275, E:L.276, E:L.276 Hydrogen bonds: V:K.126, V:D.138, V:G.140, V:A.182, V:G.191 9YF.59: 21 residues within 4Å: Chain E: I.179, P.180, V.181, I.182, W.185, M.186, A.189, P.319, F.320, H.322, I.324, V.328, A.331, V.332 Chain W: I.181, W.185, W.200, W.378, E.379 Ligands: MQ9.14, 9XX.34 16 PLIP interactions: 10 interactions with chain E, 6 interactions with chain W Hydrophobic interactions: E:P.180, E:W.185, E:W.185, E:W.185, E:W.185, E:A.189, E:F.320, E:V.332, W:I.181, W:W.378, W:W.378 Salt bridges: E:H.322, E:H.322 Hydrogen bonds: W:W.200, W:W.378, W:E.379 9YF.60: 19 residues within 4Å: Chain C: L.65, F.68, L.69, F.70, W.73 Chain E: W.185 Chain F: E.95, V.96, R.97 Chain W: A.170, L.173, V.174, I.177, G.178, G.179, I.181, K.182, N.183, K.186 18 PLIP interactions: 4 interactions with chain F, 10 interactions with chain W, 4 interactions with chain C Hydrogen bonds: F:E.95, F:R.97, W:K.182, W:N.183 Salt bridges: F:R.97, F:R.97, W:K.186 Hydrophobic interactions: W:A.170, W:L.173, W:L.173, W:V.174, W:V.174, W:I.177, W:I.181, C:L.65, C:L.69, C:L.69, C:F.70

