SMTL ID : 9gy6.1

Mycobacterial cytochrome bc1:aa3 with inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 8 residues within 4Å: Chain A: C.346, H.348, L.349, G.350, C.351, C.365, H.368, S.370 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.346, A:H.348, A:C.365, A:H.368 FES.30: 8 residues within 4Å: Chain L: C.346, H.348, L.349, G.350, C.351, C.365, H.368, S.370 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.346, L:H.348, L:C.365, L:H.368

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.2: 19 residues within 4Å: Chain A: L.212, V.213, I.216, G.217, G.218, I.220, K.221, N.222, K.225 Chain B: I.185, W.188, L.189, A.192 Chain L: F.107, L.108, W.112 Chain M: E.98, V.99, R.100 22 PLIP interactions: 10 interactions with chain A, 3 interactions with chain L, 4 interactions with chain B, 5 interactions with chain M Hydrophobic interactions: A:V.213, A:I.216, A:I.220, A:I.220, A:I.220, A:I.220, L:F.107, L:L.108, B:I.185, B:W.188, B:W.188, B:W.188 Hydrogen bonds: A:G.218, A:K.221, A:N.222, M:E.98, M:R.100, M:R.100, M:R.100 Salt bridges: A:K.225, M:R.100 Water bridges: L:W.112 9YF.12: 18 residues within 4Å: Chain B: L.278 Chain C: K.171, D.183, G.185, A.227, S.231, G.234, Y.235, G.236, G.238, M.247, I.251 Chain H: P.111, W.112, L.113, A.116 Ligands: CDL.14, MQ7.29 12 PLIP interactions: 7 interactions with chain C, 4 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: C:Y.235, C:Y.235, C:I.251, H:P.111, H:W.112, H:W.112, H:L.113, B:L.278 Hydrogen bonds: C:D.183, C:G.185, C:Y.235, C:G.236 9YF.31: 17 residues within 4Å: Chain A: L.108, W.112 Chain B: E.98, V.99, R.100 Chain L: L.212, I.216, G.217, G.218, I.220, K.221, N.222 Chain M: I.185, W.188, L.189, A.192, L.193 18 PLIP interactions: 5 interactions with chain B, 5 interactions with chain M, 8 interactions with chain L Hydrogen bonds: B:E.98, B:R.100, B:R.100, B:R.100, L:G.218, L:K.221, L:N.222 Salt bridges: B:R.100, L:K.225 Hydrophobic interactions: M:I.185, M:W.188, M:W.188, M:W.188, M:L.189, L:L.212, L:I.216, L:I.220, L:I.220 9YF.44: 15 residues within 4Å: Chain M: L.278 Chain N: K.171, D.183, G.185, S.231, G.234, Y.235, G.236, M.247, I.251 Chain S: W.112, L.113, A.116 Ligands: CDL.32, MQ7.41 11 PLIP interactions: 6 interactions with chain N, 4 interactions with chain S, 1 interactions with chain M Hydrophobic interactions: N:Y.235, N:Y.235, N:I.251, S:W.112, S:W.112, S:L.113, S:A.116, M:L.278 Hydrogen bonds: N:D.183, N:S.231, N:G.236

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 8 residues within 4Å: Chain A: L.185, S.188, L.200 Chain L: F.150, I.155 Chain M: M.254, P.255, V.259 6 PLIP interactions: 2 interactions with chain M, 1 interactions with chain A, 3 interactions with chain L Hydrophobic interactions: M:P.255, M:V.259, A:L.200, L:F.150, L:F.150, L:I.155 PLM.28: 7 residues within 4Å: Chain G: V.159, L.160, A.163, M.167 Chain H: F.130, W.134 Ligands: CDL.14 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:V.159, G:L.160, G:M.167, H:F.130, H:W.134 PLM.33: 10 residues within 4Å: Chain A: A.147, F.150 Chain B: A.9, M.254, P.255 Chain L: L.181, A.184, S.188, L.190, L.200 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain L, 3 interactions with chain A Hydrophobic interactions: B:P.255, L:A.184, L:L.190, A:F.150, A:F.150, A:F.150 PLM.59: 10 residues within 4Å: Chain R: V.156, V.159, L.160, A.163, K.166, M.167 Chain S: I.122, F.130, K.138 Ligands: CDL.40 7 PLIP interactions: 4 interactions with chain R, 3 interactions with chain S Hydrophobic interactions: R:V.156, R:V.159, R:L.160, R:M.167, S:I.122, S:F.130 Hydrogen bonds: S:K.138

