SMTL ID : 9fu0.1

CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

WUO.1: 24 residues within 4Å: Chain A: K.181, D.193, G.195, A.237, P.240, S.241, G.244, Y.245, G.246, G.248, I.261, I.262 Chain C: L.278 Chain F: P.111, W.112, L.113, A.115, A.116, F.120 Ligands: MQ9.4, CDL.5, CDL.13, CDL.14, 9YF.36 19 PLIP interactions: 13 interactions with chain A, 4 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: A:Y.245, A:I.261, A:I.262, A:I.262, F:W.112, F:L.113, F:A.115, F:A.116, C:L.278, C:L.278 Hydrogen bonds: A:K.181, A:D.193, A:A.237, A:S.241, A:S.241, A:Y.245, A:G.246, A:G.248 Salt bridges: A:K.181 WUO.19: 21 residues within 4Å: Chain D: V.68, G.69, H.70, V.71, W.74, F.75, G.78, F.79, V.82 Chain G: F.61, F.73, L.74, Q.78 Chain H: L.335 Chain K: G.27, Q.28, I.29 Ligands: HEA.26, CDL.28, 9YF.36, 9XX.37 16 PLIP interactions: 11 interactions with chain D, 3 interactions with chain G, 2 interactions with chain K Hydrophobic interactions: D:V.71, D:W.74, D:W.74, D:W.74, D:F.75, D:F.75, D:F.79, D:V.82, D:V.82, G:F.61, G:L.74 Hydrogen bonds: D:H.70, D:V.71, G:F.73, K:Q.28, K:I.29

2 x HEC: HEME C(Covalent)

HEC.2: 26 residues within 4Å: Chain A: F.99, T.103, R.105, Q.114, A.115, N.171, C.172, S.174, C.175, H.176, L.185, P.192, D.193, L.194, A.197, I.202, A.205, M.206, P.210, Q.211, N.212, M.213, P.214, F.216, I.229 Chain B: Y.343 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.99, A:L.185, A:L.194, A:A.197, A:I.202, A:I.202, A:A.205, A:P.210, A:F.216, A:I.229 Hydrogen bonds: A:D.193, A:Q.211 Water bridges: A:R.105 Salt bridges: A:R.105, A:R.105 Metal complexes: A:H.176 HEC.3: 23 residues within 4Å: Chain A: S.70, C.71, C.74, H.75, R.85, P.87, L.89, T.92, A.96, V.97, Q.100, V.101, M.106, P.107, A.108, M.109, F.122, Q.211 Chain H: W.138 Chain K: T.32, Q.35, P.37, A.38 17 PLIP interactions: 2 interactions with chain K, 14 interactions with chain A, 1 interactions with chain H, Hydrogen bonds: K:A.38, A:Q.211 Water bridges: K:T.32 Hydrophobic interactions: A:P.87, A:L.89, A:L.89, A:T.92, A:A.96, A:V.97, A:V.97, A:Q.100, A:V.101, A:M.106, A:F.122, A:Q.211, H:W.138 Metal complexes: A:H.75

