SMTL ID : 9ftz.1

CIII2/CIV respiratory supercomplex from Mycobacterium smegmatis with lansoprazole sulfide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MQ9.1: 22 residues within 4Å: Chain A: G.256, M.257, W.260, I.268 Chain C: M.121, F.128, F.129, L.148, F.303, W.307, V.340, L.343, L.344, Y.347, G.377, A.380, I.381, Y.384, L.385, T.388, M.392 Ligands: CDL.11 26 PLIP interactions: 20 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:M.121, 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:L.343, C:Y.347, C:A.380, C:I.381, C:Y.384, 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:W.260, A:I.268 Hydrogen bonds: C:Y.384 pi-Stacking: A:W.260 MQ9.5: 31 residues within 4Å: Chain A: Y.245, L.247, G.248, F.250, P.254, M.257 Chain C: L.386, F.389, A.390, M.392, I.395, I.396, K.399, F.400, I.402, T.407, I.410, G.411 Chain F: S.100, T.101, V.104, W.112, L.113 Chain G: F.131, L.134, I.135, A.138, L.170 Ligands: CDL.12, 9XX.31, 9YF.36 24 PLIP interactions: 10 interactions with chain C, 7 interactions with chain F, 2 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: C:L.386, C:F.389, C:F.389, C:I.395, C:I.396, C:K.399, C:F.400, C:F.400, C:I.402, C:I.410, F:V.104, F:V.104, F:W.112, F:W.112, F:W.112, F:L.113, A:L.247, A:P.254, G:F.131, G:L.134, G:I.135, G:A.138, G:L.170 pi-Stacking: F:W.112 MQ9.15: 22 residues within 4Å: Chain B: I.127, I.130 Chain C: E.44, Y.48, L.55, T.56, F.104, V.105, L.227, V.230, W.231, F.257, A.258, G.262, F.265, T.269 Chain N: F.194, T.198, A.201, F.202 Ligands: HEM.14, 7PH.51 11 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B, 1 interactions with chain N Hydrophobic interactions: C:L.55, C:T.56, C:F.104, C:V.105, C:V.230, C:W.231, C:F.265, C:F.265, B:I.127, B:I.130, N:F.194 MQ9.45: 23 residues within 4Å: Chain B: L.191, A.201, F.202 Chain M: F.34, P.35, F.40, E.44, L.47, I.52, L.55, T.56, F.104, V.105, V.230, W.231, H.235, F.257, A.258, S.261, G.262, F.265, T.269 Ligands: HEM.44 17 PLIP interactions: 15 interactions with chain M, 2 interactions with chain B Hydrophobic interactions: M:F.34, M:E.44, M:L.47, M:I.52, M:L.55, M:F.104, M:V.105, M:V.230, M:W.231, M:W.231, M:F.257, M:F.265, M:F.265, M:T.269, B:L.191, B:A.201 pi-Stacking: M:F.257 MQ9.46: 15 residues within 4Å: Chain C: R.19 Chain M: V.142, F.153, A.174, L.175, I.178, T.179, M.305, T.308, A.334, M.337, I.345, A.346, F.349, K.352 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:V.142, M:A.174, M:I.178, M:A.346, M:F.349, M:F.349, M:K.352

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

WUO.2: 21 residues within 4Å: Chain A: K.181, D.193, G.195, A.237, P.240, S.241, G.244, Y.245, G.246, M.257, I.261, I.262 Chain C: L.274, L.278 Chain F: P.111, W.112, L.113, A.115, A.116, F.120 Ligands: CDL.11 19 PLIP interactions: 12 interactions with chain A, 5 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: A:Y.245, A:M.257, A:I.262, F:W.112, F:W.112, F:L.113, F:A.115, F:A.116, C:L.274, C:L.278 Hydrogen bonds: A:D.193, A:D.193, A:A.237, A:S.241, A:Y.245, A:G.246, A:G.248 Water bridges: A:G.248 Salt bridges: A:K.181 WUO.18: 22 residues within 4Å: Chain D: V.68, G.69, H.70, V.71, W.74, F.75, G.78, F.79, A.85, L.86 Chain G: L.57, F.61, F.73 Chain H: L.335 Chain K: G.27, Q.28, I.29 Ligands: CDL.17, HEA.25, CDL.27, 9XX.31, 9YF.36 15 PLIP interactions: 9 interactions with chain D, 2 interactions with chain K, 1 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: D:W.74, D:W.74, D:F.75, D:F.75, D:F.79, D:A.85, D:L.86, G:L.57, G:F.61 Hydrogen bonds: D:H.70, D:V.71, K:Q.28, K:I.29, H:L.335, G:F.73

