SMTL ID : 7qhm.1

Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (stigmatellin and azide bound)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 11 residues within 4Å: Chain A: C.333, H.335, I.336, G.337, C.338, C.352, C.354, H.355, Q.356, S.357, P.371 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.333, A:H.335, A:C.352, A:H.355 FES.46: 10 residues within 4Å: Chain N: C.333, H.335, I.336, G.337, C.338, C.352, C.354, H.355, S.357, P.371 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.333, N:H.335, N:C.352, N:H.355

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.2: 25 residues within 4Å: Chain A: I.186, N.188, W.190, W.206, T.207, T.211, E.214, N.394, F.395, I.396, E.397, P.398, W.404, E.405, R.406, K.407 Chain B: I.177, I.178, T.180, W.181, M.182, L.185, N.317, Y.318 Ligands: 9YF.3 23 PLIP interactions: 12 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:I.186, A:W.404, B:I.178, B:W.181, B:W.181, B:W.181, B:W.181, B:L.185, B:Y.318 Hydrogen bonds: A:W.190, A:W.206, A:W.206, A:E.214, A:N.394, A:F.395, A:E.405, A:E.405, A:K.407, A:K.407, B:T.180, B:T.180, B:W.181, B:Y.318 IZL.47: 25 residues within 4Å: Chain N: I.186, N.188, W.190, W.206, T.207, T.211, E.214, N.394, F.395, I.396, E.397, P.398, W.404, E.405, R.406, K.407 Chain O: I.177, I.178, T.180, W.181, M.182, L.185, N.317, Y.318 Ligands: 9YF.48 15 PLIP interactions: 5 interactions with chain N, 10 interactions with chain O Hydrogen bonds: N:W.190, N:W.206, N:N.394, N:E.405, N:K.407, O:I.177, O:T.180, O:T.180, O:W.181, O:Y.318 Hydrophobic interactions: O:I.178, O:W.181, O:W.181, O:W.181, O:W.181

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.3: 16 residues within 4Å: Chain A: A.180, G.183, G.184, I.186, K.187, N.188, N.191 Chain B: W.181 Chain N: L.71, Y.74, I.75, W.79 Chain O: E.92, V.93, R.94 Ligands: IZL.2 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain O Hydrophobic interactions: A:A.180 Hydrogen bonds: A:G.183, A:G.184, A:I.186, A:N.188, O:R.94, O:R.94, O:R.94 Salt bridges: O:R.94 9YF.37: 20 residues within 4Å: Chain B: S.396, N.398, A.399, W.402, I.403, I.406 Chain C: A.109, S.192 Chain D: F.141, L.142 Chain H: C.1, S.2, I.6, Q.8 Chain I: V.59, E.60, W.63, I.67 Ligands: DGA.35, IX7.38 10 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C, 2 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: B:A.399, B:W.402, B:I.403, B:I.406, I:W.63 Hydrogen bonds: B:S.396, C:S.192, C:S.192, H:S.2, H:Q.8 9YF.48: 17 residues within 4Å: Chain A: Y.74, I.75, F.76, W.79 Chain B: E.92, V.93, R.94 Chain N: A.180, G.183, G.184, M.185, I.186, K.187, N.188, N.191 Chain O: W.181 Ligands: IZL.47 11 PLIP interactions: 5 interactions with chain N, 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: N:I.186, A:I.75, A:I.75 Hydrogen bonds: N:G.183, N:G.184, N:N.188, N:N.191, B:R.94, B:R.94, B:R.94 Salt bridges: B:R.94 9YF.83: 22 residues within 4Å: Chain O: S.396, N.398, A.399, W.402, I.403, I.406, G.407, V.410 Chain P: S.192 Chain Q: L.142 Chain U: C.1, S.2, I.6, T.7, Q.8 Chain V: V.59, E.60, W.63, I.67 Ligands: CDL.54, DGA.81, IX7.84 11 PLIP interactions: 6 interactions with chain O, 2 interactions with chain V, 1 interactions with chain P, 2 interactions with chain U Hydrophobic interactions: O:W.402, O:I.406, O:I.406, V:W.63, V:W.63 Hydrogen bonds: O:S.396, O:N.398, P:S.192, U:S.2 Water bridges: O:S.396, U:S.2