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

MQ9.4: 28 residues within 4Å: Chain A: Y.245, L.247, G.248, F.250, P.254, M.257 Chain C: F.389, A.390, M.392, N.393, I.395, K.399, F.400, I.402, I.410 Chain F: S.100, T.101, V.104, W.112, L.113 Chain G: F.131, L.134, I.135, A.138 Ligands: WUO.1, CDL.14, 9YF.36, 9XX.37 21 PLIP interactions: 3 interactions with chain G, 3 interactions with chain A, 7 interactions with chain F, 8 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:V.104, F:V.104, F:W.112, F:W.112, F:W.112, F:L.113, C:N.393, C:I.395, C:K.399, C:F.400, C:F.400, C:F.400, C:I.402, C:I.410 pi-Stacking: F:W.112 MQ9.10: 22 residues within 4Å: Chain A: M.257, W.260, I.268 Chain C: M.121, V.122, L.124, F.128, F.129, L.148, F.303, W.307, V.340, L.343, L.344, Y.347, A.380, I.381, Y.384, L.385, T.388 Ligands: CDL.5, CDL.13 27 PLIP interactions: 22 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:M.121, C:V.122, C:L.124, C:F.128, C:F.128, C:F.129, C:L.148, C:F.303, C:W.307, C:W.307, C:V.340, C:V.340, C:L.343, C:Y.347, C:A.380, C:I.381, C:Y.384, C:Y.384, C:Y.384, C:L.385, C:T.388, A:W.260, A:W.260, A:W.260, A:I.268 Hydrogen bonds: C:Y.384 pi-Stacking: A:W.260 MQ9.16: 23 residues within 4Å: Chain B: F.123, I.130, A.134 Chain C: E.44, Y.48, L.55, F.104, V.105, L.227, V.230, W.231, F.257, A.258, V.259, S.261, G.262, F.265, A.266 Chain N: F.194, T.198, A.201, F.202 Ligands: HEM.15 18 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B, 4 interactions with chain N Hydrophobic interactions: C:E.44, C:F.104, C:V.105, C:L.227, C:V.230, C:W.231, C:W.231, C:A.258, C:F.265, C:F.265, C:A.266, B:F.123, B:I.130, B:A.134, N:F.194, N:T.198, N:A.201, N:F.202 MQ9.17: 18 residues within 4Å: Chain B: L.206 Chain C: I.149, L.150, F.153, A.174, L.175, I.178, T.179, M.189, L.193, R.206, I.218, M.305, T.308, A.334, M.337 Chain M: V.58 Ligands: 9YF.7 11 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B, 1 interactions with chain M Hydrophobic interactions: C:I.149, C:L.150, C:F.153, C:A.174, C:L.175, C:L.193, C:L.193, C:I.218, C:I.218, B:L.206, M:V.58 MQ9.45: 25 residues within 4Å: Chain B: L.187, L.191, A.201, F.202 Chain M: F.34, F.40, E.44, L.47, Y.48, I.52, L.55, T.56, F.104, V.105, V.230, W.231, F.257, A.258, S.261, G.262, F.265, T.269 Chain N: I.127, I.130 Ligands: HEM.44 20 PLIP interactions: 15 interactions with chain M, 2 interactions with chain N, 3 interactions with chain B Hydrophobic interactions: M:F.34, M:F.34, M:L.47, M:I.52, M:I.52, M:L.55, M:L.55, M:F.104, M:V.105, M:W.231, M:F.257, M:F.265, M:F.265, M:T.269, N:I.127, N:I.130, B:L.187, B:L.191, B:A.201 pi-Stacking: M:F.257 MQ9.46: 8 residues within 4Å: Chain C: R.19 Chain M: E.138, L.175, M.189, A.334, I.345, F.349, K.352 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:L.175, M:I.345, M:F.349

