SMTL ID : 8ovc.1

Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: S.70, C.71, C.74, H.75, R.85, G.86, P.87, L.89, A.96, V.97, Q.100, V.101, M.106, P.107, A.108, A.115, P.210, Q.211 Chain K: T.32, Q.35, P.37, A.38 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain K, Hydrophobic interactions: A:P.87, A:L.89, A:Q.100, A:V.101, A:P.107 Hydrogen bonds: A:Q.211, K:T.32, K:T.32, K:A.38 pi-Stacking: A:H.75, A:H.75 Metal complexes: A:H.75 HEC.2: 23 residues within 4Å: Chain A: F.99, R.105, Q.114, N.171, C.172, C.175, H.176, L.185, Y.190, A.191, P.192, D.193, L.194, I.202, A.205, M.206, P.210, Q.211, N.212, M.213, P.214, I.229 Chain B: Y.343 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.99, A:L.185, A:A.191, A:P.192, A:A.205, A:P.210, A:I.229 Hydrogen bonds: A:D.193 Water bridges: A:Q.114 Salt bridges: A:R.105, A:R.105 Metal complexes: A:H.176 HEC.33: 22 residues within 4Å: Chain O: S.70, C.71, C.74, H.75, R.85, G.86, P.87, L.89, A.96, V.97, Q.100, V.101, M.106, P.107, A.108, A.115, F.122, Q.211 Chain Y: T.32, Q.35, P.37, A.38 8 PLIP interactions: 7 interactions with chain O, 1 interactions with chain Y, Hydrophobic interactions: O:P.87, O:Q.100, O:V.101, O:F.122 pi-Stacking: O:H.75, O:H.75 Metal complexes: O:H.75 Hydrogen bonds: Y:A.38 HEC.34: 22 residues within 4Å: Chain O: F.99, R.105, Q.114, N.171, C.172, C.175, H.176, L.185, Y.190, A.191, P.192, D.193, L.194, I.202, A.205, M.206, P.210, Q.211, N.212, M.213, P.214 Chain P: Y.343 11 PLIP interactions: 11 interactions with chain O, Hydrophobic interactions: O:F.99, O:L.185, O:A.191, O:P.192, O:L.194, O:A.205, O:M.213 Hydrogen bonds: O:D.193 Salt bridges: O:R.105, O:R.105 Metal complexes: O:H.176