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

MQ9.4: 39 residues within 4Å: Chain A: T.177, I.178, I.179, P.181, M.182 Chain B: L.48, L.49, V.52, L.206, I.207, P.209, A.210, I.211, L.213 Chain N: F.70, S.103, I.107 Chain O: F.44, V.46, L.48, L.49, T.50, V.52, Y.53, L.56, F.98, I.99, M.102, L.206, I.207, P.209, A.210, I.211, L.213, F.262, A.266 Ligands: HEM.7, MQ9.44, HEM.51 17 PLIP interactions: 5 interactions with chain B, 9 interactions with chain O, 2 interactions with chain A, 1 interactions with chain N Hydrophobic interactions: B:L.48, B:L.49, B:V.52, B:L.206, B:L.213, O:L.48, O:L.49, O:V.52, O:F.98, O:I.207, O:P.209, O:A.210, O:L.213, O:A.266, A:T.177, A:I.178, N:I.107 MQ9.9: 13 residues within 4Å: Chain B: F.28, E.38, L.41, Y.42, I.45, L.220, V.223, W.224, F.250, A.254, V.255, F.262 Ligands: HEM.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.28, B:Y.42, B:L.220, B:V.223, B:W.224 MQ9.44: 28 residues within 4Å: Chain A: F.70, S.103, I.107 Chain B: V.46, L.49, T.50, V.52, Y.53, L.56, F.98, I.99, M.102, F.262, A.266 Chain N: T.177, I.178, I.179, P.181, M.182, M.185 Chain O: L.144, M.151, A.203, I.207, I.208, I.211 Ligands: MQ9.4, SMA.50 14 PLIP interactions: 7 interactions with chain B, 3 interactions with chain N, 1 interactions with chain A, 3 interactions with chain O Hydrophobic interactions: B:L.49, B:T.50, B:V.52, B:L.56, B:L.56, B:F.98, B:A.266, N:I.178, N:I.178, N:P.181, A:I.107, O:I.207, O:I.208, O:I.211 MQ9.53: 16 residues within 4Å: Chain O: F.28, E.38, L.41, Y.42, I.45, L.220, V.223, W.224, H.228, F.250, A.254, V.255, G.258, L.259, F.262 Ligands: HEM.52 8 PLIP interactions: 8 interactions with chain O Hydrophobic interactions: O:F.28, O:F.28, O:L.41, O:W.224, O:F.250, O:V.255, O:L.259, O:F.262

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

3PE.5: 20 residues within 4Å: Chain A: V.145, L.148, N.149, S.151, W.152, S.155, L.157, I.163, A.167 Chain N: L.60, A.113, V.114, Y.117, I.122 Chain O: M.1, L.3, A.4, M.247, P.248, V.252 Ligand excluded by PLIP 3PE.17: 12 residues within 4Å: Chain A: L.94, P.97, I.101 Chain B: V.271, T.273 Chain C: T.244, P.245, S.246, G.249, Y.250, S.251 Ligands: 3PE.18 Ligand excluded by PLIP 3PE.18: 6 residues within 4Å: Chain B: V.271 Chain C: P.245, Y.250 Chain G: Y.115, W.116 Ligands: 3PE.17 Ligand excluded by PLIP 3PE.27: 13 residues within 4Å: Chain D: F.292, F.343, V.346, G.347, W.350, T.561 Chain E: L.50, K.73, L.75, N.78, L.81, V.84, L.85 Ligand excluded by PLIP 3PE.31: 14 residues within 4Å: Chain D: Y.237, L.241 Chain F: Y.123, V.127, T.132, I.133, Q.134, F.143, I.144, G.147, F.148, L.151 Chain G: F.113, Y.115 Ligand excluded by PLIP 3PE.40: 34 residues within 4Å: Chain D: V.295, G.296, F.299, A.300, L.302, S.303, A.306, L.307, V.336, P.337, V.340 Chain E: V.79, E.82, L.83, T.86, I.90 Chain G: G.10, P.11 Chain J: Y.27, S.32, S.33, L.34, T.39, W.40, M.43, G.44, L.46, L.47, L.50, I.94, R.98, Y.101, T.111, Q.112 Ligand excluded by PLIP 3PE.41: 16 residues within 4Å: Chain D: W.356, I.361, V.364, G.365, A.368, F.436, W.437, F.440 Chain E: L.52, I.55, G.59, K.61 Chain L: L.51, A.55, N.58, S.59 Ligand excluded by PLIP 3PE.45: 19 residues within 4Å: Chain A: V.56, L.60, V.114, Y.117, I.122 Chain B: M.1, L.3, M.247, P.248, V.252 Chain N: L.148, N.149, S.151, W.152, Q.153, S.155, L.157, I.163, A.167 Ligand excluded by PLIP 3PE.58: 14 residues within 4Å: Chain N: L.90, L.94, P.97, I.101 Chain O: V.271 Chain P: T.241, T.244, P.245, S.246, G.249, Y.250, S.251, S.254 Ligands: 3PE.76 Ligand excluded by PLIP 3PE.67: 18 residues within 4Å: Chain Q: W.356, I.361, V.364, G.365, A.368, F.436, W.437, F.440, H.444 Chain R: W.48, F.51, L.52, I.55, F.56, K.61 Chain Y: A.55, N.58, S.59 Ligand excluded by PLIP 3PE.72: 15 residues within 4Å: Chain Q: F.292, F.343, V.346, G.347, W.350, K.351, T.561 Chain R: I.46, M.47, L.50, K.73, L.75, N.78, L.81, L.85 Ligand excluded by PLIP 3PE.73: 20 residues within 4Å: Chain Q: L.233, L.236, Y.237, L.241 Chain S: Y.123, V.127, T.132, I.133, Q.134, F.143, I.144, G.147, F.148, L.151 Chain T: L.106, V.110, F.113, I.118, L.122 Ligands: 3PE.79 Ligand excluded by PLIP 3PE.76: 9 residues within 4Å: Chain O: V.271, T.272 Chain P: Y.250, G.253, F.263 Chain T: Y.115, W.116 Ligands: 3PE.58, 3PE.77 Ligand excluded by PLIP 3PE.77: 28 residues within 4Å: Chain O: V.296, L.299, I.378, T.381, V.382, G.385, V.388, Y.389, Q.392, F.393 Chain P: Y.250, L.252, G.253, L.255, V.258, A.259, L.262, F.263, W.265, V.266, F.267 Chain T: Y.112, F.113, H.114, Y.115, W.116, V.120 Ligands: 3PE.76 Ligand excluded by PLIP 3PE.79: 12 residues within 4Å: Chain Q: K.240, L.241, G.242 Chain S: G.120, Y.123, Q.134 Chain T: F.113, Y.115, I.118, A.119, L.122 Ligands: 3PE.73 Ligand excluded by PLIP 3PE.80: 15 residues within 4Å: Chain S: F.44, F.48, T.200 Chain T: A.19, V.20, I.23, F.24, M.27, H.28, V.38, W.40, S.43, V.44, V.47, L.48 Ligand excluded by PLIP 3PE.86: 30 residues within 4Å: Chain Q: V.295, G.296, F.299, A.300, L.302, S.303, A.306, V.336, P.337, V.340 Chain R: V.79, E.82, L.83, T.86, I.90 Chain T: G.10, P.11 Chain W: A.26, Y.27, S.32, S.33, L.34, T.39, M.43, G.44, L.46, L.47, I.94, R.98, Y.101 Ligand excluded by PLIP