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

MQ9.4: 40 residues within 4Å: Chain A: A.198, G.201, M.202, W.205, I.206, M.209, V.210, I.213 Chain F: M.118, V.119, L.121, A.122, F.125, F.126, W.138, L.145, M.149, F.300, M.303, W.304, L.336, V.337, F.338, L.340, L.341, Y.344, I.373, G.374, A.377, I.378, L.380, Y.381, L.382, L.384, T.385, F.386, M.389 Ligands: 9Y0.22, CDL.24, MQ9.42 25 PLIP interactions: 20 interactions with chain F, 5 interactions with chain A Hydrophobic interactions: F:M.118, F:L.121, F:F.125, F:F.125, F:L.145, F:F.300, F:V.337, F:V.337, F:L.340, F:L.340, F:Y.344, F:A.377, F:A.377, F:I.378, F:L.380, F:Y.381, F:Y.381, F:Y.381, F:L.382, F:T.385, A:W.205, A:W.205, A:W.205, A:I.206 pi-Stacking: A:W.205 MQ9.14: 28 residues within 4Å: Chain E: V.139, L.143, I.146, L.147, F.150, F.153, A.171, L.172, I.175, T.176, I.179, M.186, L.190, I.215, L.219, M.302, T.305, V.330, A.331, M.334, F.338, I.342, A.343, F.346, I.347, K.350 Ligands: 9Y0.30, 9YF.59 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:L.143, E:I.146, E:I.146, E:L.147, E:F.150, E:F.150, E:F.150, E:A.171, E:L.172, E:I.175, E:A.331, E:F.338, E:I.342, E:A.343, E:F.346, E:K.350 MQ9.15: 40 residues within 4Å: Chain C: L.161, L.165, F.168, T.172, A.175, F.176 Chain E: F.31, E.41, L.44, Y.45, I.48, I.49, L.52, T.53, W.56, G.98, F.101, V.102, V.105, L.224, V.227, W.228, H.232, F.254, A.255, V.256, S.258, G.259, A.260, F.262, A.263, T.266 Chain W: F.68, F.97, I.101, I.104, G.105, A.108 Ligands: HEM.12, CDL.17 26 PLIP interactions: 16 interactions with chain E, 4 interactions with chain W, 6 interactions with chain C Hydrophobic interactions: E:F.31, E:L.44, E:I.48, E:L.52, E:L.52, E:T.53, E:F.101, E:F.101, E:V.102, E:L.224, E:V.227, E:W.228, E:F.262, E:F.262, E:F.262, E:A.263, W:F.97, W:I.101, W:I.104, W:A.108, C:L.165, C:F.168, C:T.172, C:A.175, C:F.176, C:F.176 MQ9.19: 28 residues within 4Å: Chain F: V.139, L.143, I.146, L.147, F.150, F.153, F.154, A.171, L.172, I.175, T.176, I.179, M.186, L.190, I.215, L.219, M.302, T.305, I.309, A.331, M.334, F.338, I.342, A.343, F.346, I.347, K.350 Ligands: 9Y0.22 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:L.143, F:I.146, F:I.146, F:L.147, F:L.147, F:F.150, F:F.150, F:F.150, F:F.153, F:A.171, F:L.172, F:I.179, F:L.219, F:I.342, F:A.343, F:F.346 MQ9.25: 40 residues within 4Å: Chain C: F.68, F.97, I.101, I.104, G.105, A.108 Chain F: F.31, E.41, L.44, Y.45, I.48, I.49, L.52, T.53, W.56, G.98, F.101, V.102, V.105, L.224, V.227, W.228, H.232, F.254, A.255, V.256, S.258, G.259, A.260, F.262, A.263, T.266 