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

MQ9.3: 13 residues within 4Å: Chain A: G.256, M.257, W.260 Chain C: M.121, F.128, F.303, W.307, V.340, I.376, A.380, Y.384, M.392 Ligands: CDL.9 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.128, C:F.303, C:W.307, C:V.340, C:I.376, C:Y.384, C:Y.384, A:M.257, A:W.260, A:W.260, A:W.260 Hydrogen bonds: C:Y.384 MQ9.7: 25 residues within 4Å: Chain A: Y.245, L.247, G.248, F.250, P.254, M.257 Chain C: F.389, M.392, N.393, I.395, K.399, F.400, I.402, T.407 Chain F: L.97, S.100, T.101, V.104, W.112 Chain G: L.134, I.135, A.138 Ligands: WUO.4, 9XX.25, 9YF.29 20 PLIP interactions: 3 interactions with chain G, 3 interactions with chain A, 7 interactions with chain F, 7 interactions with chain C Hydrophobic interactions: G:L.134, G:I.135, G:A.138, A:L.247, A:P.254, A:P.254, F:L.97, F:V.104, F:W.112, F:W.112, F:W.112, F:W.112, C:F.389, C:N.393, C:I.395, C:K.399, C:F.400, C:F.400, C:I.402 pi-Stacking: F:W.112 MQ9.11: 13 residues within 4Å: Chain C: E.44, L.47, Y.48, L.150, I.215, G.217, L.220, A.221, G.224, W.231 Chain Q: L.220 Ligands: MQ9.12, CDL.41 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain Q Hydrophobic interactions: C:L.47, C:L.47, C:L.150, C:I.215, C:A.221, C:W.231, Q:L.220 MQ9.12: 18 residues within 4Å: Chain C: V.142, F.156, A.174, L.175, I.178, M.189, M.305, T.308, A.334, V.335, M.337, G.338, A.342, L.343, I.345, A.346, F.349 Ligands: MQ9.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.142, C:A.174, C:L.175, C:I.178, C:L.343, C:I.345, C:F.349 MQ9.35: 20 residues within 4Å: Chain O: Y.245, L.247, G.248, F.250, A.253, P.254, M.257 Chain Q: F.389, N.393, I.395, K.399, F.400, I.402, T.407 Chain T: S.100, T.101, W.112 Chain U: I.135, A.138 Ligands: WUO.36 18 PLIP interactions: 5 interactions with chain O, 2 interactions with chain U, 5 interactions with chain Q, 6 interactions with chain T Hydrophobic interactions: O:L.247, O:F.250, O:P.254, O:P.254, O:M.257, U:I.135, U:A.138, Q:N.393, Q:I.395, Q:K.399, Q:F.400, Q:I.402, T:W.112, T:W.112, T:W.112 pi-Stacking: T:W.112, T:W.112, T:W.112 MQ9.37: 11 residues within 4Å: Chain B: F.123, I.127 Chain C: F.104, V.105, M.254, G.262, F.265, T.269 Chain P: T.198, A.201, F.202 9 PLIP interactions: 3 interactions with chain P, 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: P:T.198, P:A.201, P:F.202, C:F.104, C:V.105, C:F.265, C:F.265, B:F.123, B:I.127 MQ9.42: 15 residues within 4Å: Chain O: M.257, W.260 Chain Q: M.121, A.125, F.128, F.303, M.306, V.340, L.343, I.376, A.380, I.381, Y.384, L.387, T.388 17 PLIP interactions: 4 interactions with chain O, 13 interactions with chain Q Hydrophobic interactions: O:W.260, O:W.260, O:W.260, Q:A.125, Q:F.128, Q:F.128, Q:F.128, Q:F.303, Q:I.376, Q:A.380, Q:I.381, Q:Y.384, Q:Y.384, Q:Y.384, Q:L.387, Q:T.388 pi-Stacking: O:W.260 MQ9.47: 14 residues within 4Å: Chain B: L.191, A.201, F.202 Chain P: F.123, A.134 Chain Q: L.55, V.105, A.258, V.259, G.262, F.265, A.266, T.269 Ligands: MQ9.48 12 PLIP interactions: 3 interactions with chain B, 7 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: B:L.191, B:A.201, B:F.202, Q:L.55, Q:V.105, Q:A.258, Q:F.265, Q:F.265, Q:A.266, Q:T.269, P:F.123, P:A.134 MQ9.48: 15 residues within 4Å: Chain C: L.213, L.214, I.218 Chain Q: E.44, I.51, L.55, L.213, P.216, G.217, L.227, V.230, F.257 Ligands: CDL.44, MQ9.47, HEM.50 7 PLIP interactions: 5 interactions with chain Q, 2 interactions with chain C Hydrophobic interactions: Q:I.51, Q:L.55, Q:L.213, Q:V.230, C:L.213, C:I.218 Hydrogen bonds: Q:S.261 MQ9.49: 8 residues within 4Å: Chain Q: A.174, L.175, T.308, M.337, F.341, A.342, I.345, A.346 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:A.174, Q:A.342, Q:I.345, Q:A.346

4 x WUO: acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)(Non-covalent)