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.6: 26 residues within 4Å: Chain A: I.336, C.354, H.355 Chain B: I.143, L.144, A.147, F.150, M.151, Y.153, L.160, S.161, V.163, G.164, I.167, M.168, I.171, I.208, S.292, Q.293, P.294, M.298, T.301, D.302, A.305, R.306, L.330 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.147, B:F.150, B:F.150, B:I.167, B:M.168 Hydrogen bonds: B:Y.153, B:G.164, A:H.355 SMA.50: 29 residues within 4Å: Chain N: I.336, C.354, H.355 Chain O: F.150, M.151, Y.153, L.160, V.163, G.164, I.167, M.168, I.171, I.172, L.175, M.182, I.186, F.200, S.292, Q.293, P.294, M.298, T.301, D.302, A.305, R.306, V.326, A.327, L.330 Ligands: MQ9.44 5 PLIP interactions: 1 interactions with chain N, 4 interactions with chain O Hydrogen bonds: N:H.355, O:Y.153, O:Y.153 Hydrophobic interactions: O:I.167, O:I.186

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

HEM.7: 33 residues within 4Å: Chain B: F.44, L.47, L.48, G.51, V.52, L.54, T.55, F.58, A.86, I.89, R.100, H.103, H.104, A.107, F.110, V.111, G.145, E.148, G.149, G.152, Y.153, L.155, P.156, Y.201, H.204, V.205, P.209, L.212, N.275, Y.297 Chain O: I.202, L.206 Ligands: MQ9.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.47, B:F.110, B:E.148, B:Y.153, B:L.155, B:Y.201, B:V.205, B:V.205, B:P.209, B:P.209 Hydrogen bonds: B:N.275 Water bridges: B:R.100, B:H.104 Salt bridges: B:R.100, B:R.100, B:H.104 pi-Stacking: B:H.204 Metal complexes: B:H.103, B:H.204 HEM.8: 29 residues within 4Å: Chain B: F.34, L.36, G.37, E.38, A.40, L.41, F.110, M.114, H.117, M.118, R.120, I.121, A.126, F.127, R.131, N.134, W.135, G.138, V.139, L.141, I.142, I.216, H.219, L.220, V.223, H.228, T.229, L.357 Ligands: MQ9.9 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:F.110, B:I.121, B:I.121, B:I.121, B:N.134, B:W.135, B:V.139, B:L.141, B:I.216, B:V.223, B:V.223 Hydrogen bonds: B:L.36, B:G.37, B:T.229, B:T.229 Water bridges: B:H.117, B:H.117, B:R.131 Salt bridges: B:H.117, B:R.120, B:R.120, B:R.131, B:H.228, B:H.228 pi-Stacking: B:H.117 Metal complexes: B:H.117, B:H.219 HEM.51: 33 residues within 4Å: Chain B: I.202, L.206 Chain O: F.44, L.47, L.48, G.51, V.52, L.54, T.55, F.58, A.86, I.89, R.100, H.103, H.104, A.107, F.110, V.111, G.145, E.148, G.149, G.152, Y.153, L.155, P.156, Y.201, H.204, V.205, P.209, L.212, N.275, Y.297 Ligands: MQ9.4 15 PLIP interactions: 15 interactions with chain O, Hydrophobic interactions: O:L.47, O:L.48, O:L.54, O:F.110, O:E.148, O:V.205, O:V.205, O:P.209 Hydrogen bonds: O:N.275 Salt bridges: O:R.100, O:R.100, O:H.104 pi-Stacking: O:H.204 Metal complexes: O:H.103, O:H.204 HEM.52: 28 residues within 4Å: Chain O: F.34, L.36, G.37, E.38, A.40, L.41, F.110, M.114, H.117, M.118, R.120, I.121, A.126, F.127, R.131, N.134, W.135, G.138, V.139, L.141, I.142, I.216, H.219, L.220, V.223, H.228, T.229 Ligands: MQ9.53 25 PLIP interactions: 25 interactions with chain O, Hydrophobic interactions: O:A.40, O:L.41, O:F.110, O:I.121, O:I.121, O:I.121, O:N.134, O:W.135, O:V.139, O:L.141, O:L.220, O:V.223 Hydrogen bonds: O:G.37, O:T.229, O:T.229 Water bridges: O:R.120, O:R.120 Salt bridges: O:H.117, O:R.120, O:R.120, O:R.131, O:H.228, O:H.228 Metal complexes: O:H.117, O:H.219