Chain W: L.161, L.165, F.168, T.172, A.175, F.176 Ligands: HEM.20, CDL.23 24 PLIP interactions: 6 interactions with chain W, 14 interactions with chain F, 4 interactions with chain C Hydrophobic interactions: W:L.165, W:F.168, W:T.172, W:A.175, W:F.176, W:F.176, F:F.31, F:L.44, F:I.48, F:L.52, F:T.53, F:F.101, F:F.101, F:V.102, F:L.224, F:V.227, F:W.228, F:F.262, F:F.262, F:A.263, C:F.97, C:I.101, C:I.104, C:A.108 MQ9.42: 32 residues within 4Å: Chain A: A.198, P.199, M.202 Chain B: F.122, L.125, I.126, A.129, I.132, L.161 Chain F: L.311, L.383, F.386, A.387, M.389, N.390, I.392, I.393, K.396, F.397, I.399, T.404, I.407, G.408 Chain L: L.97, S.100, T.101, V.104, L.108, W.112, L.113 Ligands: 9YF.3, MQ9.4 24 PLIP interactions: 7 interactions with chain L, 4 interactions with chain B, 12 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: L:L.97, L:T.101, L:W.112, L:L.113, B:F.122, B:L.125, B:A.129, B:I.132, F:F.386, F:A.387, F:I.392, F:I.393, F:I.393, F:F.397, F:F.397, F:F.397, F:F.397, F:I.399, F:T.404, F:I.407, A:P.199 pi-Stacking: L:W.112, L:W.112, L:W.112 MQ9.49: 38 residues within 4Å: Chain E: L.311, L.383, F.386, A.387, M.389, N.390, I.392, I.393, K.396, F.397, I.399, T.404, I.407, G.408 Chain G: F.122, L.125, I.126, A.129, I.132, L.161 Chain R: L.97, S.100, T.101, V.104, L.108, W.112, L.113 Chain V: Y.190, L.192, G.193, F.195, A.198, P.199, M.202 Ligands: 9YF.16, 9XX.53, MQ9.56, 9YF.57 27 PLIP interactions: 13 interactions with chain E, 8 interactions with chain R, 4 interactions with chain G, 2 interactions with chain V Hydrophobic interactions: E:F.386, E:F.386, E:A.387, E:I.392, E:I.393, E:F.397, E:F.397, E:F.397, E:F.397, E:I.399, E:T.404, E:I.407, R:L.97, R:T.101, R:V.104, R:W.112, R:W.112, R:L.113, G:F.122, G:L.125, G:A.129, G:I.132, V:P.199, V:P.199 Hydrogen bonds: E:K.396 pi-Stacking: R:W.112, R:W.112 MQ9.56: 41 residues within 4Å: Chain E: M.118, V.119, L.121, A.122, F.125, F.126, W.138, L.145, M.149, F.300, M.303, W.304, L.336, V.337, F.338, L.340, L.341, Y.344, I.373, G.374, A.377, I.378, L.380, Y.381, L.382, L.384, T.385, F.386, M.389 Chain V: A.198, G.201, M.202, W.205, I.206, M.209, V.210, I.213 Ligands: 9YF.16, CDL.18, 9Y0.30, MQ9.49 25 PLIP interactions: 19 interactions with chain E, 6 interactions with chain V Hydrophobic interactions: E:M.118, E:L.121, E:F.125, E:F.125, E:L.145, E:F.300, E:V.337, E:V.337, E:L.340, E:Y.344, E:A.377, E:A.377, E:I.378, E:L.380, E:Y.381, E:Y.381, E:Y.381, E:L.382, E:T.385, V:W.205, V:W.205, V:W.205, V:W.205, V:I.206, V:I.213