WUO.4: 19 residues within 4Å: Chain A: G.195, A.237, P.240, S.241, Y.245, G.246, G.248, M.257, I.261 Chain C: M.275, L.278, L.279 Chain F: W.112, A.115, A.116, F.120 Ligands: MQ9.7, CDL.9, CDL.10 10 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: C:L.278, C:L.278, C:L.279, F:W.112, F:A.116, F:F.120 Hydrogen bonds: A:S.241, A:Y.245, A:G.246, A:G.248 WUO.28: 18 residues within 4Å: Chain D: V.68, H.70, V.71, W.74, F.75, G.78, V.82 Chain G: F.61, F.73 Chain H: L.335 Chain K: C.24, G.27, Q.28, I.29 Ligands: CDL.14, HEA.20, 9XX.25, 9YF.29 14 PLIP interactions: 3 interactions with chain G, 7 interactions with chain D, 3 interactions with chain K, 1 interactions with chain H Hydrophobic interactions: G:F.61, G:F.73, D:V.71, D:W.74, D:F.75, D:V.82 Hydrogen bonds: G:F.73, D:H.70, D:V.71, K:C.24, K:Q.28, K:I.29, H:L.335 Salt bridges: D:H.70 WUO.36: 18 residues within 4Å: Chain O: K.181, D.193, G.195, A.237, P.240, S.241, G.244, Y.245, G.246, M.257, I.262 Chain Q: L.274, L.278, L.279 Chain T: W.112, F.120 Ligands: MQ9.35, CDL.51 15 PLIP interactions: 9 interactions with chain O, 4 interactions with chain Q, 2 interactions with chain T Hydrophobic interactions: O:Y.245, O:I.262, Q:L.274, Q:L.278, Q:L.278, Q:L.279, T:W.112, T:F.120 Hydrogen bonds: O:K.181, O:D.193, O:S.241, O:G.246, O:G.248 Water bridges: O:Y.245 Salt bridges: O:K.181 WUO.55: 18 residues within 4Å: Chain Q: I.421 Chain R: V.68, H.70, V.71, W.74, F.75, G.78, F.79, V.82 Chain U: F.61, F.73 Chain V: L.335 Chain Y: G.27, Q.28, I.29 Ligands: CDL.53, 9YF.67, 9XX.68 15 PLIP interactions: 10 interactions with chain R, 2 interactions with chain Y, 2 interactions with chain U, 1 interactions with chain Q Hydrophobic interactions: R:W.74, R:W.74, R:W.74, R:F.75, R:F.79, R:F.79, R:V.82, U:F.73, Q:I.421 Hydrogen bonds: R:H.70, R:V.71, Y:Q.28, Y:I.29, U:F.73 Salt bridges: R:H.70

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

FES.5: 9 residues within 4Å: Chain B: C.333, H.335, L.336, G.337, C.338, C.352, C.354, H.355, S.357 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.333, B:H.335, B:C.352, B:H.355 FES.39: 8 residues within 4Å: Chain P: C.333, H.335, L.336, G.337, C.338, C.352, H.355, S.357 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.333, P:H.335, P:C.352, P:H.355

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.6: 15 residues within 4Å: Chain B: V.200, G.204, G.205, L.206, I.207, K.208, N.209, K.212 Chain C: I.185, W.188, A.192 Chain P: L.95, W.99 Chain Q: E.98, R.100 14 PLIP interactions: 2 interactions with chain P, 4 interactions with chain C, 2 interactions with chain Q, 6 interactions with chain B Hydrophobic interactions: P:L.95, C:I.185, C:W.188, C:W.188, C:A.192, B:V.200, B:L.206, B:I.207 Hydrogen bonds: P:E.100, Q:R.100, B:G.204, B:N.209 Salt bridges: Q:R.100, B:K.212 9YF.29: 21 residues within 4Å: Chain A: S.187 Chain C: L.386, S.403, N.405, A.406, W.409, I.410, I.413, G.414 Chain D: E.72, F.75, F.79 Chain G: I.141 Chain K: C.24, S.25, I.29, Q.31 Ligands: MQ9.7, CDL.10, 9XX.25, WUO.28 13 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C, 1 interactions with chain K, 4 interactions with chain D, 1 interactions with chain G Hydrogen bonds: A:S.187, C:S.403, C:N.405 Hydrophobic interactions: C:L.386, C:W.409, C:I.410, C:I.413, D:F.75, D:F.75, D:F.75, D:F.79, G:I.141 Water bridges: K:S.25 9YF.38: 12 residues within 4Å: Chain B: L.95, W.99 Chain C: E.98, R.100 Chain P: V.200, G.204, G.205, I.207, K.208, N.209, K.212 Chain Q: W.188 11 PLIP interactions: 4 interactions with chain P, 3 interactions with chain Q, 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: P:V.200, P:I.207, Q:W.188, Q:W.188, Q:W.188, B:L.95 Hydrogen bonds: P:N.209, C:R.100, C:R.100 Salt bridges: P:K.212, C:R.100 9YF.67: 19 residues within 4Å: Chain O: S.187 Chain Q: L.386, S.403, N.405, A.406, W.409, I.410, I.413, G.414, V.417 Chain R: V.71, E.72, F.75, F.79 Chain U: I.141 Chain Y: C.24, S.25, I.29 Ligands: WUO.55 11 PLIP interactions: 2 interactions with chain R, 9 interactions with chain Q Hydrophobic interactions: R:F.79, Q:L.386, Q:A.406, Q:W.409, Q:I.410, Q:I.413, Q:I.413, Q:I.413, Q:V.417 Hydrogen bonds: R:E.72, Q:S.403