2 x HEC: HEME C(Covalent)

HEC.3: 25 residues within 4Å: Chain A: F.99, R.105, Q.114, A.115, N.171, C.172, C.175, H.176, L.185, Y.190, A.191, P.192, 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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.99, A:L.185, A:A.191, A:P.192, A:L.194, A:L.194, A:A.197, A:I.202, A:I.202, A:A.205, A:P.210, A:M.213, A:F.216, A:I.229 Hydrogen bonds: A:Q.100 Water bridges: A:R.105, A:Q.114, A:A.197, A:A.197 Salt bridges: A:R.105, A:R.105 Metal complexes: A:H.176 HEC.4: 22 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, M.106, P.107, A.108, A.115, F.122, Q.211 Chain H: W.138 Chain K: T.32, Q.35, P.37, A.38 13 PLIP interactions: 11 interactions with chain A, 1 interactions with chain H, 1 interactions with chain K, Hydrophobic interactions: A:P.87, A:L.89, A:L.89, A:V.97, A:Q.100, A:P.107, A:F.122, H:W.138 Hydrogen bonds: A:Q.100, A:Q.211, K:A.38 Water bridges: A:Q.211 Metal complexes: A:H.75

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: 8 residues within 4Å: Chain N: C.333, H.335, L.336, C.338, C.352, C.354, 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, I.203, 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 15 PLIP interactions: 2 interactions with chain M, 8 interactions with chain B, 2 interactions with chain N, 3 interactions with chain C Hydrogen bonds: M:R.100, B:K.208, B:K.208, B:N.209 Salt bridges: M:R.100, B:K.212 Hydrophobic interactions: B:V.200, B:I.203, B:I.207, B:I.207, N:L.95, N:F.96, C:I.185, C:W.188, C:W.188 9YF.36: 24 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: MQ9.5, CDL.11, CDL.12, WUO.18, 9XX.31 19 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A, 1 interactions with chain G, 6 interactions with chain D, 1 interactions with chain K 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, G:I.141, D:F.75, D:F.75, D:F.75, D:F.75, D:F.79, D:F.79 Hydrogen bonds: C:S.403, C:N.405, A:S.187, K:S.25 9YF.48: 13 residues within 4Å: Chain B: L.95, W.99 Chain C: E.98, R.100 Chain M: I.185, W.188 Chain N: V.200, G.204, G.205, I.207, K.208, N.209, K.212 17 PLIP interactions: 9 interactions with chain N, 2 interactions with chain C, 4 interactions with chain M, 2 interactions with chain B Hydrophobic interactions: N:V.200, N:V.200, N:I.207, N:I.207, M:I.185, M:I.185, M:W.188, M:W.188, B:L.95 Hydrogen bonds: N:K.208, N:N.209, N:K.212, N:K.212, C:R.100, B:W.99 Salt bridges: N:K.212, C:R.100

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

7PH.8: 12 residues within 4Å: Chain B: L.168, T.169, L.172, E.173, S.175, L.177, L.187 Chain M: A.6, M.254, V.259 Chain N: F.137, I.142 10 PLIP interactions: 5 interactions with chain B, 3 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: B:L.172, B:L.172, B:L.187, N:F.137, N:F.137, N:I.142, M:A.6, M:V.259 Hydrogen bonds: B:T.169 Salt bridges: B:K.178 7PH.19: 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: I.122, W.134 Ligands: CDL.16 9 PLIP interactions: 1 interactions with chain C, 6 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: C:F.502, E:F.107, E:F.107, E:V.156, E:V.159, E:L.162, E:A.163, F:I.122 Salt bridges: F:K.138 7PH.50: 13 residues within 4Å: Chain C: A.9, A.10, G.13, D.14, I.16, D.17, S.23, M.254 Chain N: R.161, K.162, V.164, A.165 Ligands: CDL.40 6 PLIP interactions: 3 interactions with chain N, 3 interactions with chain C Hydrophobic interactions: N:V.164, C:A.9, C:I.16, C:D.17 Salt bridges: N:R.161, N:K.162 7PH.51: 11 residues within 4Å: Chain B: F.137 Chain C: F.5, A.6, M.254, V.259 Chain N: L.168, T.169, L.172, L.177, K.178 Ligands: MQ9.15 9 PLIP interactions: 2 interactions with chain B, 6 interactions with chain N, 1 interactions with chain C Hydrophobic interactions: B:F.137, B:F.137, N:L.168, N:L.172, N:L.172, N:L.172, C:V.259 Salt bridges: N:K.178, 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: 14 residues within 4Å: Chain B: W.211, K.222, A.223, W.226, W.404, E.405, R.406, K.407 Chain C: V.184, I.185, T.187, W.188, G.324, H.325 14 PLIP interactions: 4 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:V.184, C:W.188 Hydrogen bonds: C:T.187, B:W.211, B:K.222, B:K.222, B:W.226, B:E.405, B:E.405, B:R.406, B:K.407 Salt bridges: C:H.325 Water bridges: B:N.209, B:N.209 IZL.49: 11 residues within 4Å: Chain M: V.184, W.188, G.324, H.325 Chain N: W.211, K.222, W.226, W.404, E.405, R.406, K.407 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:W.211, N:W.211, N:K.222, N:K.222, N:W.226, N:E.405, N:E.405, N:K.407 Salt bridges: M:H.325