16 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 16 residues within 4Å: Chain B: R.22, Q.23, A.133, A.218, A.221, L.222, W.224, Y.225 Chain O: L.10, Y.14, M.16, G.19, I.20, R.22, Q.23 Ligands: CDL.14 Ligand excluded by PLIP CDL.11: 18 residues within 4Å: Chain B: H.31, W.32, F.123, F.231, R.359, P.360, R.361, T.367, V.371, T.419, L.422, C.423, L.426 Chain C: V.273, M.277, R.282, S.283 Ligands: CDL.33 Ligand excluded by PLIP CDL.14: 22 residues within 4Å: Chain B: L.10, Y.14, M.16, G.19, I.20, R.22, Q.23, W.224 Chain O: R.22, Q.23, A.133, I.137, I.211, G.214, L.215, A.217, A.218, A.221, L.222, W.224, Y.225 Ligands: CDL.10 Ligand excluded by PLIP CDL.25: 37 residues within 4Å: Chain D: F.119, P.120, R.121, L.122, F.125, I.181, V.184, A.185, I.188, L.229 Chain F: V.25, G.28, T.29, F.32, E.36, H.152, A.155, M.158, A.159, V.162, V.163, R.166, A.179, V.182, V.183, Y.186 Chain G: F.88, S.90, M.99, V.103, L.106, L.125, I.126, I.129, L.132, N.133 Chain K: A.45 Ligand excluded by PLIP CDL.26: 36 residues within 4Å: Chain B: F.417, I.418, R.421, L.422 Chain D: G.21, A.23, R.24, K.25, G.26, S.27, K.28, A.29, M.32, M.33, I.43, M.44, I.46, I.47, M.48, F.50, S.51, F.54, F.127, T.131, V.415, F.419, M.422, T.423, F.492, I.493, V.496, F.497, W.500, R.501 Ligands: HAS.19, CDL.33 Ligand excluded by PLIP CDL.32: 15 residues within 4Å: Chain A: W.59, F.112, L.116, K.119, K.120 Chain B: F.495 Chain C: W.278 Chain F: L.106, I.109, V.161, L.164, M.165, H.168, K.169 Ligands: CDL.34 Ligand excluded by PLIP CDL.33: 29 residues within 4Å: Chain B: R.361, I.418, L.422, L.426, K.479 Chain C: L.270, V.273, A.274, M.277, R.282 Chain D: W.30, M.33 Chain G: I.94, W.95, A.97, A.98, G.101, A.102, G.104, F.105, F.108, M.117, L.124, F.127, T.128, K.131 Ligands: CDL.11, CDL.26, CDL.34 Ligand excluded by PLIP CDL.34: 26 residues within 4Å: Chain A: L.108, F.112 Chain B: I.260, F.264, L.267 Chain C: V.271, A.274, A.275, M.277, W.278 Chain F: V.157, M.158, V.161, V.162, M.165, K.169 Chain G: M.123, I.126, F.127, T.130, K.131, L.134, V.138, P.139 Ligands: CDL.32, CDL.33 Ligand excluded by PLIP CDL.39: 23 residues within 4Å: Chain B: L.115, M.118, L.119, F.122, W.135, L.336, L.337, Y.340, I.343, F.347, L.369, G.370, A.373, L.374, Y.377 Chain I: W.28, L.31, K.32, T.35, L.38, A.39, I.42 Ligands: LYC.12 Ligand excluded by PLIP CDL.54: 28 residues within 4Å: Chain O: H.31, W.32, F.123, F.231, R.359, P.360, R.361, T.367, V.371, L.374, V.375, I.378, L.379, G.407, G.411, I.414, A.415, I.418, T.419, L.422, C.423, L.426 Chain P: L.270, V.273, M.277, R.282 Ligands: CDL.75, 9YF.83 Ligand excluded by PLIP CDL.65: 44 residues within 4Å: Chain Q: F.119, P.120, R.121, L.122, F.125, I.181, V.184, A.185, I.188, L.229, L.233 Chain S: M.24, V.25, G.28, T.29, F.32, Q.35, E.36, F.39, L.151, H.152, I.154, A.155, M.158, A.159, V.162, V.163, R.166, A.175, T.178, A.179, V.182, V.183, Y.186 Chain T: S.90, M.99, V.103, L.122, L.125, I.126, I.129, L.132, N.133 Chain X: A.45 Ligand excluded by PLIP CDL.66: 32 residues within 4Å: Chain O: F.417, I.418, R.421, L.422 Chain Q: A.23, R.24, K.25, G.26, S.27, K.28, A.29, M.32, M.33, I.43, M.44, I.46, I.47, M.48, F.50, S.51, F.52, F.54, F.127, V.415, F.419, M.422, F.492, I.493, V.496, F.497, W.500, R.501 Ligand excluded by PLIP CDL.74: 22 residues within 4Å: Chain N: W.59, F.112, L.116, K.119, K.120 Chain O: F.495 Chain P: W.278 Chain S: L.106, I.109, I.110, S.113, V.116, I.117, I.154, V.157, V.161, L.164, M.165, H.168, K.169 Chain T: P.139 Ligands: CDL.78 Ligand excluded by PLIP CDL.75: 35 residues within 4Å: Chain O: R.361, I.418, L.422, L.426, K.479, Q.480, Q.483 Chain P: F.267, L.270, V.273, A.274, M.277, R.282 Chain Q: W.30, M.33, V.132 Chain T: I.94, W.95, A.97, A.98, S.100, G.101, A.102, G.104, F.105, F.108, M.117, V.120, M.123, L.124, F.127, T.128, K.131 Ligands: CDL.54, CDL.78 Ligand excluded by PLIP CDL.78: 24 residues within 4Å: Chain N: L.108, F.112 Chain O: F.264, L.267 Chain P: V.271, A.274, A.275, M.277, W.278 Chain S: M.158, V.161, V.162, M.165, K.169 Chain T: M.123, I.126, F.127, T.130, K.131, L.134, V.138, P.139 Ligands: CDL.74, CDL.75 Ligand excluded by PLIP CDL.85: 37 residues within 4Å: Chain O: L.115, M.118, L.119, F.122, W.135, V.307, M.308, P.309, W.311, M.329, L.336, L.337, Y.340, I.343, K.346, F.347, L.369, G.370, A.373, L.374, F.376, Y.377, R.405, L.408, I.409 Chain V: W.28, L.31, K.32, T.35, L.38, A.39, I.42, S.43, F.46, Y.50 Ligands: LYC.55, DGA.87 Ligand excluded by PLIP