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 24 residues within 4Å: Chain A: I.261, V.265, A.266, G.269, V.270, M.272, W.273, R.277 Chain B: K.139 Chain C: R.487, K.490 Chain F: W.91, A.119, T.123, C.126, G.127, W.134, G.135, E.137 Ligands: WUO.1, MQ9.10, CDL.13, CDL.14, 7PH.20 11 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C, 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: F:A.119, F:T.123, A:A.266, A:W.273 Hydrogen bonds: F:G.135, C:K.490, A:R.277 Salt bridges: C:R.487, C:K.490, A:R.277, B:K.139 CDL.12: 20 residues within 4Å: Chain C: Y.20, P.22, V.26, R.28, Q.29, L.47, L.220, I.223, G.224, A.225, L.227, A.228, L.229, W.231, F.232 Chain M: Y.20, H.21, A.25, R.28 Ligands: CDL.42 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain M Hydrophobic interactions: C:Y.20, C:P.22, C:P.22, C:V.26, C:L.47, C:L.220, C:I.223, C:L.227, C:L.229, C:W.231, C:F.232, C:F.232, C:F.232 Hydrogen bonds: C:Q.29, M:R.28 Salt bridges: C:R.28, M:H.21 CDL.13: 28 residues within 4Å: Chain A: I.268, M.272, R.277, A.278 Chain C: H.37, W.38, L.42, V.122, R.126, F.129, R.366, P.367, R.368, T.374, S.378, I.381, A.382, V.425, A.426, W.429, A.430, L.433, P.483 Ligands: WUO.1, CDL.5, MQ9.10, CDL.14, 9XX.37 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.38, C:L.42, C:V.122, C:F.129, C:I.381, C:A.382, C:V.425, C:A.426, C:W.429, C:W.429, A:I.268 Hydrogen bonds: C:R.366, C:R.366, C:R.368, A:A.278 Salt bridges: C:H.37, C:R.366, C:R.368 CDL.14: 21 residues within 4Å: Chain C: R.368, W.429, L.433, L.484, K.486, R.487 Chain F: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123 Chain G: Y.29, I.32 Ligands: WUO.1, MQ9.4, CDL.5, CDL.13 20 PLIP interactions: 9 interactions with chain F, 9 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: F:W.90, F:W.91, F:I.93, F:I.93, F:L.94, F:L.97, F:L.97, F:F.120, F:T.123, C:W.429, G:I.32 Hydrogen bonds: C:L.484, C:L.484, G:Y.29 Water bridges: C:R.366, C:K.486 Salt bridges: C:R.368, C:K.486, C:R.487, C:R.487 CDL.18: 25 residues within 4Å: Chain C: M.379, A.420, Y.423, F.424, R.428 Chain D: M.48, G.51, G.52, S.55, L.86, V.87, R.89, N.90, L.93, R.94, I.99 Chain G: M.21, K.24, L.27, V.46, W.493, F.496, K.497, R.500 Ligands: CDL.28 22 PLIP interactions: 8 interactions with chain G, 8 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: G:L.27, G:V.46, G:W.493, G:F.496, G:F.496, G:F.496, D:V.87, D:L.93, C:Y.423, C:Y.423, C:Y.423, C:F.424 Water bridges: G:R.500, D:R.94, D:R.100 Salt bridges: G:K.24, D:R.89, D:R.89, D:R.94, C:R.428 Hydrogen bonds: D:N.90, C:R.428 CDL.24: 24 residues within 4Å: Chain E: V.25, T.29, W.32, L.149, G.153, V.156, A.157, L.160, L.161, R.164, A.177, V.180, Y.184 Chain F: I.95, F.99, V.125, L.128, V.129 Chain G: F.118, P.119, R.120, L.121, L.124, L.180 24 PLIP interactions: 7 interactions with chain G, 9 interactions with chain E, 8 interactions with chain F Hydrophobic interactions: G:F.118, G:L.124, G:L.180, E:W.32, E:W.32, E:W.32, E:V.156, E:L.160, E:Y.184, E:Y.184, F:I.95, F:F.99, F:F.99, F:V.125, F:V.125 Hydrogen bonds: G:R.120, G:L.121 Water bridges: G:R.120, F:A.86, F:A.86, F:Y.133 Salt bridges: G:R.120, E:R.164, E:R.164 CDL.28: 23 residues within 4Å: Chain C: F.424, V.425, R.428 Chain G: M.21, G.22, P.23, K.24, G.25, N.26, L.27, I.28, I.42, M.43, C.45, V.46, A.50, W.127, V.495, W.499, R.500 Ligands: CDL.18, WUO.19, 9XX.37 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:L.27, G:I.42, G:V.46, G:A.50, G:W.127, C:F.424, C:V.425 Hydrogen bonds: G:G.22, G:G.25, G:N.26, G:L.27, G:I.28 Salt bridges: C:R.428 CDL.42: 14 residues within 4Å: Chain C: Y.20, R.28 Chain M: A.25, R.28, Q.29, L.220, I.223, G.224, A.225, L.227, A.228, L.229, F.232 Ligands: CDL.12 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain C Hydrophobic interactions: M:L.220, M:I.223, M:L.227, M:L.229, M:F.232 Hydrogen bonds: M:Q.29, C:R.28 Salt bridges: M:R.28, C:H.21 CDL.43: 18 residues within 4Å: Chain M: H.37, W.38, V.122, A.125, R.126, F.129, F.238, R.366, P.367, R.368, T.374, S.378, I.381, A.382, L.385, A.426, W.429, L.433 13 PLIP interactions: 13 interactions with chain M Hydrophobic interactions: M:V.122, M:F.129, M:T.374, M:I.381, M:A.382, M:L.385, M:A.426, M:W.429, M:L.433 Hydrogen bonds: M:R.368 Salt bridges: M:H.37, M:H.37, M:R.368

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

FES.6: 8 residues within 4Å: Chain B: C.333, H.335, L.336, 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.47: 7 residues within 4Å: Chain N: C.333, H.335, L.336, C.338, C.352, H.355, S.357 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.333, N:H.335, N:C.352, N:H.355