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

CU.5: 5 residues within 4Å: Chain B: H.255, V.258, H.304, H.305 Ligands: HEA.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.255, B:H.304, B:H.305 CU.26: 5 residues within 4Å: Chain G: H.255, V.258, H.304, H.305 Ligands: HEA.27 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.255, G:H.304, G:H.305 CU.37: 7 residues within 4Å: Chain K: H.206, G.207, C.247, E.249, C.251, H.255, M.258 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.247, K:C.251, K:H.255 CU.38: 7 residues within 4Å: Chain K: F.110, Q.111, W.112, V.204, H.206, C.251, M.258 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:H.206, K:H.206 CU.44: 6 residues within 4Å: Chain P: H.206, C.247, T.248, E.249, C.251, H.255 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.247, P:E.249, P:C.251, P:H.255 CU.45: 7 residues within 4Å: Chain P: F.110, Q.111, W.112, H.206, C.247, C.251, M.258 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:H.206, P:H.206

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

HEA.6: 46 residues within 4Å: Chain B: L.82, W.142, T.143, W.251, V.258, Y.259, I.261, A.262, F.266, H.304, H.305, Y.307, T.321, I.324, A.325, V.326, T.328, G.329, F.332, F.333, F.360, L.361, G.364, L.365, G.367, V.368, L.370, A.371, D.376, T.380, D.381, V.385, H.388, F.389, V.392, L.393, T.396, I.397, R.450 Chain K: V.34, V.38, P.76, I.79, I.80 Ligands: CU.5, HEA.7 29 PLIP interactions: 26 interactions with chain B, 3 interactions with chain K, Hydrophobic interactions: B:V.258, B:V.258, B:T.321, B:A.325, B:T.328, B:F.360, B:L.361, B:V.368, B:L.370, B:L.370, B:F.389, B:F.389, B:V.392, B:L.393, B:L.393, K:V.34, K:P.76, K:I.80 Hydrogen bonds: B:Y.259, B:H.304, B:T.328, B:T.328, B:D.381 Salt bridges: B:R.450 pi-Stacking: B:H.388, B:H.388 pi-Cation interactions: B:H.255, B:H.304 Metal complexes: B:H.388 HEA.7: 42 residues within 4Å: Chain B: F.43, L.44, V.45, G.47, L.48, A.50, L.51, M.53, R.54, L.57, F.70, F.74, T.75, H.77, G.78, M.81, L.82, Y.85, A.86, G.141, W.142, T.143, Y.383, I.386, F.389, H.390, L.393, F.394, I.397, V.398, T.436, F.437, Q.440, R.450, R.451, Y.452, A.472, L.475, G.476, M.479 Ligands: HEA.6, CDL.8 28 PLIP interactions: 28 interactions with chain B, Hydrophobic interactions: B:F.43, B:F.43, B:L.44, B:L.48, B:L.48, B:A.50, B:L.51, B:F.74, B:M.81, B:F.389, B:F.389, B:L.393, B:I.397, B:A.472 Hydrogen bonds: B:F.74, B:W.142, B:Y.383, B:R.451, B:Y.452 Salt bridges: B:R.450, B:R.451 pi-Stacking: B:H.77, B:H.77, B:H.390, B:H.390, B:F.437, B:F.437 Metal complexes: B:H.77 HEA.27: 45 residues within 4Å: Chain G: L.82, W.142, T.143, W.251, V.258, Y.259, I.261, A.262, F.266, H.304, H.305, Y.307, T.321, I.324, A.325, T.328, G.329, F.332, F.333, F.360, L.361, G.364, L.365, G.367, V.368, L.370, A.371, D.376, T.380, D.381, V.385, H.388, F.389, V.392, L.393, T.396, I.397, R.450 Chain P: V.34, V.38, P.76, I.79, I.80 Ligands: CU.26, HEA.28 29 PLIP interactions: 26 interactions with chain G, 3 interactions with chain P, Hydrophobic interactions: G:V.258, G:A.262, G:T.321, G:F.360, G:L.361, G:V.368, G:V.368, G:L.370, G:L.370, G:A.371, G:V.385, G:V.385, G:F.389, G:F.389, G:V.392, G:L.393, G:L.393, P:V.34, P:P.76, P:I.80 Hydrogen bonds: G:Y.259, G:D.381 Salt bridges: G:H.305, G:R.450 pi-Stacking: G:H.388, G:H.388 pi-Cation interactions: G:H.255, G:H.304 Metal complexes: G:H.388 HEA.28: 43 residues within 4Å: Chain G: F.43, L.44, V.45, G.47, L.48, A.50, L.51, M.53, R.54, L.57, F.70, F.74, T.75, H.77, G.78, M.81, L.82, Y.85, A.86, G.141, W.142, Y.383, I.386, F.389, H.390, L.393, F.394, I.397, V.398, F.433, T.436, F.437, Q.440, R.450, R.451, Y.452, A.472, L.475, G.476, M.479 Ligands: HEA.27, CDL.29, PLM.52 36 PLIP interactions: 36 interactions with chain G, Hydrophobic interactions: G:F.43, G:F.43, G:L.44, G:L.44, G:V.45, G:L.48, G:L.48, G:A.50, G:L.51, G:R.54, G:F.74, G:M.81, G:L.82, G:L.82, G:I.386, G:F.389, G:F.389, G:L.393, G:I.397, G:F.437, G:A.472 Hydrogen bonds: G:F.74, G:W.142, G:Y.383, G:Q.440, G:R.451, G:Y.452 Salt bridges: G:R.450, G:R.451 pi-Stacking: G:H.77, G:H.77, G:H.390, G:H.390, G:H.390, G:F.437 Metal complexes: G:H.390