2 x LYC: LYCOPENE(Non-covalent)

LYC.12: 31 residues within 4Å: Chain B: V.111, L.115, M.118, I.142, M.146, Y.297, W.300, L.333, V.334, L.336, L.337, L.369, M.372, A.373, F.376, Y.377, L.408, I.409, P.412, A.413 Chain C: W.265 Chain I: I.36, A.39, G.40, S.43, L.71, G.74, L.75, I.77, H.78 Ligands: CDL.39 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain I Hydrophobic interactions: B:L.115, B:W.300, B:L.333, B:L.337, B:A.373, B:F.376, B:Y.377, B:A.413, I:L.71, I:L.75, I:I.77, I:H.78 LYC.55: 31 residues within 4Å: Chain O: V.111, L.115, M.118, I.142, M.146, Y.297, W.300, L.333, V.334, L.336, L.337, M.372, A.373, F.376, Y.377, L.408, I.409, V.410, P.412, A.413 Chain P: W.265 Chain V: I.36, A.39, G.40, S.43, L.71, G.74, L.75, I.77, H.78 Ligands: CDL.85 15 PLIP interactions: 10 interactions with chain O, 5 interactions with chain V Hydrophobic interactions: O:L.115, O:I.142, O:W.300, O:W.300, O:L.333, O:L.333, O:L.337, O:A.373, O:Y.377, O:A.413, V:A.39, V:L.71, V:L.75, V:I.77, V:H.78

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.13: 15 residues within 4Å: Chain B: A.4, T.5, G.7, N.8, L.10, D.11, M.16, A.17, I.20 Chain N: E.138, R.141, R.142, I.144, V.145, L.148 7 PLIP interactions: 3 interactions with chain N, 4 interactions with chain B Hydrophobic interactions: N:I.144, B:D.11, B:A.17, B:I.20 Hydrogen bonds: N:R.141, B:A.4 Salt bridges: N:R.141 LMT.49: 16 residues within 4Å: Chain A: E.138, R.141, R.142, I.144, V.145, L.148 Chain O: L.3, A.4, G.7, N.8, L.10, D.11, M.16, A.17, I.20, I.24 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain O Hydrophobic interactions: A:I.144, A:L.148, O:D.11, O:I.20 Salt bridges: A:R.141 Hydrogen bonds: O:A.4, O:A.4

4 x HEC: HEME C(Covalent)