3 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.7: 16 residues within 4Å: Chain B: V.200, G.204, G.205, I.207, K.208, N.209, K.212 Chain C: I.185, W.188, M.189 Chain M: E.98, R.100 Chain N: L.95, F.96, W.99 Ligands: MQ9.17 13 PLIP interactions: 5 interactions with chain B, 2 interactions with chain M, 3 interactions with chain C, 3 interactions with chain N Hydrophobic interactions: B:V.200, B:I.207, C:I.185, C:W.188, C:W.188, N:L.95, N:L.95, N:F.96 Hydrogen bonds: B:K.208, B:K.208, B:N.209, M:R.100 Salt bridges: M:R.100 9YF.36: 23 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, L.418 Chain D: V.71, E.72, F.75, F.79 Chain G: I.141 Chain K: C.24, S.25, I.29, Q.31 Ligands: WUO.1, MQ9.4, WUO.19, 9XX.37 18 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D, 2 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: C:L.386, C:W.409, C:I.410, C:I.410, C:I.410, C:I.413, C:I.413, C:L.418, D:E.72, D:F.75, D:F.75, D:F.79, D:F.79 Hydrogen bonds: C:S.403, C:N.405, K:S.25, K:Q.31, A:S.187 9YF.48: 11 residues within 4Å: Chain B: L.95, W.99 Chain C: E.98, R.100 Chain M: I.185, W.188 Chain N: G.205, I.207, K.208, N.209, K.212 14 PLIP interactions: 3 interactions with chain M, 3 interactions with chain C, 6 interactions with chain N, 2 interactions with chain B Hydrophobic interactions: M:I.185, M:W.188, M:W.188, N:I.207, N:I.207, N:I.207, B:L.95 Hydrogen bonds: C:R.100, N:G.205, N:N.209, B:W.99 Water bridges: C:E.98 Salt bridges: C:R.100, N:K.212

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

7PH.8: 10 residues within 4Å: Chain B: L.168, T.169, L.172, E.173, S.175, L.177, K.178 Chain M: F.5, V.259 Chain N: F.137 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: B:L.168, B:L.177, M:F.5, M:V.259, N:F.137 Hydrogen bonds: B:T.169 Salt bridges: B:K.178 7PH.20: 12 residues within 4Å: Chain C: F.502 Chain E: F.107, V.159, L.162, A.163, K.166, M.167 Chain F: C.126, F.130, W.134, K.138 Ligands: CDL.5 8 PLIP interactions: 6 interactions with chain E, 1 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: E:F.107, E:F.107, E:V.159, E:L.162, C:F.502 Salt bridges: E:K.166, E:K.166, F:K.138 7PH.50: 14 residues within 4Å: Chain C: A.9, A.10, Q.12, G.13, D.14, D.17, P.22, S.23 Chain N: R.161, K.162, V.164, A.165, L.168 Ligands: 7PH.51 6 PLIP interactions: 4 interactions with chain N, 2 interactions with chain C Hydrophobic interactions: N:V.164, N:L.168, C:Q.12, C:D.17 Salt bridges: N:R.161, N:K.162 7PH.51: 10 residues within 4Å: Chain C: A.6, A.9, V.259 Chain N: L.168, T.169, L.172, L.177, K.178, G.184 Ligands: 7PH.50 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:L.168, N:L.168, N:L.172, N:L.177 Salt bridges: N:K.178

2 x IZL: [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate(Non-covalent)

IZL.9: 12 residues within 4Å: Chain B: W.211, K.222, W.226, W.404, E.405, R.406, K.407 Chain C: V.184, I.185, W.188, G.324, H.325 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:V.184, C:I.185, C:W.188 Salt bridges: C:H.325 Hydrogen bonds: B:W.211, B:K.222, B:K.222, B:W.226, B:E.405, B:E.405, B:E.405, B:K.407 Water bridges: B:N.209 IZL.49: 11 residues within 4Å: Chain M: V.184, I.185, W.188, H.325 Chain N: W.211, K.222, W.226, W.404, E.405, R.406, K.407 8 PLIP interactions: 6 interactions with chain N, 2 interactions with chain M Hydrogen bonds: N:W.211, N:K.222, N:K.222, N:E.405, N:E.405, N:K.407 Hydrophobic interactions: M:I.185 Salt bridges: M:H.325