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

HEM.10: 22 residues within 4Å: Chain C: F.50, L.53, L.54, G.57, V.58, L.60, T.61, F.64, R.106, H.109, H.110, A.113, F.116, E.154, G.158, Y.159, L.161, P.162, Y.208, H.211, N.282 Chain M: L.213 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain M, Hydrophobic interactions: C:F.50, C:L.53, C:L.53, C:L.54, C:L.60, C:F.64, C:H.110, C:F.116, C:E.154, C:Y.159, C:L.161, C:Y.208, M:L.213 Hydrogen bonds: C:R.106, C:N.282 Salt bridges: C:R.106, C:H.110 pi-Stacking: C:H.109, C:H.211 Metal complexes: C:H.109, C:H.211 HEM.14: 24 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, L.147, I.223, H.226, V.230, H.235, T.236 Ligands: MQ9.15 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:A.46, C:F.116, C:I.120, C:I.120, C:I.127, C:I.127, C:W.141, C:L.147, C:I.223 Hydrogen bonds: C:G.43, C:R.137, C:T.236 Water bridges: C:L.42, C:L.42 Salt bridges: C:H.123, C:R.126, C:R.126, C:H.235, C:H.235 Metal complexes: C:H.123, C:H.226 HEM.41: 24 residues within 4Å: Chain M: F.50, L.53, L.54, G.57, V.58, L.60, T.61, F.64, R.106, H.109, H.110, A.113, E.154, G.155, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, N.282, Y.304 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:F.50, M:L.53, M:L.53, M:L.54, M:L.60, M:F.64, M:E.154, M:L.161, M:Y.208, M:I.212, M:I.212, M:P.216 Hydrogen bonds: M:N.282 Salt bridges: M:R.106, M:R.106, M:H.110 Metal complexes: M:H.109, M:H.211 HEM.44: 22 residues within 4Å: Chain M: 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, W.141, G.144, S.145, L.147, H.226, V.230, H.235, T.236 Ligands: MQ9.45 21 PLIP interactions: 21 interactions with chain M, Hydrophobic interactions: M:A.46, M:F.116, M:I.120, M:I.120, M:I.120, M:I.127, M:I.127, M:I.127, M:A.132, M:W.141, M:L.147 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.226