HEC.15: 31 residues within 4Å: Chain C: A.66, C.67, T.69, C.70, H.71, R.81, G.82, P.83, L.85, V.88, A.92, V.93, Q.96, V.97, M.102, P.103, I.104, L.105, A.111, R.117, Y.118, I.126, V.130, Q.216 Chain E: W.125, Y.264 Chain H: T.9, S.10, Q.12, A.14, A.15 18 PLIP interactions: 15 interactions with chain C, 2 interactions with chain H, 1 interactions with chain E, Hydrophobic interactions: C:A.66, C:L.85, C:L.85, C:V.88, C:Q.96, C:V.97, C:M.102, C:I.104, C:I.104, C:I.126, C:Q.216, E:W.125 Water bridges: C:Q.96, C:Q.216, C:Q.216 Metal complexes: C:H.71 Hydrogen bonds: H:Q.12, H:A.15 HEC.16: 36 residues within 4Å: Chain A: S.341, L.342, Y.343, E.344 Chain C: F.95, Q.96, R.101, Q.110, A.111, R.113, F.173, N.176, C.177, S.179, C.180, H.181, L.190, Y.195, A.196, P.197, L.199, A.201, A.202, E.206, I.207, A.210, M.211, P.215, Q.216, N.217, M.218, P.219, F.221, L.226, I.234, I.238 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:F.95, C:L.190, C:L.199, C:A.202, C:I.207, C:A.210, C:I.234 Hydrogen bonds: C:Q.110, C:P.215, C:Q.216 Salt bridges: C:R.101, C:R.101, C:R.113 Metal complexes: C:H.181 HEC.56: 32 residues within 4Å: Chain P: Y.63, A.66, C.67, T.69, C.70, H.71, R.81, G.82, P.83, L.85, V.88, A.92, V.93, Q.96, V.97, M.102, P.103, I.104, L.105, N.107, A.111, Y.118, I.126, V.130, Q.216 Chain R: W.125, Y.264 Chain U: T.9, S.10, Q.12, A.14, A.15 14 PLIP interactions: 12 interactions with chain P, 1 interactions with chain R, 1 interactions with chain U, Hydrophobic interactions: P:P.83, P:L.85, P:L.85, P:A.92, P:Q.96, P:V.97, P:P.103, P:I.104, P:I.104, P:I.126, R:W.125 Water bridges: P:Q.96 Metal complexes: P:H.71 Hydrogen bonds: U:A.15 HEC.57: 35 residues within 4Å: Chain N: L.342, Y.343, E.344 Chain P: F.95, Q.96, S.99, R.101, Q.110, A.111, R.113, F.173, N.176, C.177, S.179, C.180, H.181, L.190, Y.195, A.196, P.197, L.199, A.202, E.206, I.207, A.210, M.211, P.215, Q.216, N.217, M.218, P.219, F.221, L.226, I.234, I.238 17 PLIP interactions: 17 interactions with chain P, Hydrophobic interactions: P:F.95, P:L.190, P:P.197, P:L.199, P:I.207, P:A.210, P:P.215, P:M.218, P:F.221, P:I.234 Hydrogen bonds: P:P.215, P:Q.216 Water bridges: P:R.113 Salt bridges: P:R.101, P:R.101, P:R.113 Metal complexes: P:H.181

4 x HAS: HEME-AS(Non-covalent)

HAS.19: 41 residues within 4Å: Chain D: S.51, F.53, F.54, L.55, G.57, L.58, A.60, L.61, I.63, R.64, F.80, F.84, T.85, H.87, G.88, M.91, L.92, Y.95, G.151, W.152, Y.393, I.396, F.399, H.400, L.403, F.404, V.407, V.408, T.446, F.447, Q.450, R.460, R.461, Y.462, S.482, L.485, G.486, V.489, I.493 Ligands: HAS.20, CDL.26 31 PLIP interactions: 31 interactions with chain D, Hydrophobic interactions: D:F.53, D:F.53, D:F.54, D:F.54, D:F.54, D:F.54, D:A.60, D:L.61, D:F.84, D:M.91, D:L.92, D:I.396, D:F.399, D:F.399, D:L.403, D:F.404, D:F.404, D:V.407, D:V.408, D:F.447, D:V.489, D:V.489 Hydrogen bonds: D:R.64, D:R.64, D:W.152, D:R.461 Salt bridges: D:R.460, D:R.461 pi-Stacking: D:F.447 Metal complexes: D:H.87, D:H.400 HAS.20: 47 residues within 4Å: Chain D: L.92, W.152, T.153, W.261, V.268, Y.269, L.271, A.272, H.314, H.315, T.331, I.334, S.335, V.336, T.338, G.339, F.342, F.343, F.370, L.371, G.374, L.375, G.377, I.378, L.380, A.381, D.386, A.390, D.391, L.395, H.398, F.399, T.402, L.403, T.406, R.460 Chain E: V.36, A.39, A.40, I.43, M.47, P.89, I.92, V.93, L.96 Ligands: HAS.19, AZI.24 32 PLIP interactions: 27 interactions with chain D, 5 interactions with chain E, Hydrophobic interactions: D:W.261, D:V.268, D:V.268, D:T.331, D:T.338, D:F.342, D:F.342, D:F.343, D:F.370, D:F.370, D:L.375, D:I.378, D:L.395, D:F.399, D:F.399, D:T.402, D:L.403, E:A.39, E:I.43, E:I.43, E:P.89, E:I.92 Hydrogen bonds: D:W.152, D:Y.269, D:Y.269, D:G.377, D:D.391 Water bridges: D:H.315, D:F.317 Salt bridges: D:R.460 pi-Cation interactions: D:H.265 Metal complexes: D:H.398 HAS.59: 44 residues within 4Å: Chain Q: F.53, F.54, G.57, L.58, A.60, L.61, I.63, R.64, L.67, F.80, F.84, T.85, H.87, G.88, M.91, L.92, Y.95, G.151, W.152, L.271, Y.393, I.396, F.399, H.400, L.403, F.404, V.407, V.408, T.446, F.447, Q.450, R.460, R.461, Y.462, S.482, F.483, L.485, G.486, L.487, V.489, I.490 Chain Y: L.38, A.42 Ligands: HAS.60 23 PLIP interactions: 23 interactions with chain Q, Hydrophobic interactions: Q:F.53, Q:A.60, Q:R.64, Q:M.91, Q:L.92, Q:I.396, Q:I.396, Q:F.399, Q:L.403, Q:L.403, Q:V.408, Q:L.487 Hydrogen bonds: Q:R.64, Q:W.152, Q:Q.450, Q:R.461, Q:Y.462 Salt bridges: Q:R.460, Q:R.461 pi-Stacking: Q:F.399, Q:F.447 Metal complexes: Q:H.87, Q:H.400 HAS.60: 49 residues within 4Å: Chain Q: L.92, W.152, W.261, H.265, V.268, Y.269, L.271, A.272, H.314, H.315, F.317, T.331, I.334, S.335, T.338, G.339, F.342, F.343, F.370, L.371, G.374, L.375, G.377, I.378, M.379, L.380, A.381, D.386, A.390, D.391, L.395, H.398, F.399, T.402, L.403, T.406, V.407, R.460 Chain R: V.36, A.39, A.40, I.43, M.47, P.89, I.92, V.93, L.96 Ligands: HAS.59, AZI.63 28 PLIP interactions: 5 interactions with chain R, 23 interactions with chain Q, Hydrophobic interactions: R:A.39, R:A.40, R:I.43, R:I.43, R:I.92, Q:V.268, Q:V.268, Q:T.331, Q:F.342, Q:F.343, Q:F.370, Q:F.370, Q:L.371, Q:I.378, Q:I.378, Q:F.399, Q:F.399, Q:T.402, Q:L.403, Q:L.403 Hydrogen bonds: Q:W.152, Q:Y.269, Q:H.314, Q:H.315, Q:G.377, Q:D.391 Salt bridges: Q:R.460 Metal complexes: Q:H.398

