SMTL ID : 9dm1.1

Mycobacterial supercomplex malate:quinone oxidoreductase assembly

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.255, H.304, H.305 Ligands: HEA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.255, A:H.304, A:H.305 CU.20: 4 residues within 4Å: Chain D: H.255, H.304, H.305 Ligands: HEA.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.255, D:H.304, D:H.305 CU.28: 4 residues within 4Å: Chain G: C.247, C.251, H.255, M.258 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.247, G:C.251, G:H.255 CU.29: 5 residues within 4Å: Chain G: F.110, V.204, H.206, C.251, M.258 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.206, G:H.206 CU.40: 5 residues within 4Å: Chain N: C.247, T.248, E.249, C.251, H.255 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.247, N:E.249, N:C.251, N:H.255 CU.41: 5 residues within 4Å: Chain N: F.110, H.206, C.247, C.251, M.258 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:H.206, N:H.206

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

HEA.2: 31 residues within 4Å: Chain A: T.143, W.251, V.258, Y.259, A.262, H.304, H.305, T.321, I.324, A.325, T.328, G.329, F.360, L.361, G.364, G.367, V.368, L.370, A.371, D.376, T.380, V.385, H.388, F.389, V.392, L.393, R.450 Chain G: V.34, P.76, I.80 Ligands: CU.1 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain G, Hydrophobic interactions: A:V.258, A:V.258, A:T.321, A:A.325, A:T.328, A:F.360, A:L.361, A:V.368, A:L.370, A:L.370, A:F.389, A:F.389, A:V.392, A:L.393, A:L.393, G:V.34, G:P.76, G:I.80 Hydrogen bonds: A:Y.259, A:Y.259, A:D.381 Salt bridges: A:R.450 pi-Stacking: A:H.388, A:H.388 pi-Cation interactions: A:H.255, A:H.304 Metal complexes: A:H.388 HEA.3: 32 residues within 4Å: Chain A: F.43, L.44, V.45, G.47, L.48, A.50, L.51, R.54, F.70, F.74, H.77, G.78, M.81, L.82, G.141, W.142, Y.383, F.389, H.390, L.393, F.394, I.397, T.436, F.437, R.450, R.451, Y.452, A.472, L.475, G.476, M.479 Ligands: CDL.4 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:F.43, A:F.43, A:L.44, A:L.48, A:L.48, A:A.50, A:L.51, A:F.74, A:M.81, A:F.389, A:F.389, A:L.393, A:I.397, A:A.472 Hydrogen bonds: A:F.74, A:W.142, A:R.451, A:Y.452 Salt bridges: A:R.450, A:R.451 pi-Stacking: A:H.77, A:H.77, A:H.390, A:H.390, A:F.437, A:F.437 Metal complexes: A:H.77 HEA.21: 32 residues within 4Å: Chain D: W.142, T.143, W.251, V.258, Y.259, A.262, H.304, H.305, T.321, I.324, G.329, 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, R.450 Chain N: V.34, P.76, I.80 Ligands: CU.20 28 PLIP interactions: 25 interactions with chain D, 3 interactions with chain N, Hydrophobic interactions: D:V.258, D:A.262, D:T.321, D:F.360, D:L.361, D:V.368, D:V.368, D:L.370, D:L.370, D:A.371, D:V.385, D:V.385, D:F.389, D:F.389, D:V.392, D:L.393, D:L.393, N:V.34, N:P.76, N:I.80 Hydrogen bonds: D:D.381 Salt bridges: D:H.305, D:R.450 pi-Stacking: D:H.388, D:H.388 pi-Cation interactions: D:H.255, D:H.304 Metal complexes: D:H.388 HEA.22: 35 residues within 4Å: Chain D: F.43, L.44, V.45, G.47, L.48, A.50, L.51, M.53, R.54, F.70, F.74, H.77, G.78, M.81, L.82, G.141, W.142, Y.383, I.386, F.389, H.390, L.393, F.394, I.397, T.436, F.437, Q.440, R.450, R.451, Y.452, A.472, L.475, G.476, M.479 Ligands: CDL.23 35 PLIP interactions: 35 interactions with chain D, Hydrophobic interactions: D:F.43, D:F.43, D:L.44, D:L.44, D:V.45, D:L.48, D:L.48, D:A.50, D:L.51, D:R.54, D:F.74, D:M.81, D:L.82, D:L.82, D:I.386, D:F.389, D:F.389, D:L.393, D:I.397, D:F.437, D:A.472 Hydrogen bonds: D:F.74, D:W.142, D:Q.440, D:R.451, D:Y.452 Salt bridges: D:R.450, D:R.451 pi-Stacking: D:H.77, D:H.77, D:H.390, D:H.390, D:H.390, D:F.437 Metal complexes: D:H.390