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

HEM.8: 18 residues within 4Å: Chain C: F.50, L.53, L.54, G.57, L.60, I.95, R.106, H.109, H.110, A.113, E.154, G.158, Y.159, H.211, I.212, P.216, N.282 Chain Q: L.213 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain Q, Hydrophobic interactions: C:F.50, C:L.53, C:L.53, C:L.54, C:L.60, C:E.154, C:Y.159, C:I.212, C:P.216, Q:L.213 Salt bridges: C:R.106, C:R.106, C:H.110 pi-Stacking: C:H.109 pi-Cation interactions: C:H.109 Metal complexes: C:H.109, C:H.211 HEM.13: 21 residues within 4Å: Chain C: 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, H.226, V.230, H.235, T.236 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:A.46, C:F.116, C:I.120, C:I.120, C:L.124, C:I.127, C:I.127, C:W.141, C:V.230, C:V.230 Hydrogen bonds: C:G.43, C:R.137 Salt bridges: C:H.123, C:R.126, C:R.126, C:H.235, C:H.235 pi-Cation interactions: C:H.123 Metal complexes: C:H.123, C:H.226 HEM.43: 19 residues within 4Å: Chain C: L.213 Chain Q: L.53, L.54, G.57, L.60, T.61, R.106, H.109, H.110, A.113, E.154, G.155, G.158, Y.159, P.162, Y.208, H.211, I.212, N.282 19 PLIP interactions: 18 interactions with chain Q, 1 interactions with chain C, Hydrophobic interactions: Q:L.53, Q:L.53, Q:L.54, Q:L.60, Q:L.60, Q:T.61, Q:A.113, Q:E.154, Q:Y.159, Q:Y.208, Q:I.212, Q:I.212, C:L.213 Hydrogen bonds: Q:N.282 Salt bridges: Q:R.106, Q:R.106, Q:H.110 Metal complexes: Q:H.109, Q:H.211 HEM.50: 18 residues within 4Å: Chain Q: F.40, G.43, A.46, I.120, H.123, L.124, R.126, I.127, A.132, R.137, W.141, G.144, L.147, H.226, V.230, H.235, T.236 Ligands: MQ9.48 20 PLIP interactions: 20 interactions with chain Q, Hydrophobic interactions: Q:A.46, Q:I.120, Q:I.120, Q:I.127, Q:I.127, Q:I.127, Q:A.132, Q:W.141, Q:L.147, Q:V.230 Hydrogen bonds: Q:G.43, Q:T.236 Salt bridges: Q:H.123, Q:R.126, Q:R.126, Q:R.137, Q:H.235, Q:H.235 pi-Cation interactions: Q:H.123 Metal complexes: Q:H.226