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.11: 29 residues within 4Å: Chain A: I.268, M.272, R.277, A.278 Chain C: H.37, W.38, L.42, V.122, A.125, R.126, F.129, R.366, P.367, R.368, T.374, S.378, I.381, L.385, V.425, A.426, W.429, A.430, L.433, P.483 Ligands: MQ9.1, WUO.2, CDL.12, 9XX.31, 9YF.36 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.38, C:L.42, C:V.122, C:A.125, C:F.129, C:F.129, C:F.129, C:I.381, C:A.426, C:W.429, C:L.433, A:I.268, 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.12: 18 residues within 4Å: Chain C: R.368, W.429, L.433, L.484, K.486, R.487 Chain F: W.90, S.98, T.101, F.120, S.124 Chain G: Y.29, I.32, F.131 Ligands: MQ9.5, CDL.11, CDL.16, 9YF.36 17 PLIP interactions: 13 interactions with chain C, 2 interactions with chain G, 1 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: C:W.429, G:F.131, F:F.120 Hydrogen bonds: C:L.484, C:L.484, C:K.486, G:Y.29 Water bridges: C:R.366, C:R.366, C:R.366, C:R.368, C:R.368, C:R.487 Salt bridges: C:R.368, C:K.486, C:R.487, A:R.277 CDL.16: 21 residues within 4Å: Chain A: I.261, V.265, A.266, I.268, G.269, M.272, W.273, R.277 Chain B: K.139 Chain C: R.487, K.490 Chain F: W.91, A.119, I.122, T.123, C.126, W.134, G.135, E.137 Ligands: CDL.12, 7PH.19 15 PLIP interactions: 4 interactions with chain C, 4 interactions with chain F, 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:K.490, C:K.490 Salt bridges: C:R.487, C:K.490, A:R.277, B:K.139 Hydrophobic interactions: F:W.91, F:A.119, F:I.122, F:T.123, A:I.261, A:V.265, A:A.266, A:I.268, A:W.273 CDL.17: 26 residues within 4Å: Chain C: M.379, A.420, Y.423, F.424, R.428 Chain D: I.45, M.48, H.49, G.51, G.52, 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: WUO.18, CDL.27 18 PLIP interactions: 5 interactions with chain D, 7 interactions with chain G, 6 interactions with chain C Hydrophobic interactions: D:V.87, G:L.27, G:V.46, G:W.493, G:W.493, G:F.496, G:F.496, C:A.420, C:Y.423, C:Y.423, C:F.424 Hydrogen bonds: D:N.90, C:R.428 Salt bridges: D:R.89, D:R.89, D:R.94, G:K.24, C:R.428 CDL.23: 19 residues within 4Å: Chain E: M.24, V.25, G.28, T.29, W.32, L.161, R.164, A.177, V.180, V.181, Y.184 Chain F: F.99, V.125, L.128, V.129 Chain G: F.118, P.119, R.120, L.121 17 PLIP interactions: 5 interactions with chain G, 9 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: G:F.118, G:L.121, E:W.32, E:W.32, E:V.180, E:Y.184, E:Y.184, F:V.125, F:V.125, F:V.129 Hydrogen bonds: G:R.120, G:L.121 Salt bridges: G:R.120, E:R.164, E:R.164 Water bridges: E:R.164, E:R.164 CDL.27: 22 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, V.47, F.126, W.127, V.495, W.499, R.500 Ligands: CDL.17, WUO.18, 9XX.31 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:L.27, G:I.28, G:I.42, G:V.47, G:F.126, G:W.127, G:V.495, G:W.499, 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: G:R.500, C:R.428 CDL.40: 18 residues within 4Å: Chain C: Y.20, P.22, A.25, R.28, Q.29, A.221, G.224, A.225, A.228, L.229, W.231, F.232 Chain M: Y.20, H.21, P.22, R.28 Ligands: CDL.42, 7PH.50 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain M Hydrophobic interactions: C:P.22, C:P.22, C:A.25, C:Q.29, C:L.229, C:F.232 Hydrogen bonds: C:Q.29, M:R.28 Salt bridges: C:R.28, M:H.21 Water bridges: M:R.28 CDL.42: 18 residues within 4Å: Chain C: Y.20, H.21, R.28, I.143 Chain M: Y.20, A.25, R.28, Q.29, L.220, A.221, I.223, G.224, A.225, L.227, A.228, L.229, F.232 Ligands: CDL.40 14 PLIP interactions: 11 interactions with chain M, 3 interactions with chain C Hydrophobic interactions: M:Y.20, M:L.220, M:I.223, M:A.225, M:L.227, M:L.227, M:A.228, M:L.229, M:F.232, M:F.232, C:I.143 Salt bridges: M:R.28, C:H.21 Hydrogen bonds: C:R.28 CDL.43: 18 residues within 4Å: Chain M: H.37, W.38, M.121, A.125, F.129, T.130, F.238, R.366, P.367, R.368, T.374, S.378, I.381, A.382, V.425, A.426, W.429, L.433 12 PLIP interactions: 12 interactions with chain M Hydrophobic interactions: M:F.129, M:F.129, M:T.130, M:I.381, M:A.382, M:V.425, M:A.426, M:L.433 Hydrogen bonds: M:R.368 Salt bridges: M:H.37, M:H.37, M:R.368

1 x 01: Lansoprazole sulfide

01.13: 14 residues within 4Å: Chain B: H.355 Chain C: F.156, G.170, A.173, A.174, I.178, T.179, S.299, P.301, T.308, D.309, I.312, A.334, M.337 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.173, C:I.178 Hydrogen bonds: C:D.309

5 x TRD: TRIDECANE(Non-covalent)