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

HEM.4: 23 residues within 4Å: Chain B: S.39, 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, L.147, I.223, H.226, L.227, V.230, H.235, T.236 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.116, B:I.120, B:I.120, B:I.127, B:I.127, B:I.127, B:W.141, B:L.147, B:L.227, B:V.230, B:V.230 Hydrogen bonds: B:G.43, B:T.236 Salt bridges: B:H.123, B:R.126, B:R.126, B:R.137, B:H.235, B:H.235 pi-Cation interactions: B:H.123 Metal complexes: B:H.226 HEM.5: 25 residues within 4Å: Chain B: 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.155, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, N.282 Chain M: L.213 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain M, Hydrophobic interactions: B:F.50, B:L.53, B:L.53, B:L.54, B:V.58, B:L.60, B:T.61, B:F.64, B:F.116, B:E.154, B:Y.159, B:L.161, B:Y.208, B:I.212, B:I.212, B:P.216, M:L.213 Hydrogen bonds: B:N.282 Salt bridges: B:R.106, B:R.106, B:H.110 Metal complexes: B:H.109, B:H.211 HEM.34: 23 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, N.140, W.141, G.144, L.147, I.223, H.226, L.227, V.230, H.235, T.236 27 PLIP interactions: 27 interactions with chain M, Hydrophobic interactions: M:A.46, M:F.116, M:I.120, M:I.120, M:L.124, M:L.124, M:I.127, M:I.127, M:I.127, M:A.132, M:W.141, M:L.147, M:L.227, M:V.230, M:V.230 Hydrogen bonds: M:G.43, M:T.236 Water bridges: M:H.123, M:H.123 Salt bridges: M:H.123, M:R.126, M:R.126, M:R.137, M:H.235, M:H.235 pi-Cation interactions: M:H.123 Metal complexes: M:H.226 HEM.35: 25 residues within 4Å: Chain B: L.213 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, F.116, E.154, G.155, G.158, Y.159, L.161, P.162, Y.208, H.211, I.212, P.216, N.282 22 PLIP interactions: 21 interactions with chain M, 1 interactions with chain B, Hydrophobic interactions: M:F.50, M:L.53, M:L.53, M:L.54, M:V.58, M:L.60, M:T.61, M:F.64, M:F.116, M:E.154, M:L.161, M:Y.208, M:I.212, M:I.212, M:P.216, B:L.213 Hydrogen bonds: M:N.282 Salt bridges: M:R.106, M:R.106, M:H.110 Metal complexes: M:H.109, M:H.211

17 x CDL: CARDIOLIPIN(Covalent)(Non-covalent)