16 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 23 residues within 4Å: Chain A: M.272, R.277, A.278 Chain C: H.37, W.38, V.122, F.129, R.366, P.367, R.368, T.374, S.378, L.385, W.429, A.430, L.433, P.483 Ligands: MQ9.3, WUO.4, CDL.10, CDL.17, CDL.22, 9XX.25 Ligand excluded by PLIP CDL.10: 22 residues within 4Å: Chain C: R.368, W.429, L.433, L.484, K.486, R.487 Chain F: W.90, W.91, L.94, L.97, S.98, T.101, F.120, T.123, S.124 Chain G: Y.29, I.32 Ligands: WUO.4, CDL.9, CDL.17, CDL.22, 9YF.29 Ligand excluded by PLIP CDL.14: 20 residues within 4Å: Chain C: A.420, I.421, F.424, R.428 Chain D: M.48, G.52, F.79, I.83, L.86, V.87, R.89, N.90, R.94 Chain G: M.21, K.24, W.493, F.496 Ligands: CDL.22, 9XX.25, WUO.28 Ligand excluded by PLIP CDL.17: 15 residues within 4Å: Chain A: M.272, W.273, R.277 Chain C: R.487, K.490 Chain F: W.91, I.122, T.123, C.126, G.127, W.134, G.135 Ligands: CDL.9, CDL.10, 7PH.16 Ligand excluded by PLIP CDL.18: 14 residues within 4Å: Chain E: V.25, W.32, L.160, R.164, V.180, Y.184 Chain F: V.125, V.129 Chain G: F.118, P.119, R.120, L.121, L.124 Chain N: X.11 Ligand excluded by PLIP CDL.22: 17 residues within 4Å: Chain C: F.424, R.428 Chain G: M.21, G.22, G.25, N.26, L.27, I.28, L.31, V.46, W.127, V.495, W.499 Ligands: CDL.9, CDL.10, CDL.14, 9XX.25 Ligand excluded by PLIP CDL.40: 15 residues within 4Å: Chain O: W.273 Chain P: L.75, W.79, I.132, L.136, K.140 Chain Q: F.502 Chain S: V.159, L.162, A.163, K.166 Chain T: F.130, W.134, K.138 Ligands: CDL.51 Ligand excluded by PLIP CDL.41: 14 residues within 4Å: Chain C: Y.20, V.26, R.28, Q.29, A.228, L.229, W.231, F.232, S.261 Chain Q: Y.20, H.21, R.28 Ligands: MQ9.11, CDL.44 Ligand excluded by PLIP CDL.44: 14 residues within 4Å: Chain C: Y.20, H.21, P.22, R.28 Chain Q: Y.20, A.25, V.26, R.28, Q.29, L.229, W.231, F.232 Ligands: CDL.41, MQ9.48 Ligand excluded by PLIP CDL.45: 17 residues within 4Å: Chain O: M.272, A.278 Chain Q: H.37, W.38, V.122, F.129, R.366, P.367, R.368, S.378, A.426, W.429, A.430, L.433, P.483 Ligands: CDL.46, CDL.51 Ligand excluded by PLIP CDL.46: 17 residues within 4Å: Chain Q: R.368, W.429, L.433, L.484, K.486, R.487 Chain T: W.90, I.93, L.94, L.97, S.98, F.120, S.124 Chain U: Y.29, I.32 Ligands: CDL.45, CDL.51 Ligand excluded by PLIP CDL.51: 18 residues within 4Å: Chain O: I.262, A.266, M.272, W.273, R.277 Chain Q: R.487, K.490 Chain T: W.91, I.122, T.123, C.126, G.127, W.134, E.137 Ligands: WUO.36, CDL.40, CDL.45, CDL.46 Ligand excluded by PLIP CDL.53: 15 residues within 4Å: Chain Q: Y.423, F.424, R.428 Chain R: M.48, V.82, A.85, L.86, R.89, N.90, L.93 Chain U: M.21, F.496 Ligands: CDL.54, WUO.55, CDL.63 Ligand excluded by PLIP CDL.54: 14 residues within 4Å: Chain R: V.84, A.85, G.88, R.89, W.91, W.92, R.96, W.98 Chain U: V.492, W.493, F.496, K.497, R.500 Ligands: CDL.53 Ligand excluded by PLIP CDL.57: 17 residues within 4Å: Chain S: W.32, L.149, G.153, A.157, L.160, L.161, R.164, V.180, Y.184 Chain T: F.99, V.125, L.128 Chain U: F.118, P.119, R.120, L.121 Ligands: 7PH.56 Ligand excluded by PLIP CDL.63: 19 residues within 4Å: Chain Q: F.424, R.428 Chain U: M.21, G.22, P.23, K.24, G.25, N.26, L.27, I.28, L.31, I.42, C.45, V.46, V.495, F.496, W.499, R.500 Ligands: CDL.53 Ligand excluded by PLIP

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

7PH.15: 5 residues within 4Å: Chain E: V.125, T.130, P.132, Y.141 Chain G: L.240 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.240 7PH.16: 11 residues within 4Å: Chain C: F.502 Chain E: F.107, V.156, V.159, L.162, A.163, K.166, M.167 Chain F: C.126, W.134 Ligands: CDL.17 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.107, E:V.156, E:V.159, E:V.159, E:L.162, C:F.502 7PH.56: 9 residues within 4Å: Chain S: Y.121, V.125, T.130, I.131, P.132, Y.141, L.142 Chain U: L.240 Ligands: CDL.57 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain U Hydrophobic interactions: S:Y.121, S:L.142, U:L.240 Hydrogen bonds: S:T.130, S:I.131