TRD.20: 4 residues within 4Å: Chain E: F.48, R.51, T.198, V.202 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.48, E:V.202 TRD.22: 5 residues within 4Å: Chain E: F.44, F.48 Chain F: V.34, W.36, T.39 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:V.34, F:W.36, F:W.36, F:T.39, E:F.44, E:F.48 TRD.29: 2 residues within 4Å: Chain G: T.444, L.447 No protein-ligand interaction detected (PLIP) TRD.30: 6 residues within 4Å: Chain G: L.371, S.375, L.447, H.450, W.451 Chain H: L.33 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:L.371, G:L.447, G:L.447, G:H.450, G:W.451 TRD.35: 2 residues within 4Å: Chain G: W.451 Chain H: A.30 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:W.451, G:W.451

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

3PE.21: 8 residues within 4Å: Chain E: Y.121, V.125, T.130, I.131, P.132, Y.141, G.145 Chain G: L.240 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:Y.121, E:V.125, E:I.131, E:Y.141, G:L.240 Hydrogen bonds: E:I.131

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

HEA.24: 30 residues within 4Å: Chain G: W.151, T.152, W.260, V.267, Y.268, H.313, H.314, T.330, I.333, A.334, T.337, 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, T.405, R.459 Chain H: V.60, I.106 Ligands: CU.26 26 PLIP interactions: 2 interactions with chain H, 24 interactions with chain G, Hydrophobic interactions: H:V.60, H:I.106, G:W.151, G:W.260, G:V.267, G:T.330, G:A.334, G:T.337, G:L.370, G:V.377, G:L.379, G:F.398, G:F.398, G:V.401, G:V.401, G:L.402 Hydrogen bonds: G:W.151, G:Y.268, G:Y.268, G:T.389 Water bridges: G:H.314, G:H.314 Salt bridges: G:R.459 pi-Cation interactions: G:H.264, G:H.397 Metal complexes: G:H.397 HEA.25: 30 residues within 4Å: Chain G: F.52, L.53, G.56, L.57, A.59, F.79, F.83, H.86, G.87, M.90, L.91, G.150, W.151, Y.392, I.395, F.398, H.399, L.402, F.403, I.406, V.407, F.446, Q.449, R.459, R.460, A.481, L.484, G.485, M.488 Ligands: WUO.18 22 PLIP interactions: 22 interactions with chain G, Hydrophobic interactions: G:F.52, G:F.52, G:M.90, G:L.91, G:L.91, G:I.395, G:F.398, G:L.402, G:I.406, G:V.407, G:A.481, G:L.484 Hydrogen bonds: G:F.83, G:W.151, G:Q.449, G:R.460 Water bridges: G:R.459 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.26: 4 residues within 4Å: Chain G: H.264, H.313, H.314 Ligands: HEA.24 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: 5 residues within 4Å: Chain H: C.273, E.275, C.277, H.281 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.28: 5 residues within 4Å: Chain G: E.65, M.68, P.69, 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.10

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

9XX.31: 12 residues within 4Å: Chain C: L.418 Chain G: F.61, L.134, F.140, I.141 Chain K: C.24 Ligands: MQ9.5, CDL.11, WUO.18, CDL.27, 9YF.36, PLM.37 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:L.134, G:I.141, C:L.418 9XX.39: 5 residues within 4Å: Chain C: F.320, P.322, W.332 Chain L: C.21 Ligands: PLM.38 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.320, C:F.320, C:F.320, C:F.320, C:P.322, C:W.332 9XX.53: 6 residues within 4Å: Chain M: F.320, Y.321, P.322, I.327, W.332 Chain O: C.21 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:F.320, M:F.320, M:F.320, M:P.322, M:I.327, M:W.332

1 x MG: MAGNESIUM ION(Non-covalent)

MG.32: 2 residues within 4Å: Chain G: D.390 Chain H: E.275 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.390

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

PLM.37: 6 residues within 4Å: Chain G: Q.78, Q.81, F.140, G.145 Chain K: C.24 Ligands: 9XX.31 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Q.78, G:F.140 PLM.38: 7 residues within 4Å: Chain C: W.318, E.319, F.320 Chain D: F.58, V.61 Chain L: C.21 Ligands: 9XX.39 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:F.320, D:F.58, D:V.61 Water bridges: C:E.319 PLM.52: 5 residues within 4Å: Chain M: W.318, E.319, F.320, W.332 Chain O: C.21 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:W.318, M:W.318, M:F.320, M:W.332

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.
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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]

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