CDL.6: 20 residues within 4Å: Chain B: Y.20, P.22, A.25, R.28, Q.29, L.47, L.220, A.221, I.223, G.224, A.225, L.227, A.228, L.229, W.231, F.232 Chain M: Y.20, H.21, A.25 Ligands: CDL.36 Ligand excluded by PLIP CDL.7: 26 residues within 4Å: Chain B: H.37, W.38, A.125, R.126, F.129, F.238, R.366, P.367, R.368, S.378, I.381, A.382, L.385, I.421, V.425, A.426, W.429, A.430, L.433, P.483 Chain C: M.262, R.267, A.268 Ligands: CDL.8, MQ9.13, CDL.25 Ligand excluded by PLIP CDL.8: 22 residues within 4Å: Chain B: R.366, R.368, W.429, L.433, L.484, K.486, R.487 Chain F: Y.29, I.32 Chain H: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123 Ligands: CDL.7, CDL.14, CDL.25, MQ7.29 Ligand excluded by PLIP CDL.14: 21 residues within 4Å: Chain B: R.487, K.490 Chain C: I.251, V.255, A.256, G.259, M.262, W.263, R.267 Chain H: W.91, A.119, F.120, T.123, C.126, G.127, W.134, G.135, E.137 Ligands: CDL.8, 9YF.12, PLM.28 Ligand excluded by PLIP CDL.15: 30 residues within 4Å: Chain B: I.376, M.379, M.415, A.420, Y.423, F.424, R.428 Chain D: I.29, M.32, G.35, G.36, S.39, A.69, L.70, V.71, R.73, N.74, R.78, I.83 Chain F: M.21, K.24, L.27, V.46, A.50, F.51, V.54, F.496 Ligands: 9Y0.16, CDL.17, CDL.25 Ligand excluded by PLIP CDL.17: 19 residues within 4Å: Chain D: V.68, A.69, G.72, R.73, W.76, L.77, R.80, W.82 Chain F: L.53, V.492, W.493, F.496, K.497, R.500, Y.501 Chain J: M.46 Ligands: CDL.15, HEA.21, CDL.25 Ligand excluded by PLIP CDL.24: 24 residues within 4Å: Chain F: F.118, P.119, R.120, L.121, L.124, L.180 Chain G: V.25, G.28, T.29, W.32, L.149, H.150, G.153, V.156, L.160, R.164, A.177, V.180, Y.184 Chain H: I.95, I.122, V.125, L.128, V.129 Ligand excluded by PLIP CDL.25: 28 residues within 4Å: Chain B: F.424, V.425, R.428 Chain F: M.21, G.22, P.23, K.24, G.25, N.26, L.27, I.28, L.31, I.42, M.43, C.45, V.46, V.47, F.49, L.105, L.130, F.418, F.491, V.495, W.499 Ligands: CDL.7, CDL.8, CDL.15, CDL.17 Ligand excluded by PLIP CDL.32: 16 residues within 4Å: Chain L: L.88, Y.91, W.92, L.95, L.141, I.145, L.149, K.153 Chain M: M.267, L.274, M.275 Chain N: I.252, V.260, W.263 Ligands: CDL.40, 9YF.44 Ligand excluded by PLIP CDL.36: 19 residues within 4Å: Chain B: Y.20, H.21, P.22, A.25, R.28 Chain M: Y.20, P.22, A.25, V.26, R.28, Q.29, L.220, G.224, A.225, A.228, L.229, W.231, F.232 Ligands: CDL.6 Ligand excluded by PLIP CDL.37: 27 residues within 4Å: Chain M: H.37, W.38, V.122, R.126, F.129, R.366, P.367, R.368, T.374, S.378, I.381, A.382, L.385, L.418, V.422, A.426, W.429, A.430, L.433, P.483 Chain N: I.258, M.262, R.267, A.268 Ligands: CDL.38, MQ9.45, CDL.56 Ligand excluded by PLIP CDL.38: 24 residues within 4Å: Chain M: R.368, W.429, L.433, S.436, P.483, L.484, K.486, R.487, K.490 Chain N: M.262 Chain Q: Y.29, I.32 Chain S: W.90, W.91, I.93, L.94, L.97, S.98, T.101, F.120, T.123 Ligands: CDL.37, CDL.40, CDL.56 Ligand excluded by PLIP CDL.40: 22 residues within 4Å: Chain M: R.487, K.490 Chain N: I.251, V.255, A.256, G.259, M.262, W.263, R.267 Chain R: K.166 Chain S: W.91, A.119, F.120, T.123, C.126, G.127, W.134, G.135, E.137 Ligands: CDL.32, CDL.38, PLM.59 Ligand excluded by PLIP CDL.46: 31 residues within 4Å: Chain M: M.379, L.383, M.415, A.420, Y.423, F.424, R.428 Chain O: M.27, I.29, M.32, H.33, G.35, G.36, S.39, V.66, A.69, L.70, V.71, R.73, N.74, R.78, I.83 Chain Q: M.21, L.27, V.46, A.50, F.51, F.496 Ligands: 9Y0.47, CDL.48, CDL.56 Ligand excluded by PLIP CDL.48: 20 residues within 4Å: Chain O: A.65, G.72, R.73, W.76, L.77, R.80, W.82 Chain Q: L.53, L.489, V.492, W.493, F.496, K.497, R.500, Y.501 Chain U: M.46 Ligands: CDL.46, 9Y0.47, HEA.52, CDL.56 Ligand excluded by PLIP CDL.55: 22 residues within 4Å: Chain Q: F.118, P.119, R.120, L.121, L.180 Chain R: V.25, G.28, T.29, W.32, E.36, L.149, G.153, V.156, A.157, L.160, R.164, A.177, V.180, Y.184 Chain S: V.125, L.128, V.129 Ligand excluded by PLIP CDL.56: 31 residues within 4Å: Chain M: F.424, V.425, R.428 Chain Q: 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.47, F.49, L.105, W.127, I.414, W.417, F.418, F.491, V.495, F.496, W.499, R.500 Ligands: CDL.37, CDL.38, CDL.46, CDL.48 Ligand excluded by PLIP