16 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 27 residues within 4Å: Chain A: M.12, G.13, P.14, G.16, N.17, L.18, I.19, L.22, I.33, M.34, V.37, V.38, F.117, W.118, V.486, W.490, R.491 Chain C: I.418, F.421, V.422, R.425 Ligands: HEA.3, CDL.15, CDL.32, CDL.35, PLM.61, 9XX.62 Ligand excluded by PLIP CDL.9: 24 residues within 4Å: Chain B: 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 C: Y.17, H.18, P.19, R.25, A.136 Ligands: MQ9.8, CDL.14 Ligand excluded by PLIP CDL.10: 30 residues within 4Å: Chain B: H.34, W.35, S.36, V.119, A.122, R.123, F.126, T.127, 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 Chain U: I.213, M.217, R.222, A.223 Ligands: CDL.46, 9YF.53, MQ9.56 Ligand excluded by PLIP CDL.14: 22 residues within 4Å: Chain B: Y.17, H.18, P.19 Chain C: 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.9, MQ9.19 Ligand excluded by PLIP CDL.15: 31 residues within 4Å: Chain C: H.34, W.35, S.36, V.119, A.122, R.123, F.126, T.127, 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 Chain M: I.213, M.217, R.222, A.223 Ligands: CDL.4, MQ9.18, CDL.32, 9YF.63 Ligand excluded by PLIP CDL.23: 30 residues within 4Å: Chain B: I.418, F.421, V.422, R.425 Chain D: M.12, G.13, P.14, G.16, N.17, L.18, I.19, L.22, L.30, I.33, M.34, V.37, V.38, A.41, V.45, F.117, W.118, L.121, V.486, W.490, R.491 Ligands: HEA.22, CDL.46, CDL.48, PLM.51, 9XX.52 Ligand excluded by PLIP CDL.30: 21 residues within 4Å: Chain A: F.109, R.111, L.112, L.171, L.175 Chain H: V.25, G.28, T.29, W.32, E.36, L.149, H.150, G.153, A.157, R.164, A.177, V.180, V.181, Y.184 Chain I: F.99 Ligands: 9Y0.31 Ligand excluded by PLIP CDL.32: 19 residues within 4Å: Chain A: Y.20, I.23 Chain C: R.365, W.426, L.430, R.484 Chain I: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123 Chain M: M.217 Ligands: CDL.4, CDL.15, CDL.34 Ligand excluded by PLIP CDL.33: 18 residues within 4Å: Chain H: L.155, V.156, V.159, A.163, K.166, M.167 Chain I: I.122, C.126, F.130, W.134 Chain M: W.218 Chain X: L.49, W.53, L.102, I.106, L.110, K.114 Ligands: CDL.34 Ligand excluded by PLIP CDL.34: 21 residues within 4Å: Chain C: R.484, K.487 Chain I: W.91, I.122, T.123, C.126, G.127, W.134, G.135, E.137 Chain M: I.207, V.210, A.211, G.214, V.215, M.217, W.218, R.222 Ligands: CDL.32, CDL.33, 9YF.39 Ligand excluded by PLIP CDL.35: 27 residues within 4Å: Chain A: M.12, V.37, A.41, F.487 Chain C: M.376, M.412, P.416, A.417, I.418, Y.420, F.421, R.425 Chain L: I.45, M.48, H.49, G.51, G.52, S.55, I.83, A.85, L.86, V.87, R.89, N.90, R.94 Ligands: CDL.4, 9XX.62 Ligand excluded by PLIP CDL.42: 18 residues within 4Å: Chain O: L.155, V.156, V.159, A.163, K.166, M.167 Chain P: I.122, C.126, F.130, W.134 Chain U: W.218 Chain V: L.49, W.53, L.102, I.106, L.110, K.114 Ligands: CDL.47 Ligand excluded by PLIP CDL.43: 21 residues within 4Å: Chain D: F.109, R.111, L.112, L.171, L.175 Chain O: V.25, G.28, T.29, W.32, E.36, L.149, H.150, G.153, A.157, R.164, A.177, V.180, V.181, Y.184 Chain P: F.99 Ligands: 9Y0.44 Ligand excluded by PLIP CDL.46: 18 residues within 4Å: Chain B: R.365, W.426, L.430, R.484 Chain D: Y.20, I.23 Chain P: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123 Ligands: CDL.10, CDL.23, CDL.47 Ligand excluded by PLIP CDL.47: 16 residues within 4Å: Chain P: W.91, A.119, I.122, T.123, C.126, G.127, W.134 Chain U: I.207, V.210, A.211, M.217, W.218, R.222 Ligands: CDL.42, CDL.46, 9YF.57 Ligand excluded by PLIP CDL.48: 27 residues within 4Å: Chain B: M.376, L.380, M.412, P.416, A.417, I.418, Y.420, F.421, R.425 Chain D: M.12, V.37, A.41, F.487 Chain S: I.45, M.48, H.49, G.51, S.55, I.83, A.85, L.86, V.87, R.89, N.90, R.94 Ligands: CDL.23, 9XX.52 Ligand excluded by PLIP