16 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 35 residues within 4Å: Chain B: M.12, G.13, P.14, K.15, G.16, N.17, L.18, I.19, L.22, I.23, L.30, I.33, M.34, V.37, V.38, F.40, A.41, V.45, F.117, W.118, L.121, F.482, V.483, V.486, F.487, W.490, R.491 Chain F: I.418, F.421, V.422, R.425 Ligands: HEA.7, CDL.24, CDL.39, CDL.43 Ligand excluded by PLIP CDL.11: 35 residues within 4Å: Chain B: F.109, R.111, L.112, L.115, L.171, L.175, V.178 Chain D: R.15, V.25, G.28, T.29, W.32, E.36, F.146, L.149, H.150, I.152, G.153, V.156, A.157, L.160, L.161, R.164, A.177, V.180, V.181, Y.184 Chain L: F.99, V.118, V.121, I.122, V.125, L.128, V.129 Ligands: 9Y0.10 Ligand excluded by PLIP CDL.17: 26 residues within 4Å: Chain E: I.13, Y.17, P.19, A.22, V.23, R.25, Q.26, L.217, A.218, I.220, G.221, A.222, L.224, A.225, L.226, W.228, F.229 Chain F: Y.17, H.18, P.19, A.22, R.25, A.136, L.226 Ligands: MQ9.15, CDL.23 Ligand excluded by PLIP CDL.18: 35 residues within 4Å: Chain E: H.34, W.35, S.36, L.39, V.119, A.122, R.123, F.126, T.127, F.235, R.363, P.364, R.365, T.371, S.375, I.378, L.382, L.415, I.418, V.419, V.422, A.423, W.426, A.427, L.430, P.480 Chain V: I.213, M.217, R.222, A.223 Ligands: 9YF.16, CDL.29, CDL.50, 9XX.53, MQ9.56 Ligand excluded by PLIP CDL.23: 26 residues within 4Å: Chain E: Y.17, H.18, P.19, A.22, R.25, A.136, L.226 Chain F: I.13, Y.17, P.19, A.22, V.23, R.25, Q.26, L.217, A.218, I.220, G.221, A.222, L.224, A.225, L.226, W.228, F.229 Ligands: CDL.17, MQ9.25 Ligand excluded by PLIP CDL.24: 34 residues within 4Å: Chain A: I.213, M.217, R.222, A.223 Chain F: H.34, W.35, S.36, L.39, V.119, A.122, R.123, F.126, T.127, F.235, R.363, P.364, R.365, T.371, S.375, I.378, A.379, L.382, L.415, I.418, V.419, V.422, A.423, W.426, A.427, L.430, P.480 Ligands: MQ9.4, CDL.8, CDL.39 Ligand excluded by PLIP CDL.29: 37 residues within 4Å: Chain E: I.418, F.421, V.422, R.425 Chain G: M.12, G.13, P.14, K.15, G.16, N.17, L.18, I.19, L.22, I.23, L.30, I.33, M.34, V.37, V.38, F.40, A.41, V.45, F.117, W.118, L.121, F.482, V.483, V.486, F.487, W.490, R.491 Ligands: CDL.18, HEA.28, CDL.32, CDL.50, PLM.52, 9XX.53 Ligand excluded by PLIP CDL.32: 35 residues within 4Å: Chain E: M.376, L.380, M.412, V.413, V.414, P.416, A.417, I.418, Y.420, F.421, R.425 Chain G: M.12, V.37, V.38, A.41, L.121, F.487 Chain H: I.45, M.48, H.49, G.51, G.52, S.55, V.82, I.83, A.85, L.86, V.87, R.89, N.90, L.93, R.94 Ligands: CDL.29, 9Y0.30, 9XX.53 Ligand excluded by PLIP CDL.39: 25 residues within 4Å: Chain A: M.217, R.222 Chain B: Y.20, I.23, F.122 Chain F: R.363, R.365, V.422, W.426, L.430, K.483, R.484 Chain L: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123, S.124 Ligands: CDL.8, CDL.24, CDL.41 Ligand excluded by PLIP CDL.40: 24 residues within 4Å: Chain A: A.211, W.218 Chain C: L.49, W.53, L.102, I.106, L.110, K.114 Chain D: F.107, I.152, L.155, V.156, V.159, A.163, K.166, M.167 Chain F: V.268, L.271 Chain L: I.122, C.126, F.130, W.134 Ligands: 9YF.3, CDL.41 Ligand excluded by PLIP CDL.41: 21 residues within 4Å: Chain A: I.207, V.210, A.211, G.214, V.215, M.217, W.218, R.222 Chain F: K.487 Chain L: W.91, A.119, F.120, I.122, T.123, C.126, G.127, F.130, W.134 Ligands: 9YF.3, CDL.39, CDL.40 Ligand excluded by PLIP CDL.43: 34 residues within 4Å: Chain B: M.12, K.15, V.37, V.38, A.41, L.121, F.487 Chain F: M.376, L.380, M.412, V.413, V.414, P.416, A.417, I.418, Y.420, F.421, R.425 Chain O: I.45, M.48, H.49, G.51, G.52, S.55, I.83, A.85, L.86, V.87, R.89, N.90, L.93, R.94 Ligands: CDL.8, 9Y0.22 Ligand excluded by PLIP CDL.47: 24 residues within 4Å: Chain E: V.268, L.271 Chain Q: F.107, I.152, L.155, V.156, V.159, A.163, K.166, M.167 Chain R: I.122, C.126, F.130, W.134 Chain V: A.211, W.218 Chain W: L.49, W.53, L.102, I.106, L.110, K.114 Ligands: CDL.51, 9YF.57 Ligand excluded by PLIP CDL.48: 35 residues within 4Å: Chain G: F.109, R.111, L.112, L.115, L.171, L.175, V.178 Chain Q: R.15, V.25, G.28, T.29, W.32, E.36, F.146, L.149, H.150, I.152, G.153, V.156, A.157, L.160, L.161, R.164, A.177, V.180, V.181, Y.184 Chain R: F.99, V.118, V.121, I.122, V.125, L.128, V.129 Ligands: 9Y0.46 Ligand excluded by PLIP CDL.50: 25 residues within 4Å: Chain E: R.365, V.422, W.426, L.430, K.483, R.484 Chain G: Y.20, I.23, F.122 Chain R: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123, S.124 Chain V: M.217, R.222 Ligands: 9YF.16, CDL.18, CDL.29, CDL.51 Ligand excluded by PLIP CDL.51: 20 residues within 4Å: Chain R: W.91, A.119, F.120, I.122, T.123, C.126, G.127, F.130, W.134 Chain V: I.207, V.210, A.211, G.214, V.215, M.217, W.218, R.222 Ligands: CDL.47, CDL.50, 9YF.57 Ligand excluded by PLIP