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

HEA.19: 31 residues within 4Å: Chain G: W.151, T.152, W.260, H.264, V.267, Y.268, H.313, H.314, T.330, A.334, T.337, G.338, F.341, L.370, G.373, G.376, V.377, L.379, A.380, D.385, T.389, V.394, H.397, F.398, V.401, L.402, R.459 Chain H: P.102, I.105, I.106 Ligands: CU.21 21 PLIP interactions: 19 interactions with chain G, 2 interactions with chain H, Hydrophobic interactions: G:W.260, G:V.267, G:T.330, G:A.334, G:F.341, G:L.370, G:V.377, G:L.379, G:F.398, G:F.398, G:F.398, G:V.401, G:V.401, G:L.402, H:I.105, H:I.106 Hydrogen bonds: G:W.151, G:Y.268, G:Y.268, G:T.389 Salt bridges: G:R.459 HEA.20: 27 residues within 4Å: Chain G: F.52, L.53, G.56, L.57, A.59, L.60, R.63, F.83, T.84, H.86, G.87, M.90, L.91, W.151, Y.392, I.395, F.398, H.399, L.402, F.403, I.406, F.446, R.459, R.460, L.484, G.485 Ligands: WUO.28 21 PLIP interactions: 21 interactions with chain G, Hydrophobic interactions: G:F.52, G:L.60, G:M.90, G:L.91, G:L.91, G:I.395, G:L.402, G:I.406, G:F.446 Hydrogen bonds: G:R.63, G:F.83, G:W.151, G:Q.449, G:R.459, G:R.460 Salt bridges: G:R.460 pi-Stacking: G:F.398, G:H.399, G:F.446 Metal complexes: G:H.86, G:H.399 HEA.58: 27 residues within 4Å: Chain U: W.151, W.260, V.267, Y.268, H.313, H.314, T.330, A.334, G.338, L.370, G.373, G.376, V.377, L.379, A.380, D.385, T.389, V.394, H.397, F.398, V.401, L.402, R.459 Chain V: P.102, I.105, I.106 Ligands: CU.60 18 PLIP interactions: 3 interactions with chain V, 15 interactions with chain U, Hydrophobic interactions: V:P.102, V:I.105, V:I.106, U:W.151, U:W.260, U:V.267, U:V.267, U:T.330, U:L.370, U:V.377, U:F.398, U:F.398, U:V.401, U:V.401, U:L.402 Hydrogen bonds: U:W.151, U:Y.268 Salt bridges: U:R.459 HEA.59: 29 residues within 4Å: Chain U: F.52, L.53, G.56, L.60, 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, F.446, R.459, R.460, Y.461, A.481, L.484, G.485, M.488 Ligands: 9XX.68 20 PLIP interactions: 20 interactions with chain U, Hydrophobic interactions: U:F.52, U:F.52, U:L.60, U:I.395, U:F.398, U:F.398, U:L.402, U:L.402, U:F.446, U:A.481 Hydrogen bonds: U:R.63, U:W.151, U:Y.392, U:Q.449, U:R.460, U:Y.461 Salt bridges: U:R.459, U:R.460 Metal complexes: U:H.86, U:H.399

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

CU.21: 4 residues within 4Å: Chain G: H.264, H.313, H.314 Ligands: HEA.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.264, G:H.313, G:H.314 CU.26: 5 residues within 4Å: Chain H: C.273, M.276, C.277, H.281 Ligands: CU.27 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.273, H:C.277, H:H.281 CU.27: 5 residues within 4Å: Chain H: H.232, C.273, C.277, M.284 Ligands: CU.26 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.232, H:C.273, H:C.277 CU.60: 4 residues within 4Å: Chain U: H.264, H.313, H.314 Ligands: HEA.58 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:H.264, U:H.313, U:H.314 CU.65: 5 residues within 4Å: Chain V: C.273, E.275, C.277, H.281 Ligands: CU.66 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.273, V:E.275, V:C.277, V:H.281 CU.66: 5 residues within 4Å: Chain V: H.232, C.273, C.277, M.284 Ligands: CU.65 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:H.232, V:C.273, V:C.277