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

HEM.11: 24 residues within 4Å: Chain C: F.50, L.53, L.54, G.57, V.58, L.60, T.61, I.95, R.106, H.109, H.110, A.113, F.116, E.154, G.155, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, N.282 Chain M: L.213 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain M, Hydrophobic interactions: C:F.50, C:F.50, C:L.53, C:L.53, C:L.54, C:V.58, C:L.60, C:L.60, C:F.116, C:E.154, C:Y.159, C:L.161, C:Y.208, C:I.212, M:L.213 Hydrogen bonds: C:R.106, C:N.282 Salt bridges: C:R.106, C:R.106, C:H.110 Metal complexes: C:H.109, C:H.211 HEM.15: 25 residues within 4Å: Chain C: F.40, G.43, E.44, 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, K.234, H.235, T.236 Ligands: MQ9.16 28 PLIP interactions: 28 interactions with chain C, Hydrophobic interactions: C:F.116, C:I.120, C:I.120, C:I.120, C:I.127, C:I.127, C:I.127, C:A.132, C:W.141, C:L.147, C:L.227, C:V.230, C:V.230 Hydrogen bonds: C:G.43, C:E.44, C:T.236 Water bridges: C:L.42, C:R.137, C:N.140 Salt bridges: C:H.123, C:R.126, C:R.126, C:R.137, C:H.235, C:H.235 pi-Stacking: C:H.226 Metal complexes: C:H.123, C:H.226 HEM.41: 25 residues within 4Å: Chain C: L.213 Chain M: F.50, L.53, L.54, G.57, V.58, L.60, T.61, R.106, H.109, H.110, A.113, F.116, E.154, G.155, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, N.282, Y.304 20 PLIP interactions: 19 interactions with chain M, 1 interactions with chain C, Hydrophobic interactions: M:F.50, M:L.53, M:L.53, M:L.53, M:L.54, M:L.60, M:L.60, M:H.110, M:F.116, M:E.154, M:L.161, M:Y.208, M:I.212, M:I.212, M:P.216, C:L.213 Hydrogen bonds: M:N.282 Salt bridges: M:R.106, M:H.110 Metal complexes: M:H.211 HEM.44: 23 residues within 4Å: Chain M: F.40, G.43, E.44, L.47, 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: MQ9.45 24 PLIP interactions: 24 interactions with chain M, Hydrophobic interactions: M:L.47, M:I.120, M:I.120, M:I.120, M:I.127, M:I.127, M:A.132, M:W.141, M:L.147, M:L.147, M:I.223, M:L.227, M:V.230, M:V.230 Hydrogen bonds: M:G.43, M:E.44, M:T.236 Salt bridges: M:H.123, M:R.126, M:R.126, M:R.137, M:H.235, M:H.235 Metal complexes: M:H.123

5 x TRD: TRIDECANE(Non-covalent)

TRD.21: 5 residues within 4Å: Chain E: F.48, R.51, V.202 Chain F: W.36 Ligands: TRD.23 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:F.48, E:V.202, F:W.36 TRD.23: 4 residues within 4Å: Chain E: F.48 Chain F: V.34, W.36 Ligands: TRD.21 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:V.34, F:W.36, F:W.36, E:F.48 TRD.30: 6 residues within 4Å: Chain G: H.443, T.444, L.447, V.448, I.476 Ligands: TRD.31 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:H.443, G:L.447, G:V.448, G:I.476 TRD.31: 7 residues within 4Å: Chain G: S.375, L.447, H.450, W.451 Chain H: L.33 Ligands: TRD.30, TRD.35 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:L.447, G:L.447, G:H.450, G:W.451, G:W.451 TRD.35: 6 residues within 4Å: Chain G: L.371, W.451 Chain H: D.29, A.30, F.58 Ligands: TRD.31 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.371, G:W.451, G:W.451, H:A.30, H:F.58

1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.22: 7 residues within 4Å: Chain E: Y.121, V.125, T.130, I.131, P.132, Y.141 Chain G: L.240 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:Y.121, E:V.125, E:Y.141, G:L.240 Hydrogen bonds: E:I.131