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

FES.9: 10 residues within 4Å: Chain C: C.307, H.309, L.310, C.312, C.326, C.328, H.329, S.331, P.345, A.346 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.307, C:H.309, C:H.309, C:C.326, C:H.329 FES.58: 10 residues within 4Å: Chain W: C.307, H.309, L.310, C.312, C.326, C.328, H.329, S.331, P.345, A.346 5 PLIP interactions: 5 interactions with chain W, Metal complexes: W:C.307, W:H.309, W:H.309, W:C.326, W:H.329

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

9Y0.10: 26 residues within 4Å: Chain B: M.164, A.167, V.168, F.223, A.226, A.227, H.230, L.231 Chain D: Y.121, V.125, T.130, I.131, P.132, Y.141, L.142, G.145, F.146, L.149 Chain L: F.99, A.102, A.103, A.106, W.109, I.114, V.118 Ligands: CDL.11 13 PLIP interactions: 4 interactions with chain L, 3 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: L:A.103, L:A.106, L:W.109, L:I.114, B:A.226, B:A.227, B:L.231, D:Y.121, D:Y.121, D:V.125, D:Y.141, D:Y.141, D:L.149 9Y0.22: 22 residues within 4Å: Chain F: L.340, Y.344, I.347, K.350, V.351, T.352, I.373, M.376, A.377, L.380, P.416 Chain O: V.22, T.26, G.27, W.40, H.42, M.43, P.44, V.47 Ligands: MQ9.4, MQ9.19, CDL.43 8 PLIP interactions: 3 interactions with chain O, 5 interactions with chain F Hydrophobic interactions: O:W.40, O:P.44, O:V.47, F:Y.344, F:I.347, F:I.347, F:K.350, F:I.373 9Y0.30: 22 residues within 4Å: Chain E: L.340, Y.344, I.347, K.350, V.351, T.352, I.373, M.376, A.377, L.380, P.416 Chain H: V.22, T.26, G.27, W.40, H.42, M.43, P.44, V.47 Ligands: MQ9.14, CDL.32, MQ9.56 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain E Hydrophobic interactions: H:W.40, H:P.44, H:V.47, E:Y.344, E:I.347, E:I.347, E:I.373 9Y0.31: 21 residues within 4Å: Chain G: L.48, F.52, F.64, L.65, Q.69 Chain H: V.68, G.69, H.70, V.71, W.74, F.75, G.78, F.79, V.82 Chain P: L.309 Chain U: C.1, G.4, Q.5, I.6 Ligands: 9YF.16, 9XX.53 10 PLIP interactions: 1 interactions with chain U, 7 interactions with chain H, 1 interactions with chain G, 1 interactions with chain P Hydrophobic interactions: U:I.6, H:H.70, H:V.71, H:W.74, H:W.74, H:F.75, H:F.75, H:F.79, G:F.52, P:L.309 9Y0.46: 26 residues within 4Å: Chain G: M.164, A.167, V.168, F.223, A.226, A.227, H.230, L.231 Chain Q: Y.121, V.125, T.130, I.131, P.132, Y.141, L.142, G.145, F.146, L.149 Chain R: F.99, A.102, A.103, A.106, W.109, I.114, V.118 Ligands: CDL.48 19 PLIP interactions: 9 interactions with chain Q, 5 interactions with chain R, 5 interactions with chain G Hydrophobic interactions: Q:Y.121, Q:Y.121, Q:V.125, Q:Y.141, Q:Y.141, Q:L.142, Q:F.146, Q:L.149, R:A.103, R:A.106, R:W.109, R:W.109, R:I.114, G:F.223, G:F.223, G:A.226, G:A.227, G:L.231 Hydrogen bonds: Q:I.131