2 x MG: MAGNESIUM ION(Non-covalent)

MG.23: 2 residues within 4Å: Chain G: D.390 Chain H: E.275 No protein-ligand interaction detected (PLIP) MG.61: 2 residues within 4Å: Chain U: D.390 Chain V: E.275 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:D.390

2 x CA: CALCIUM ION(Non-covalent)

CA.24: 5 residues within 4Å: Chain G: E.65, L.66, M.68, G.70, Q.72 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.65, G:M.68, G:G.70 CA.62: 4 residues within 4Å: Chain U: E.65, M.68, G.70, Q.72 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.65, U:E.65, U:M.68, U:G.70

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

9XX.25: 13 residues within 4Å: Chain C: L.418 Chain D: F.75, F.79 Chain G: F.140, I.141 Chain K: C.24 Ligands: MQ9.7, CDL.9, CDL.14, CDL.22, WUO.28, 9YF.29, PLM.30 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: D:F.79, C:L.418, G:I.141 9XX.32: 4 residues within 4Å: Chain C: F.320, Y.321, I.327 Chain L: C.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.320, C:F.320, C:I.327 9XX.52: 5 residues within 4Å: Chain Q: F.320, Y.321, P.322 Chain Z: C.21 Ligands: PLM.69 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:F.320, Q:F.320, Q:F.320 Hydrogen bonds: Q:Y.321 9XX.68: 7 residues within 4Å: Chain U: V.54, I.137, I.141 Chain Y: C.24 Ligands: WUO.55, HEA.59, PLM.64 4 PLIP interactions: 4 interactions with chain U Hydrophobic interactions: U:V.54, U:V.54, U:I.137, U:I.141

4 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.30: 4 residues within 4Å: Chain G: F.140, G.144 Chain K: C.24 Ligands: 9XX.25 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain G Hydrogen bonds: K:C.24 Hydrophobic interactions: G:F.140 PLM.31: 4 residues within 4Å: Chain C: W.318, E.319 Chain D: R.64 Chain L: C.21 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain C Hydrogen bonds: L:C.21 Hydrophobic interactions: C:W.318 PLM.64: 8 residues within 4Å: Chain U: Q.81, F.140, P.143, G.144, G.145 Chain Y: C.24, A.26 Ligands: 9XX.68 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Y Hydrophobic interactions: U:F.140 Hydrogen bonds: Y:A.26 PLM.69: 5 residues within 4Å: Chain Q: W.318, F.320 Chain R: R.64 Chain Z: C.21 Ligands: 9XX.52 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain Z Hydrophobic interactions: Q:W.318, Q:W.318, Q:W.318, Q:F.320 Hydrogen bonds: Z:C.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riepl, D. et al., Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex. Nat Commun (2024)

Release Date

2024-07-17

Peptides

Cytochrome bc1 complex cytochrome c subunit: AO
Cytochrome bc1 complex cytochrome c subunit: BP
Cytochrome bc1 complex cytochrome b subunit: CQ
Transmembrane protein: DR
Probable cytochrome c oxidase subunit 3: ES
Cytochrome c oxidase polypeptide 4: FT
Cytochrome c oxidase subunit 1: GU
cytochrome-c oxidase: HV
Cytochrome c oxidase subunit: IW
Uncharacterized protein MSMEG_4692/MSMEI_4575: JX
LpqE protein: KY
Superoxide dismutase [Cu-Zn]: LZ
Co-purified unknown peptide: M1
Co-purified unknown peptide: N0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

O
C

B
M

P
G

C
N

Q
H

D
P

R
I

E
S

S
J

F
T

T
K

G
R

U
L

H
Q

V
X

I
U

W
Z

J
V

X
a

K
W

Y
b

L
Y

Z
c

M
E

1
f

N
F

0
e

Membrane

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

Cytochrome bc1 complex cytochrome c subunit

Cytochrome bc1 complex cytochrome b subunit

Transmembrane protein

Probable cytochrome c oxidase subunit 3

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit 1

cytochrome-c oxidase

Cytochrome c oxidase subunit

Uncharacterized protein MSMEG_4692/MSMEI_4575

LpqE protein

Superoxide dismutase [Cu-Zn]

Co-purified unknown peptide

Co-purified unknown peptide

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