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

HEM.5: 26 residues within 4Å: Chain B: S.36, F.37, G.40, E.41, L.44, F.113, I.117, H.120, L.121, R.123, I.124, A.129, R.134, N.137, W.138, G.141, S.142, L.144, L.145, I.220, H.223, L.224, V.227, H.232, T.233 Ligands: MQ9.8 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:L.44, B:F.113, B:I.117, B:I.117, B:I.117, B:I.124, B:I.124, B:A.129, B:N.137, B:W.138, B:L.144, B:L.145, B:I.220, B:I.220, B:L.224, B:V.227, B:V.227 Hydrogen bonds: B:G.40, B:T.233 Salt bridges: B:H.120, B:R.123, B:R.123, B:R.134, B:H.232, B:H.232 pi-Cation interactions: B:H.120 Metal complexes: B:H.120 HEM.6: 25 residues within 4Å: Chain B: F.47, L.50, L.51, G.54, V.55, L.57, T.58, F.61, R.103, H.106, H.107, A.110, E.151, G.152, G.155, Y.156, L.158, P.159, Y.205, H.208, I.209, P.213, N.279, Y.301 Chain C: L.210 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.47, B:L.50, B:L.50, B:L.51, B:V.55, B:L.57, B:L.57, B:H.107, B:L.158, B:Y.205, B:I.209, B:I.209, B:P.213, C:L.210 Hydrogen bonds: B:R.103, B:N.279 Salt bridges: B:R.103, B:R.103, B:H.107 Metal complexes: B:H.106, B:H.208 HEM.12: 26 residues within 4Å: Chain C: S.36, F.37, G.40, E.41, L.44, F.113, I.117, H.120, L.121, R.123, I.124, A.129, R.134, N.137, W.138, G.141, S.142, L.144, L.145, I.220, H.223, L.224, V.227, H.232, T.233 Ligands: MQ9.19 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:F.113, C:I.117, C:I.117, C:I.117, C:I.124, C:I.124, C:A.129, C:W.138, C:L.144, C:L.145, C:I.220, C:I.220, C:L.224, C:V.227, C:V.227 Hydrogen bonds: C:L.39, C:G.40, C:T.233 Salt bridges: C:H.120, C:R.123, C:R.123, C:R.134, C:H.232, C:H.232 pi-Stacking: C:H.120 Metal complexes: C:H.120 HEM.13: 26 residues within 4Å: Chain B: L.210 Chain C: F.47, L.50, L.51, G.54, V.55, L.57, T.58, F.61, R.103, H.106, H.107, A.110, E.151, G.152, G.155, Y.156, L.158, P.159, Y.205, H.208, I.209, P.213, I.216, N.279, Y.301 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:F.47, C:L.50, C:L.50, C:L.51, C:V.55, C:L.57, C:L.57, C:H.107, C:E.151, C:L.158, C:Y.205, C:I.209, C:P.213, C:I.216, B:L.210 Hydrogen bonds: C:R.103, C:N.279 Salt bridges: C:R.103, C:R.103, C:H.107 Metal complexes: C:H.106, C:H.208