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

HEM.12: 30 residues within 4Å: Chain E: S.36, F.37, L.39, G.40, E.41, A.43, L.44, F.113, I.117, H.120, L.121, R.123, I.124, A.129, F.130, R.134, N.137, W.138, G.141, S.142, L.144, L.145, I.216, I.220, H.223, L.224, V.227, H.232, T.233 Ligands: MQ9.15 27 PLIP interactions: 27 interactions with chain E, Hydrophobic interactions: E:L.44, E:F.113, E:I.117, E:I.117, E:I.117, E:I.124, E:I.124, E:A.129, E:N.137, E:W.138, E:L.144, E:L.145, E:I.220, E:I.220, E:L.224, E:V.227, E:V.227 Hydrogen bonds: E:G.40, E:T.233 Salt bridges: E:H.120, E:R.123, E:R.123, E:R.134, E:H.232, E:H.232 pi-Cation interactions: E:H.120 Metal complexes: E:H.120 HEM.13: 31 residues within 4Å: Chain E: F.47, L.50, L.51, G.54, V.55, L.57, T.58, F.61, A.89, I.92, R.103, H.106, H.107, A.110, F.113, A.148, E.151, G.152, G.155, Y.156, L.158, P.159, Y.205, H.208, I.209, P.213, I.216, N.279, D.299, Y.301 Chain F: L.210 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:F.47, E:L.50, E:L.50, E:L.51, E:V.55, E:L.57, E:L.57, E:H.107, E:L.158, E:Y.205, E:I.209, E:I.209, E:P.213, F:L.210 Hydrogen bonds: E:R.103, E:N.279 Salt bridges: E:R.103, E:R.103, E:H.107 Metal complexes: E:H.106, E:H.208 HEM.20: 31 residues within 4Å: Chain F: S.36, F.37, L.39, G.40, E.41, A.43, L.44, F.113, I.117, H.120, L.121, R.123, I.124, A.129, F.130, R.134, N.137, W.138, G.141, S.142, L.144, L.145, A.148, I.216, I.220, H.223, L.224, V.227, H.232, T.233 Ligands: MQ9.25 26 PLIP interactions: 26 interactions with chain F, Hydrophobic interactions: F:F.113, F:I.117, F:I.117, F:I.117, F:I.124, F:I.124, F:A.129, F:W.138, F:L.144, F:L.145, F:I.220, F:I.220, F:L.224, F:V.227, F:V.227 Hydrogen bonds: F:L.39, F:G.40, F:T.233 Salt bridges: F:H.120, F:R.123, F:R.123, F:R.134, F:H.232, F:H.232 pi-Stacking: F:H.120 Metal complexes: F:H.120 HEM.21: 31 residues within 4Å: Chain E: L.210 Chain F: F.47, L.50, L.51, G.54, V.55, L.57, T.58, F.61, A.89, I.92, R.103, H.106, H.107, A.110, F.113, A.148, E.151, G.152, G.155, Y.156, L.158, P.159, Y.205, H.208, I.209, P.213, I.216, N.279, D.299, Y.301 22 PLIP interactions: 21 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:F.47, F:L.50, F:L.50, F:L.51, F:V.55, F:L.57, F:L.57, F:H.107, F:E.151, F:L.158, F:Y.205, F:I.209, F:P.213, F:I.216, E:L.210 Hydrogen bonds: F:R.103, F:N.279 Salt bridges: F:R.103, F:R.103, F:H.107 Metal complexes: F:H.106, F:H.208