2 x 01: 6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide

01.9: 21 residues within 4Å: Chain A: L.349, C.367, H.368 Chain B: F.153, Y.156, L.166, G.170, A.173, A.174, I.178, T.179, M.182, L.189, S.299, Q.300, P.301, M.305, T.308, E.309, A.312, M.337 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.153, B:A.173, B:A.174, B:I.178, B:I.178, B:E.309, B:A.312, A:L.349 Hydrogen bonds: B:T.308 pi-Stacking: B:Y.156 Halogen bonds: B:L.166 01.39: 20 residues within 4Å: Chain L: H.368 Chain M: F.153, Y.156, Y.159, L.166, G.170, A.173, A.174, I.178, T.179, M.182, L.189, S.299, Q.300, P.301, M.305, T.308, E.309, A.312, M.337 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:A.173, M:A.174, M:I.178, M:E.309, M:A.312 Hydrogen bonds: M:T.308, M:T.308 pi-Stacking: M:Y.156 Halogen bonds: M:L.166

4 x HEC: HEME C(Covalent)

HEC.10: 19 residues within 4Å: Chain C: S.60, C.61, C.64, H.65, R.75, P.77, L.79, T.82, A.86, V.87, Q.90, V.91, M.96, P.97, A.98, A.105, F.112, P.200, Q.201 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:P.77, C:L.79, C:L.79, C:A.86, C:Q.90, C:V.91, C:P.97, C:A.98, C:F.112 Hydrogen bonds: C:A.105 Metal complexes: C:H.65 HEC.11: 26 residues within 4Å: Chain A: Y.356 Chain C: F.89, T.93, R.95, Q.104, N.161, C.162, C.165, H.166, L.175, Y.180, A.181, P.182, L.184, A.187, I.192, A.195, M.196, P.200, Q.201, N.202, M.203, P.204, F.206, L.211, I.219 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:F.89, C:L.175, C:L.175, C:A.181, C:L.184, C:I.192, C:A.195, C:P.200, C:P.204, C:F.206, C:L.211, C:I.219 Hydrogen bonds: C:Q.201 Salt bridges: C:R.95, C:R.95 Metal complexes: C:H.166 HEC.42: 21 residues within 4Å: Chain N: S.60, C.61, S.63, C.64, H.65, R.75, P.77, L.79, T.82, A.86, V.87, Q.90, V.91, M.96, P.97, A.98, A.105, F.112, P.200, Q.201 Ligands: HEC.43 12 PLIP interactions: 12 interactions with chain N, Hydrophobic interactions: N:P.77, N:L.79, N:L.79, N:Q.90, N:V.91, N:M.96, N:P.97, N:A.98, N:F.112 Hydrogen bonds: N:Q.90, N:Q.201 Metal complexes: N:H.65 HEC.43: 29 residues within 4Å: Chain L: Y.356 Chain N: F.89, Q.90, T.93, R.95, Q.104, A.105, N.161, C.162, C.165, H.166, L.175, Y.180, A.181, P.182, L.184, D.186, A.187, I.192, A.195, M.196, P.200, Q.201, N.202, M.203, P.204, F.206, I.219 Ligands: HEC.42 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:F.89, N:L.175, N:L.175, N:A.181, N:L.184, N:I.192, N:A.195, N:P.200, N:Q.201, N:P.204, N:F.206, N:I.219 Hydrogen bonds: N:Q.90 Salt bridges: N:R.95, N:R.95 Metal complexes: N:H.166