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

MQ9.7: 19 residues within 4Å: Chain B: L.143, I.146, L.147, F.150, A.171, L.172, I.175, T.176, I.179, M.186, I.215, M.302, A.331, M.334, F.338, I.342, A.343, F.346, K.350 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.143, B:I.146, B:I.146, B:L.147, B:F.150, B:F.150, B:F.150, B:A.171, B:L.172, B:I.175, B:A.331, B:F.338, B:I.342, B:A.343, B:F.346, B:K.350 MQ9.8: 29 residues within 4Å: Chain B: F.31, E.41, L.44, Y.45, I.48, L.52, T.53, F.101, V.102, L.224, V.227, W.228, F.254, V.256, G.259, A.260, F.262, A.263 Chain V: F.97, I.101, I.104, A.108 Chain X: L.165, F.168, T.172, A.175, F.176 Ligands: HEM.5, CDL.9 26 PLIP interactions: 16 interactions with chain B, 6 interactions with chain X, 4 interactions with chain V Hydrophobic interactions: B:F.31, B:L.44, B:I.48, B:L.52, B:L.52, B:T.53, B:F.101, B:F.101, B:V.102, B:L.224, B:V.227, B:W.228, B:F.262, B:F.262, B:F.262, B:A.263, X:L.165, X:F.168, X:T.172, X:A.175, X:F.176, X:F.176, V:F.97, V:I.101, V:I.104, V:A.108 MQ9.11: 17 residues within 4Å: Chain C: L.143, I.146, L.147, F.150, F.153, A.171, L.172, I.175, T.176, I.179, I.215, L.219, M.302, M.334, I.342, A.343, F.346 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.143, C:I.146, C:I.146, C:L.147, C:L.147, C:F.150, C:F.150, C:F.150, C:F.153, C:A.171, C:L.172, C:I.179, C:L.219, C:I.342, C:A.343, C:F.346 MQ9.17: 29 residues within 4Å: Chain A: F.122, L.125, I.126, A.129, I.132 Chain C: F.386, A.387, M.389, I.392, I.393, K.396, F.397, I.399, T.404, I.407, G.408 Chain I: L.97, S.100, T.101, V.104, W.112, L.113 Chain M: Y.190, L.192, G.193, P.199, M.202 Ligands: 9YF.39, 9YF.63 30 PLIP interactions: 7 interactions with chain A, 11 interactions with chain I, 9 interactions with chain C, 3 interactions with chain M Hydrophobic interactions: A:F.122, A:F.122, A:L.125, A:I.126, A:I.126, A:A.129, A:I.132, I:L.97, I:T.101, I:V.104, I:W.112, I:W.112, I:W.112, I:W.112, I:L.113, I:L.113, C:F.386, C:A.387, C:I.392, C:I.393, C:F.397, C:F.397, C:F.397, C:I.399, C:I.407, M:L.192, M:P.199, M:M.202 pi-Stacking: I:W.112, I:W.112 MQ9.18: 27 residues within 4Å: Chain C: M.118, V.119, L.121, A.122, F.125, L.145, M.149, F.300, W.304, V.337, L.340, L.341, Y.344, A.377, I.378, L.380, Y.381, L.382, T.385, F.386, M.389 Chain M: G.201, M.202, W.205, I.206, I.213 Ligands: CDL.15 29 PLIP interactions: 23 interactions with chain C, 6 interactions with chain M Hydrophobic interactions: C:M.118, C:V.119, C:L.121, C:F.125, C:F.125, C:L.145, C:F.300, C:V.337, C:V.337, C:V.337, C:L.340, C:L.340, C:Y.344, C:A.377, C:I.378, C:I.378, C:L.380, C:Y.381, C:Y.381, C:Y.381, C:L.382, C:T.385, M:W.205, M:W.205, M:W.205, M:W.205, M:I.206, M:I.213 Hydrogen bonds: C:Y.381 MQ9.19: 28 residues within 4Å: Chain C: F.31, E.41, L.44, Y.45, I.48, L.52, T.53, F.101, V.102, L.224, V.227, W.228, V.256, G.259, A.260, F.262, A.263 Chain V: L.165, F.168, T.172, A.175, F.176 Chain X: F.97, I.101, I.104, A.108 Ligands: HEM.12, CDL.14 24 PLIP interactions: 14 interactions with chain C, 4 interactions with chain X, 6 interactions with chain V Hydrophobic interactions: C:F.31, C:L.44, C:I.48, C:L.52, C:T.53, C:F.101, C:F.101, C:V.102, C:L.224, C:V.227, C:W.228, C:F.262, C:F.262, C:A.263, X:F.97, X:I.101, X:I.104, X:A.108, V:L.165, V:F.168, V:T.172, V:A.175, V:F.176, V:F.176 MQ9.45: 29 residues within 4Å: Chain B: F.386, A.387, M.389, I.392, I.393, K.396, F.397, I.399, T.404, I.407, G.408 Chain D: F.122, L.125, I.126, A.129, I.132 Chain P: L.97, S.100, T.101, V.104, W.112, L.113 Chain U: Y.190, L.192, G.193, P.199, M.202 Ligands: 9YF.53, 9YF.57 26 PLIP interactions: 8 interactions with chain P, 12 interactions with chain B, 2 interactions with chain U, 4 interactions with chain D Hydrophobic interactions: P:L.97, P:T.101, P:V.104, P:W.112, P:W.112, P:L.113, B:F.386, B:F.386, B:A.387, B:I.392, B:I.393, B:F.397, B:F.397, B:F.397, B:F.397, B:I.399, B:T.404, B:I.407, U:P.199, U:P.199, D:F.122, D:L.125, D:A.129, D:I.132 pi-Stacking: P:W.112, P:W.112 MQ9.56: 25 residues within 4Å: Chain B: M.118, L.121, A.122, F.125, L.145, M.149, F.300, V.337, L.340, L.341, Y.344, A.377, I.378, L.380, Y.381, L.382, T.385, F.386, M.389 Chain U: M.202, W.205, I.206, I.213 Ligands: CDL.10, 9Y0.49 26 PLIP interactions: 6 interactions with chain U, 20 interactions with chain B Hydrophobic interactions: U:W.205, U:W.205, U:W.205, U:W.205, U:I.206, U:I.213, B:M.118, B:L.121, B:F.125, B:F.125, B:L.145, B:F.300, B:V.337, B:V.337, B:L.340, B:Y.344, B:A.377, B:A.377, B:I.378, B:L.380, B:Y.381, B:Y.381, B:Y.381, B:L.382, B:T.385 Hydrogen bonds: B:Y.381