3 x PLM: PALMITIC ACID(Covalent)

PLM.33: 10 residues within 4Å: Chain E: W.312, W.315, E.316, F.317, W.329 Chain H: F.58, V.61, R.64 Chain I: C.1 Ligands: 9XX.34 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:W.315, E:W.315, E:F.317, E:F.317, E:W.329, H:V.61 PLM.35: 10 residues within 4Å: Chain F: W.312, W.315, E.316, F.317, W.329 Chain J: C.1 Chain O: F.58, V.61, R.64 Ligands: 9XX.36 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain O Hydrophobic interactions: F:W.315, F:W.315, F:F.317, F:F.317, F:W.329, O:V.61 PLM.52: 19 residues within 4Å: Chain G: V.45, L.48, M.49, F.52, Q.69, Q.72, L.73, I.128, F.131, T.133, P.134, G.136, A.137 Chain U: C.1, S.2, A.3 Ligands: HEA.28, CDL.29, 9XX.53 6 PLIP interactions: 2 interactions with chain U, 4 interactions with chain G Hydrogen bonds: U:S.2, U:A.3 Hydrophobic interactions: G:V.45, G:V.45, G:L.73, G:F.131

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

9XX.34: 10 residues within 4Å: Chain E: F.317, Y.318, P.319, I.324, V.328, W.329, V.332 Chain I: C.1 Ligands: PLM.33, 9YF.59 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.317, E:F.317, E:F.317, E:F.317, E:F.317, E:F.317, E:P.319, E:W.329, E:W.329, E:V.332 9XX.36: 9 residues within 4Å: Chain F: F.317, Y.318, P.319, I.324, V.328, W.329, V.332 Chain J: C.1 Ligands: PLM.35 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.317, F:F.317, F:F.317, F:F.317, F:F.317, F:P.319, F:W.329, F:W.329, F:V.332 9XX.53: 21 residues within 4Å: Chain E: L.415, I.418 Chain G: F.52, Q.69, L.121, L.125, I.128, A.129, F.131, I.132 Chain H: V.71, F.75, F.79 Chain U: C.1 Ligands: 9YF.16, CDL.18, CDL.29, 9Y0.31, CDL.32, MQ9.49, PLM.52 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:F.75, G:L.125, G:I.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanofsky, D.J. et al., Structure of mycobacterial CIII 2 CIV 2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203). Elife (2021)

Release Date

2021-08-04

Peptides

Cytochrome bc1 complex cytochrome c subunit: AV
Cytochrome c oxidase subunit 1: BG
Cytochrome bc1 complex Rieske iron-sulfur subunit: CW
Cytochrome aa3 subunit 3: DQ
Cytochrome bc1 complex cytochrome b subunit: EF
Putative conserved transmembrane protein: HO
Superoxide dismutase [Cu-Zn]: IJ
Cytochrome aa3 subunit 2: KP
Cytochrome c oxidase polypeptide 4: LR
Cytochrome c oxidase subunit CtaJ: MS
Uncharacterized protein MSMEG_4692/MSMEI_4575: NT
LpqE protein: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

V
I

B
R

G
L

C
M

W
Y

D
S

Q
X

E
E

F
F

H
J

O
P

I
D

J
G

K
Q

P
K

L
T

R
Z

M
U

S
a

N
V

T
b

U
c

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bc1 complex cytochrome c subunit

Cytochrome c oxidase subunit 1

Cytochrome bc1 complex Rieske iron-sulfur subunit

Cytochrome aa3 subunit 3

Cytochrome bc1 complex cytochrome b subunit

Putative conserved transmembrane protein

Superoxide dismutase [Cu-Zn]

Cytochrome aa3 subunit 2

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit CtaJ

Uncharacterized protein MSMEG_4692/MSMEI_4575

LpqE protein

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