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

MQ9.13: 23 residues within 4Å: Chain B: M.121, V.122, L.124, A.125, F.128, F.303, W.307, V.340, A.380, I.381, L.383, Y.384, L.385, T.388, M.392 Chain C: A.243, G.246, M.247, W.250, I.251, M.254, I.258 Ligands: CDL.7 28 PLIP interactions: 20 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:M.121, B:L.124, B:A.125, B:F.128, B:F.128, B:F.128, B:F.303, B:W.307, B:I.381, B:I.381, B:L.383, B:Y.384, B:Y.384, B:Y.384, B:Y.384, B:Y.384, B:Y.384, B:L.385, B:T.388, C:M.247, C:W.250, C:W.250, C:W.250, C:I.251, C:M.254, C:I.258 Hydrogen bonds: B:Y.384 pi-Stacking: C:W.250 MQ9.45: 22 residues within 4Å: Chain M: M.121, L.124, F.128, F.129, L.148, M.152, F.303, V.340, L.344, I.376, A.380, I.381, Y.384, L.385, T.388, F.389 Chain N: M.247, W.250, I.251, M.254, I.258 Ligands: CDL.37 27 PLIP interactions: 19 interactions with chain M, 8 interactions with chain N Hydrophobic interactions: M:M.121, M:L.124, M:L.124, M:F.128, M:F.128, M:F.129, M:L.148, M:F.303, M:V.340, M:L.344, M:I.376, M:A.380, M:I.381, M:Y.384, M:Y.384, M:Y.384, M:L.385, M:T.388, M:F.389, N:W.250, N:W.250, N:W.250, N:W.250, N:I.251, N:M.254, N:I.258 pi-Stacking: N:W.250

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

9Y0.16: 12 residues within 4Å: Chain D: I.29, G.30, V.31, H.33, I.34, G.35, L.37, V.68, W.75, R.78, R.79 Ligands: CDL.15 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.37, D:V.68, D:W.75 Salt bridges: D:H.33, D:H.33 9Y0.27: 14 residues within 4Å: Chain F: M.173, L.240 Chain G: Y.121, V.125, T.130, I.131, P.132, Y.141, L.142, G.145, F.146 Chain H: F.99, A.106, W.109 11 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F, 4 interactions with chain H Hydrophobic interactions: G:Y.121, G:I.131, G:Y.141, G:L.142, G:F.146, F:L.240, H:F.99, H:F.99, H:A.106, H:W.109 Hydrogen bonds: G:I.131 9Y0.47: 14 residues within 4Å: Chain O: I.29, G.30, V.31, H.33, I.34, L.37, L.38, V.68, G.72, W.75, R.78, R.79 Ligands: CDL.46, CDL.48 7 PLIP interactions: 7 interactions with chain O Hydrophobic interactions: O:V.31, O:V.31, O:L.37, O:L.38, O:V.68, O:W.75 Hydrogen bonds: O:R.78 9Y0.58: 13 residues within 4Å: Chain Q: M.173, A.236, L.240 Chain R: Y.121, V.125, T.130, I.131, P.132, Y.141, F.146 Chain S: F.99, A.102, A.103 6 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain S, 2 interactions with chain R Hydrophobic interactions: Q:A.236, Q:L.240, S:F.99, S:A.103, R:Y.121, R:F.146