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

9Y0.16: 14 residues within 4Å: Chain C: L.340, Y.344, I.347, K.350, V.351, I.373, M.376, A.377 Chain L: V.22, W.40, H.42, M.43, P.44, V.47 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain L Hydrophobic interactions: C:Y.344, C:I.347, C:I.347, C:K.350, C:I.373, L:W.40, L:P.44, L:V.47 9Y0.31: 20 residues within 4Å: Chain A: M.164, F.223, A.226, A.227, L.231 Chain H: Y.121, V.125, T.130, I.131, P.132, Y.141, G.145, F.146, L.149 Chain I: F.99, A.103, A.106, W.109, I.114 Ligands: CDL.30 13 PLIP interactions: 6 interactions with chain H, 4 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: H:Y.121, H:Y.121, H:V.125, H:Y.141, H:Y.141, H:L.149, I:A.103, I:A.106, I:W.109, I:I.114, A:A.226, A:A.227, A:L.231 9Y0.36: 16 residues within 4Å: Chain A: F.52, F.64, Q.69 Chain G: L.309 Chain L: V.68, H.70, V.71, W.74, F.75, G.78, F.79 Chain W: G.4, Q.5, I.6 Ligands: 9XX.62, 9YF.63 10 PLIP interactions: 8 interactions with chain L, 1 interactions with chain W, 1 interactions with chain G Hydrophobic interactions: L:V.71, L:V.71, L:W.74, L:F.75, L:F.79, W:I.6, G:L.309 Salt bridges: L:H.70, L:H.70, L:H.70 9Y0.44: 21 residues within 4Å: Chain D: M.164, F.223, A.226, A.227, L.231 Chain O: Y.121, V.125, T.130, I.131, P.132, Y.141, L.142, G.145, F.146, L.149 Chain P: F.99, A.103, A.106, W.109, I.114 Ligands: CDL.43 19 PLIP interactions: 5 interactions with chain P, 9 interactions with chain O, 5 interactions with chain D Hydrophobic interactions: P:A.103, P:A.106, P:W.109, P:W.109, P:I.114, O:Y.121, O:Y.121, O:V.125, O:Y.141, O:Y.141, O:L.142, O:F.146, O:L.149, D:F.223, D:F.223, D:A.226, D:A.227, D:L.231 Hydrogen bonds: O:I.131 9Y0.49: 15 residues within 4Å: Chain B: Y.344, I.347, K.350, V.351, I.373, M.376, A.377 Chain S: V.22, T.26, W.40, H.42, M.43, P.44, V.47 Ligands: MQ9.56 7 PLIP interactions: 3 interactions with chain S, 4 interactions with chain B Hydrophobic interactions: S:W.40, S:P.44, S:V.47, B:Y.344, B:I.347, B:I.347, B:I.373 9Y0.50: 14 residues within 4Å: Chain D: F.52, F.64, Q.69 Chain N: L.309 Chain S: V.68, H.70, V.71, W.74, F.75, G.78, F.79 Chain T: I.6 Ligands: 9XX.52, 9YF.53 10 PLIP interactions: 7 interactions with chain S, 1 interactions with chain N, 1 interactions with chain D, 1 interactions with chain T Hydrophobic interactions: S:H.70, S:V.71, S:W.74, S:W.74, S:F.75, S:F.75, S:F.79, N:L.309, D:F.52, T:I.6