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

CU.21: 4 residues within 4Å: Chain D: H.265, H.314, H.315 Ligands: AZI.24 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.265, D:H.314, D:H.315 CU.61: 4 residues within 4Å: Chain Q: H.265, H.314, H.315 Ligands: AZI.63 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:H.265, Q:H.314, Q:H.315

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.22: 3 residues within 4Å: Chain D: Y.155, D.391 Chain E: E.259 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:Y.155, D:D.391, E:E.259 MN.68: 4 residues within 4Å: Chain Q: Y.155, D.391 Chain R: D.228, E.259 4 PLIP interactions: 1 interactions with chain R, 3 Ligand-Water interactions Metal complexes: R:E.259, H2O.12, H2O.14, H2O.15

2 x CA: CALCIUM ION(Non-covalent)

CA.23: 5 residues within 4Å: Chain D: E.66, T.69, G.71, L.72, Q.73 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.66, D:E.66, D:T.69, D:G.71, H2O.5 CA.62: 5 residues within 4Å: Chain Q: E.66, T.69, G.71, L.72, Q.73 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.66, Q:E.66, Q:T.69, Q:G.71, H2O.13

2 x AZI: AZIDE ION(Non-covalent)

AZI.24: 6 residues within 4Å: Chain D: H.265, V.268, H.314, H.315 Ligands: HAS.20, CU.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.315, D:H.315 AZI.63: 6 residues within 4Å: Chain Q: H.265, V.268, H.314, H.315 Ligands: HAS.60, CU.61 No protein-ligand interaction detected (PLIP)

4 x CUA: DINUCLEAR COPPER ION(Non-covalent)(Covalent)

CUA.28: 5 residues within 4Å: Chain E: H.216, C.257, C.261, M.268 Ligands: CUA.29 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.216, E:C.257, E:C.261 CUA.29: 6 residues within 4Å: Chain E: C.257, E.259, M.260, C.261, H.265 Ligands: CUA.28 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.257, E:E.259, E:C.261, E:H.265 CUA.69: 6 residues within 4Å: Chain R: W.125, H.216, C.257, C.261, M.268 Ligands: CUA.70 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:H.216, R:C.257, R:C.261 CUA.70: 6 residues within 4Å: Chain R: C.257, E.259, M.260, C.261, H.265 Ligands: CUA.69 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.257, R:E.259, R:C.261, R:H.265

6 x DGA: DIACYL GLYCEROL(Covalent)

DGA.30: 11 residues within 4Å: Chain E: C.1, V.3, F.32, W.35, V.36, V.38, A.39, I.42, V.95, L.96, F.99 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.35, E:W.35, E:V.38, E:A.39, E:I.42, E:V.95 DGA.35: 9 residues within 4Å: Chain D: F.141 Chain H: C.1 Chain I: V.59, I.62, W.63, V.66 Ligands: PLM.36, 9YF.37, IX7.38 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:I.62, I:W.63, I:W.63, I:V.66 DGA.42: 11 residues within 4Å: Chain B: M.308, W.311, E.312, L.313, W.325, V.328 Chain I: L.45, F.46, G.49, F.52 Chain M: C.1 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.311, B:W.311, B:W.325, B:W.325, B:W.325 Hydrogen bonds: B:W.325 DGA.71: 12 residues within 4Å: Chain R: C.1, V.3, F.32, W.35, V.36, V.38, A.39, I.42, I.92, V.95, L.96, F.99 10 PLIP interactions: 10 interactions with chain R Hydrophobic interactions: R:W.35, R:W.35, R:V.36, R:A.39, R:I.42, R:I.92, R:V.95, R:L.96, R:F.99, R:F.99 DGA.81: 12 residues within 4Å: Chain Q: F.141, L.142 Chain U: C.1 Chain V: V.59, I.62, W.63, V.66, I.67, L.70 Ligands: PLM.82, 9YF.83, IX7.84 6 PLIP interactions: 6 interactions with chain V Hydrophobic interactions: V:V.59, V:I.62, V:W.63, V:W.63, V:V.66, V:V.66 DGA.87: 15 residues within 4Å: Chain O: M.308, W.311, E.312, L.313, W.325, V.328, M.329, I.332 Chain V: L.45, F.46, G.49, F.52 Chain Z: C.1 Ligands: CDL.85, PLM.88 12 PLIP interactions: 9 interactions with chain O, 3 interactions with chain V Hydrophobic interactions: O:W.311, O:W.311, O:W.325, O:W.325, O:W.325, O:W.325, O:V.328, O:M.329, V:F.46, V:F.46, V:F.52 Hydrogen bonds: O:W.325