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

CU.18: 6 residues within 4Å: Chain E: H.232, C.273, C.277, H.281, M.284 Ligands: CU.19 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.232, E:C.273, E:C.277 CU.19: 6 residues within 4Å: Chain E: H.232, C.273, E.275, C.277, M.284 Ligands: CU.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.232, E:C.273, E:C.277 CU.22: 4 residues within 4Å: Chain F: H.264, H.313, H.314 Ligands: HEA.20 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.264, F:H.313, F:H.314 CU.23: 3 residues within 4Å: Chain E: E.275 Chain F: T.389, D.390 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.390 CU.49: 6 residues within 4Å: Chain P: H.232, C.273, E.275, C.277, H.281 Ligands: CU.50 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.273, P:E.275, P:C.277, P:H.281 CU.50: 5 residues within 4Å: Chain P: H.232, C.273, C.277, M.284 Ligands: CU.49 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:H.232, P:C.273, P:C.277 CU.53: 3 residues within 4Å: Chain Q: H.264, H.313, H.314 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:H.264, Q:H.264, Q:H.313, Q:H.314 CU.54: 3 residues within 4Å: Chain P: E.275 Chain Q: Y.154, D.390 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain P Metal complexes: Q:D.390, Q:D.390, P:E.275

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

HEA.20: 33 residues within 4Å: Chain E: V.60, I.105 Chain F: 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.342, 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, T.405, R.459 Ligands: CU.22 24 PLIP interactions: 22 interactions with chain F, 2 interactions with chain E, Hydrophobic interactions: F:W.151, F:W.260, F:V.267, F:Y.268, F:A.271, F:T.330, F:A.334, F:T.337, F:F.341, F:F.341, F:F.342, F:F.369, F:L.370, F:F.398, F:F.398, F:L.402, E:V.60, E:I.105 Hydrogen bonds: F:W.151, F:Y.268, F:H.314 Salt bridges: F:R.459 pi-Stacking: F:H.264 Metal complexes: F:H.397 HEA.21: 33 residues within 4Å: Chain F: F.52, L.53, G.56, L.57, A.59, L.60, M.62, R.63, F.83, T.84, 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, T.445, F.446, Q.449, R.459, R.460, Y.461, A.481, L.484, G.485 Ligands: CDL.17 25 PLIP interactions: 25 interactions with chain F, Hydrophobic interactions: F:F.52, F:L.57, F:A.59, F:L.60, F:M.90, F:L.91, F:I.395, F:F.398, F:F.398, F:F.403, F:I.406, F:A.481 Hydrogen bonds: F:R.63, F:F.83, F:W.151, F:Y.392, F:Q.449, F:R.460, F:Y.461 Water bridges: F:R.459 Salt bridges: F:R.459, F:R.460 pi-Stacking: F:H.399 Metal complexes: F:H.86, F:H.399 HEA.51: 31 residues within 4Å: Chain P: V.60, V.64, I.105 Chain Q: 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 25 PLIP interactions: 22 interactions with chain Q, 3 interactions with chain P, Hydrophobic interactions: Q:W.260, Q:V.267, Q:Y.268, Q:T.330, Q:A.334, Q:T.337, Q:F.341, Q:F.369, Q:L.370, Q:F.398, Q:F.398, Q:V.401, Q:L.402, P:V.60, P:V.64, P:I.105 Hydrogen bonds: Q:W.151, Q:Y.268, Q:Y.268, Q:H.314, Q:T.389 Salt bridges: Q:R.459 pi-Stacking: Q:H.264 pi-Cation interactions: Q:H.264 Metal complexes: Q:H.397 HEA.52: 34 residues within 4Å: Chain Q: F.52, L.53, G.56, L.57, A.59, L.60, M.62, R.63, F.79, F.83, T.84, H.86, G.87, M.90, L.91, G.150, W.151, Y.392, I.395, F.398, H.399, L.402, F.403, V.407, F.446, Q.449, R.459, R.460, Y.461, A.481, L.484, G.485, M.488 Ligands: CDL.48 24 PLIP interactions: 24 interactions with chain Q, Hydrophobic interactions: Q:F.52, Q:L.53, Q:L.57, Q:A.59, Q:L.60, Q:L.60, Q:L.91, Q:I.395, Q:I.395, Q:F.398, Q:F.398, Q:V.407, Q:A.481 Hydrogen bonds: Q:R.63, Q:W.151, Q:Q.449, Q:R.460, Q:Y.461 Salt bridges: Q:R.459, Q:R.460 pi-Stacking: Q:H.399, Q:F.446 Metal complexes: Q:H.86, Q:H.399