4 x PLM: PALMITIC ACID(Covalent)

PLM.24: 7 residues within 4Å: Chain B: W.315, E.316, F.317, W.329 Chain E: C.1 Chain S: V.61, R.64 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain S Hydrophobic interactions: B:W.315, B:W.315, B:F.317, B:F.317, B:W.329, S:V.61 PLM.26: 8 residues within 4Å: Chain C: W.315, E.316, F.317, W.329 Chain F: C.1 Chain L: V.61, R.64 Ligands: 9XX.27 6 PLIP interactions: 1 interactions with chain L, 5 interactions with chain C Hydrophobic interactions: L:V.61, C:W.315, C:W.315, C:F.317, C:F.317, C:W.329 PLM.51: 13 residues within 4Å: Chain D: V.45, M.49, Q.69, Q.72, L.73, F.131, T.133, P.134 Chain T: C.1, S.2, A.3 Ligands: CDL.23, 9XX.52 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain T Hydrophobic interactions: D:V.45, D:V.45, D:L.73, D:F.131 Hydrogen bonds: T:S.2, T:A.3 PLM.61: 13 residues within 4Å: Chain A: V.45, F.52, Q.69, Q.72, L.73, F.131, T.133, P.134, G.136 Chain W: C.1, S.2 Ligands: CDL.4, 9XX.62 4 PLIP interactions: 1 interactions with chain W, 3 interactions with chain A Hydrogen bonds: W:S.2 Hydrophobic interactions: A:V.45, A:V.45, A:F.52

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

9XX.25: 7 residues within 4Å: Chain B: F.317, Y.318, P.319, I.324, W.329, V.332 Chain E: C.1 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.317, B:F.317, B:F.317, B:F.317, B:F.317, B:F.317, B:P.319, B:W.329, B:W.329, B:V.332 9XX.27: 7 residues within 4Å: Chain C: F.317, Y.318, P.319, W.329, V.332 Chain F: C.1 Ligands: PLM.26 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.317, C:F.317, C:F.317, C:F.317, C:F.317, C:P.319, C:W.329, C:W.329, C:V.332 9XX.52: 12 residues within 4Å: Chain D: L.125, I.128, F.131, I.132 Chain S: V.71, F.75 Chain T: C.1 Ligands: CDL.23, CDL.48, 9Y0.50, PLM.51, 9YF.53 3 PLIP interactions: 1 interactions with chain S, 2 interactions with chain D Hydrophobic interactions: S:F.75, D:L.125, D:I.132 9XX.62: 11 residues within 4Å: Chain A: I.128, A.129, F.131, I.132 Chain L: V.82 Chain W: C.1 Ligands: CDL.4, CDL.35, 9Y0.36, PLM.61, 9YF.63 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain W, 1 interactions with chain L Hydrophobic interactions: A:I.128, A:F.131, A:I.132, L:V.82 Hydrogen bonds: W:C.1

4 x HEC: HEME C(Non-covalent)