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

HEA.25: 32 residues within 4Å: Chain G: W.151, T.152, W.260, V.267, Y.268, A.271, H.313, H.314, T.330, A.334, T.337, G.338, F.341, F.369, 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: V.60, I.105, I.106 Ligands: CU.27 29 PLIP interactions: 26 interactions with chain G, 3 interactions with chain H, Hydrophobic interactions: G:V.267, G:V.267, G:A.271, G:T.330, G:A.334, G:T.337, G:F.341, G:F.341, G:F.369, G:L.370, G:V.377, G:F.398, G:F.398, G:V.401, G:L.402, G:L.402, H:V.60, H:I.105, H:I.106 Hydrogen bonds: G:W.151, G:Y.268, G:Y.268, G:T.389 Water bridges: G:T.152, G:D.390, G:D.390 Salt bridges: G:R.459 pi-Cation interactions: G:H.264 Metal complexes: G:H.397 HEA.26: 29 residues within 4Å: Chain G: F.52, L.53, G.56, L.57, A.59, L.60, R.63, 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, Q.449, R.459, R.460, A.481, L.484, G.485, M.488 Ligands: WUO.19 21 PLIP interactions: 21 interactions with chain G, Hydrophobic interactions: G:F.52, G:L.53, G:L.53, G:L.57, G:L.60, G:R.63, G:M.90, G:L.91, G:I.395, G:F.398, G:F.398, G:L.402, G:A.481 Hydrogen bonds: G:R.63, G:W.151, G:R.460 Salt bridges: G:R.459, G:R.460 pi-Stacking: G:H.399 Metal complexes: G:H.86, G:H.399

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

CU.27: 4 residues within 4Å: Chain G: H.264, H.313, H.314 Ligands: HEA.25 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.264, G:H.313, G:H.314 CU.33: 5 residues within 4Å: Chain H: H.232, C.273, C.277, M.284 Ligands: CU.34 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.232, H:C.273, H:C.277 CU.34: 6 residues within 4Å: Chain H: C.273, E.275, C.277, H.281, M.284 Ligands: CU.33 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.273, H:E.275, H:C.277, H:H.281

1 x CA: CALCIUM ION(Non-covalent)

CA.29: 4 residues within 4Å: Chain G: E.65, M.68, G.70, Q.72 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.65, G:E.65, G:M.68, G:G.70, H2O.8

1 x MG: MAGNESIUM ION(Non-covalent)

MG.32: 2 residues within 4Å: Chain G: D.390 Chain H: E.275 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:D.390, H:E.275, H2O.8

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

9XX.37: 12 residues within 4Å: Chain C: L.418 Chain G: F.61, I.137, F.140, I.141 Chain K: C.24 Ligands: MQ9.4, CDL.13, WUO.19, CDL.28, 9YF.36, PLM.38 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:F.61, G:I.137, G:I.141, C:L.418 9XX.40: 5 residues within 4Å: Chain C: F.320, P.322, F.323, I.327 Chain L: C.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.320, C:F.323, C:I.327 9XX.53: 1 residues within 4Å: Chain O: C.21 No protein-ligand interaction detected (PLIP)

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

PLM.38: 5 residues within 4Å: Chain G: Q.78, Q.81, F.140 Chain K: C.24 Ligands: 9XX.37 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: G:Q.78, G:F.140, G:F.140 Hydrogen bonds: G:Q.78, K:C.24 PLM.39: 7 residues within 4Å: Chain C: W.318, E.319, W.332 Chain D: F.58, V.61, R.64 Chain L: C.21 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.318, C:W.318, C:W.318, C:W.332, D:F.58, D:V.61 Water bridges: C:E.319 PLM.52: 3 residues within 4Å: Chain M: W.318, F.320 Chain O: C.21 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:W.318, M:W.318, M:W.318, M:F.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalova, T. et al., Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-11-20

Peptides

Cytochrome bc1 complex cytochrome c subunit: A
Cytochrome bc1 complex cytochrome c subunit: BN
Cytochrome bc1 complex cytochrome b subunit: CM
Transmembrane protein: D
Probable cytochrome c oxidase subunit 3: E
Cytochrome c oxidase polypeptide 4: F
Cytochrome c oxidase subunit 1: G
cytochrome-c oxidase: H
Cytochrome c oxidase subunit: I
Uncharacterized protein MSMEG_4692/MSMEI_4575: J
LpqE protein: K
Superoxide dismutase [Cu-Zn]: LO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
M

N
G

C
N

M
H

D
P

E
S

F
T

G
R

H
Q

I
U

J
V

K
W

L
Y

O
c

Membrane

We predict this structure to be a membrane protein.
Show / Hide

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]

Related Entries With Identical Sequence