2 x CA: CALCIUM ION(Non-covalent)

CA.26: 5 residues within 4Å: Chain F: E.65, M.68, P.69, G.70, Q.72 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.65, F:E.65, F:M.68, F:G.70 CA.57: 4 residues within 4Å: Chain Q: E.65, M.68, G.70, Q.72 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.65, Q:E.65, Q:M.68, Q:G.70

2 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.29: 18 residues within 4Å: Chain B: M.392, I.395, K.399, F.400 Chain C: Y.235, L.237, G.238, F.240, P.244, M.247 Chain F: I.135, A.138 Chain H: L.97, T.101, V.104, W.112 Ligands: CDL.8, 9YF.12 17 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C, 7 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: B:I.395, B:K.399, B:F.400, B:F.400, B:F.400, B:F.400, C:Y.235, C:L.237, C:P.244, H:L.97, H:V.104, H:W.112, H:W.112, F:A.138 pi-Stacking: H:W.112, H:W.112, H:W.112 MQ7.41: 17 residues within 4Å: Chain M: M.392, I.395, I.396, F.400, I.402 Chain N: Y.235, L.237, G.238, F.240, P.244, M.247 Chain Q: F.131, I.135, A.138 Chain S: T.101, W.112 Ligands: 9YF.44 14 PLIP interactions: 4 interactions with chain M, 3 interactions with chain Q, 2 interactions with chain N, 5 interactions with chain S Hydrophobic interactions: M:I.395, M:I.396, M:F.400, M:I.402, Q:F.131, Q:I.135, Q:A.138, N:P.244, N:P.244, S:W.112, S:W.112 pi-Stacking: S:W.112, S:W.112, S:W.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verma, A.K. et al., Structural and mechanistic study of a novel inhibitor analogue of M. tuberculosis cytochrome bc 1 :aa 3 . NPJ Drug Discov (2025)

Release Date

2025-04-09

Peptides

Cytochrome bc1 complex Rieske iron-sulfur subunit: AL
Cytochrome bc1 complex cytochrome b subunit: BM
Cytochrome bc1 complex cytochrome c subunit: CN
Transmembrane protein: DO
Cytochrome c oxidase subunit 2: EP
Cytochrome c oxidase subunit 1: FQ
Cytochrome c oxidase subunit 3: GR
Cytochrome c oxidase polypeptide 4: HS
Secreted protein: IT
DUF5130 domain-containing protein: JU
Superoxide dismutase [Cu-Zn]: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
M

B
B

M
N

C
C

N
O

D
D

O
P

E
E

P
Q

F
F

Q
R

G
G

R
S

H
H

S
T

I
I

T
U

J
J

U
V

K
L

V
X

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bc1 complex Rieske iron-sulfur subunit

Cytochrome bc1 complex cytochrome b subunit

Cytochrome bc1 complex cytochrome c subunit

Transmembrane protein

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 3

Cytochrome c oxidase polypeptide 4

Secreted protein

DUF5130 domain-containing protein

Superoxide dismutase [Cu-Zn]

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