HEC.37: 25 residues within 4Å: Chain G: W.112 Chain M: S.15, C.16, C.19, H.20, R.30, P.32, L.34, T.37, A.41, V.42, Q.45, V.46, M.51, A.53, A.60, F.67, L.75, T.153, G.154, Q.156 Chain W: T.9, Q.12, P.14, A.15 17 PLIP interactions: 1 interactions with chain W, 15 interactions with chain M, 1 interactions with chain G, Hydrogen bonds: W:A.15, M:Q.45, M:Q.156 Hydrophobic interactions: M:P.32, M:L.34, M:L.34, M:T.37, M:A.41, M:V.42, M:V.46, M:M.51, M:A.53, M:F.67, M:L.75, M:Q.156, G:W.112 Metal complexes: M:H.20 HEC.38: 27 residues within 4Å: Chain M: F.44, Q.45, T.48, R.50, Q.59, A.60, N.116, C.117, C.120, H.121, L.130, Y.135, P.137, D.138, L.139, A.142, I.147, A.150, M.151, P.155, Q.156, N.157, M.158, P.159, F.161, I.174 Chain X: Y.317 17 PLIP interactions: 17 interactions with chain M, Hydrophobic interactions: M:F.44, M:N.116, M:L.130, M:L.130, M:L.139, M:A.142, M:I.147, M:I.147, M:A.150, M:P.155, M:P.159, M:I.174 Hydrogen bonds: M:Q.45, M:Q.59 Salt bridges: M:R.50, M:R.50 Metal complexes: M:H.121 HEC.54: 26 residues within 4Å: Chain N: W.112 Chain T: T.9, Q.12, P.14, A.15 Chain U: S.15, C.16, C.19, H.20, R.30, P.32, L.34, T.37, A.41, V.42, Q.45, V.46, M.51, P.52, A.53, A.60, F.67, T.153, G.154, P.155, Q.156 11 PLIP interactions: 9 interactions with chain U, 1 interactions with chain T, 1 interactions with chain N, Hydrophobic interactions: U:P.32, U:L.34, U:T.37, U:A.41, U:V.42, U:V.46, U:F.67, N:W.112 Hydrogen bonds: U:Q.156, T:A.15 Metal complexes: U:H.20 HEC.55: 26 residues within 4Å: Chain U: F.44, Q.45, R.50, Q.59, A.60, N.116, C.117, C.120, H.121, L.130, Y.135, P.137, D.138, L.139, A.142, I.147, A.150, M.151, P.155, Q.156, N.157, M.158, P.159, F.161, I.174 Chain V: Y.317 18 PLIP interactions: 18 interactions with chain U, Hydrophobic interactions: U:F.44, U:N.116, U:L.130, U:A.142, U:I.147, U:I.147, U:A.150, U:P.155, U:Q.156, U:M.158, U:P.159, U:F.161 Hydrogen bonds: U:Q.45, U:D.138, U:Q.156 Salt bridges: U:R.50, U:R.50 Metal complexes: U:H.121

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.39: 19 residues within 4Å: Chain C: L.275, L.276 Chain I: P.111, W.112, A.116, F.120 Chain M: K.126, D.138, G.140, A.182, S.186, G.189, Y.190, G.191, L.192, M.202, I.207 Ligands: MQ9.17, CDL.34 16 PLIP interactions: 10 interactions with chain M, 5 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: M:Y.190, M:Y.190, M:Y.190, M:L.192, M:I.207, M:I.207, I:P.111, I:W.112, I:W.112, I:A.116, I:F.120, C:L.276 Hydrogen bonds: M:D.138, M:G.140, M:S.186, M:G.191 9YF.53: 23 residues within 4Å: Chain B: F.386, S.400, N.402, A.403, W.406, I.407, I.410, G.411, L.415 Chain D: I.132 Chain S: V.71, E.72, F.75, F.79 Chain T: C.1, S.2, I.6, Q.8 Chain U: S.132 Ligands: CDL.10, MQ9.45, 9Y0.50, 9XX.52 17 PLIP interactions: 10 interactions with chain B, 4 interactions with chain S, 1 interactions with chain T, 1 interactions with chain U, 1 interactions with chain D Hydrophobic interactions: B:F.386, B:W.406, B:I.407, B:I.407, B:I.407, B:I.410, B:I.410, B:L.415, S:F.75, S:F.75, S:F.75, S:F.79, D:I.132 Hydrogen bonds: B:S.400, B:N.402, T:S.2, U:S.132 9YF.57: 17 residues within 4Å: Chain B: L.275, L.276 Chain P: P.111, W.112, A.116 Chain U: K.126, D.138, G.140, A.182, S.186, G.189, Y.190, G.191, M.202, I.207 Ligands: MQ9.45, CDL.47 12 PLIP interactions: 1 interactions with chain B, 4 interactions with chain P, 7 interactions with chain U Hydrophobic interactions: B:L.276, P:P.111, P:W.112, P:W.112, P:A.116, U:Y.190, U:Y.190, U:I.207 Hydrogen bonds: U:D.138, U:G.140, U:S.186, U:G.191 9YF.59: 16 residues within 4Å: Chain B: P.180, V.181, I.182, W.185, M.186, A.189, F.320, H.322, V.328, A.331, V.332 Chain V: I.181, W.185, W.200, W.378, E.379 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain V Hydrophobic interactions: B:P.180, B:V.181, B:W.185, B:W.185, B:W.185, B:W.185, B:A.189, B:F.320, B:V.328, B:A.331, B:V.332, V:I.181, V:W.378, V:W.378 Salt bridges: B:H.322, B:H.322 Hydrogen bonds: V:W.200 9YF.60: 16 residues within 4Å: Chain C: E.95, V.96, R.97 Chain V: A.170, L.173, V.174, I.177, G.178, G.179, I.181, K.182, N.183, K.186 Chain X: L.65, L.69, W.73 17 PLIP interactions: 11 interactions with chain V, 3 interactions with chain C, 3 interactions with chain X Hydrophobic interactions: V:L.173, V:L.173, V:V.174, V:I.177, V:I.181, V:I.181, X:L.65, X:L.69, X:L.69 Hydrogen bonds: V:G.178, V:G.179, V:K.182, V:N.183, C:R.97 Salt bridges: V:K.186, C:R.97, C:R.97 9YF.63: 24 residues within 4Å: Chain A: I.132 Chain C: F.386, S.400, N.402, A.403, W.406, I.407, I.410, G.411, L.415 Chain L: H.70, V.71, E.72, F.75, F.79 Chain M: S.132 Chain W: C.1, S.2, I.6, Q.8 Ligands: CDL.15, MQ9.17, 9Y0.36, 9XX.62 18 PLIP interactions: 2 interactions with chain W, 5 interactions with chain L, 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: W:S.2, W:Q.8, C:S.400, C:N.402 Hydrophobic interactions: L:F.75, L:F.75, L:F.75, L:F.79, L:F.79, C:F.386, C:W.406, C:I.407, C:I.407, C:I.407, C:I.410, C:I.410, C:L.415, A:I.132 9YF.64: 14 residues within 4Å: Chain C: P.180, V.181, I.182, W.185, M.186, A.189, H.322, A.331, V.332 Chain X: I.181, W.185, W.200, W.378, E.379 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain X Hydrophobic interactions: C:P.180, C:V.181, C:W.185, C:W.185, C:W.185, C:W.185, C:A.189, C:A.331, C:V.332, X:I.181, X:W.378, X:W.378, X:E.379 Salt bridges: C:H.322, C:H.322 Hydrogen bonds: X:W.200 9YF.65: 16 residues within 4Å: Chain B: V.96, R.97 Chain V: L.65, L.69, F.70, W.73 Chain X: 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 B, 11 interactions with chain X, 3 interactions with chain V Hydrogen bonds: B:R.97, B:R.97, X:G.178, X:G.179, X:I.181, X:N.183 Salt bridges: B:R.97, B:R.97, X:K.186 Hydrophobic interactions: X:L.173, X:L.173, X:V.174, X:V.174, X:I.177, X:I.181, V:L.65, V:L.69, V:F.70