4 x PLM: PALMITIC ACID(Covalent)

PLM.36: 21 residues within 4Å: Chain D: L.55, L.58, M.59, L.62, Q.79, Q.82, L.83, L.138, F.141, L.142, T.143, P.144, G.145, G.146, A.147 Chain H: C.1, S.2, A.3, G.4 Ligands: DGA.35, IX7.38 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:L.55, D:L.62, D:L.138, D:L.138, D:F.141, D:F.141 Hydrogen bonds: D:Q.79, H:A.3 PLM.43: 4 residues within 4Å: Chain B: L.313, Y.314 Chain M: C.1, S.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.314 PLM.82: 21 residues within 4Å: Chain Q: L.55, L.58, M.59, L.62, Q.79, Q.82, L.83, L.138, T.139, F.141, L.142, T.143, P.144, G.145, G.146, A.147 Chain U: C.1, S.2, A.3 Ligands: DGA.81, IX7.84 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain U Hydrophobic interactions: Q:L.83 Hydrogen bonds: Q:Q.79, U:A.3 PLM.88: 6 residues within 4Å: Chain O: L.313, Y.314, L.315 Chain Z: C.1, S.2 Ligands: DGA.87 3 PLIP interactions: 2 interactions with chain O, 1 interactions with chain Z Hydrophobic interactions: O:L.313 Hydrogen bonds: O:Y.314, Z:S.2

2 x IX7: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate(Non-covalent)

IX7.38: 19 residues within 4Å: Chain D: L.58, L.62, F.74, L.75, Q.79 Chain E: T.319, R.322 Chain H: C.1, G.4, Q.5, I.6 Chain I: K.56, G.57, H.58, V.59, I.62 Ligands: DGA.35, PLM.36, 9YF.37 7 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I, 2 interactions with chain E Hydrogen bonds: H:Q.5, H:I.6, I:H.58, E:R.322, E:R.322 Hydrophobic interactions: I:I.62 Salt bridges: I:H.58 IX7.84: 19 residues within 4Å: Chain Q: L.58, L.62, F.74, L.75, Q.79 Chain R: R.322 Chain U: C.1, G.4, Q.5, I.6 Chain V: K.56, G.57, H.58, V.59, I.62, V.66 Ligands: DGA.81, PLM.82, 9YF.83 13 PLIP interactions: 3 interactions with chain U, 2 interactions with chain R, 5 interactions with chain V, 3 interactions with chain Q Hydrogen bonds: U:Q.5, U:I.6, R:R.322, R:R.322, V:K.56, V:H.58, V:V.59, Q:F.74 Water bridges: U:C.1, Q:Q.79 Hydrophobic interactions: V:I.62, Q:L.62 Salt bridges: V:H.58

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.64: 8 residues within 4Å: Chain Q: T.89, L.93, W.152, W.172, V.176, L.228, F.260, F.263 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kao, W.C. et al., Structural basis for safe and efficient energy conversion in a respiratory supercomplex. Nat Commun (2022)

Release Date

2022-05-18

Peptides

Cytochrome bc1 complex Rieske iron-sulfur subunit: AN
Cytochrome bc1 complex cytochrome b subunit: BO
Cytochrome bc1 complex cytochrome c subunit: CP
Cytochrome c oxidase subunit 1: DQ
Cytochrome c oxidase subunit 2: ER
Cytochrome c oxidase subunit 3: FS
Cytochrome c oxidase polypeptide 4: GT
Uncharacterized protein Cgl2664/cg2949: HU
Uncharacterized membrane protein Cgl2017/cg2211: IV
Hypothetical membrane protein: JW
Actinobacterial supercomplex, subunit C (AscC): KX
Hypothetical membrane protein: LY
Thiamine biosynthesis protein X: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
N

B
B

O
O

C
C

P
P

D
D

Q
Q

E
E

R
R

F
F

S
S

G
G

T
T

H
H

U
U

I
I

V
V

J
J

W
W

K
K

X
X

L
L

Y
Y

M
M

Z
Z

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

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase polypeptide 4

Uncharacterized protein Cgl2664/cg2949

Uncharacterized membrane protein Cgl2017/cg2211

Hypothetical membrane protein

Actinobacterial supercomplex, subunit C (AscC)

Hypothetical membrane protein

Thiamine biosynthesis protein X

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