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

FES.58: 8 residues within 4Å: Chain V: C.307, H.309, L.310, C.312, C.326, C.328, H.329, S.331 5 PLIP interactions: 5 interactions with chain V, Metal complexes: V:C.307, V:H.309, V:H.309, V:C.326, V:H.329 FES.66: 8 residues within 4Å: Chain X: C.307, H.309, L.310, C.312, C.326, C.328, H.329, S.331 5 PLIP interactions: 5 interactions with chain X, Metal complexes: X:C.307, X:H.309, X:H.309, X:C.326, X:H.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Trani, J.M. et al., Cryo-EM of native membranes reveals an intimate connection between Krebs cycle and respiration in mycobacteria. To Be Published

Release Date

2024-10-23

Peptides

Cytochrome c oxidase subunit 1: AD
Cytochrome bc1 complex cytochrome b subunit: BC
Superoxide dismutase [Cu-Zn]: EF
Cytochrome aa3 subunit 2: GN
Cytochrome aa3 subunit 3: HO
Cytochrome c oxidase polypeptide 4: IP
Cytochrome c oxidase subunit CtaJ: JQ
Uncharacterized protein MSMEG_4692/MSMEI_4575: KR
Conserved transmembrane protein: LS
Cytochrome bc1 complex cytochrome c subunit: MU
LpqE protein: TW
Cytochrome bc1 complex Rieske iron-sulfur subunit: VX
Probable malate:quinone oxidoreductase: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

D
L

B
E

C
F

E
D

F
G

G
Q

N
K

H
S

O
X

I
T

P
Z

J
U

Q
a

K
V

R
b

L
P

S
J

M
O

U
I

T
c

W
W

V
Y

X
M

Y
A

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome bc1 complex cytochrome b subunit

Superoxide dismutase [Cu-Zn]

Cytochrome aa3 subunit 2

Cytochrome aa3 subunit 3

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit CtaJ

Uncharacterized protein MSMEG_4692/MSMEI_4575

Conserved transmembrane protein

Cytochrome bc1 complex cytochrome c subunit

LpqE protein

Cytochrome bc1 complex Rieske iron-sulfur subunit

Probable malate:quinone oxidoreductase

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