SMTL ID : 7vuw.1 (1 other biounit)

Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

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

Ligands

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

HEA.1: 38 residues within 4Å: Chain A: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: EDO.37 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:R.38, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.378, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CYN.6 37 PLIP interactions: 32 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:T.349, A:L.353, A:I.356, A:I.356, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.438 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CYN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.7, H2O.12, H2O.13

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43

1 x CYN: CYANIDE ION(Non-covalent)

CYN.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.7: 12 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16 Ligands: EDO.35, EDO.169 17 PLIP interactions: 5 interactions with chain M, 5 interactions with chain A, 4 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: M:P.12, M:Q.15, M:A.16, A:T.408, A:W.409, A:W.409, A:W.409, D:A.81, D:F.84, D:F.84, D:F.84, K:F.4, K:F.4 Water bridges: M:A.3, M:K.4 Hydrogen bonds: A:T.408 Salt bridges: K:H.5 PGV.8: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151, L.152, I.158, P.200 Chain C: H.7, V.9, G.18, A.22, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88 Ligands: PEK.64 19 PLIP interactions: 11 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.84, C:F.84, C:F.84, A:F.148, A:L.152, A:I.158, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.66: 23 residues within 4Å: Chain C: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: CDL.68 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:I.208, C:I.208, C:T.211, C:F.212, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Water bridges: C:S.63, C:R.219, C:H.229, C:H.229, F:Q.12, F:E.17 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.67: 14 residues within 4Å: Chain A: F.237, D.298 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.18 Ligands: EDO.16, CHD.62, EDO.80, EDO.137, EDO.139 8 PLIP interactions: 2 interactions with chain A, 1 interactions with chain H, 5 interactions with chain C Hydrophobic interactions: A:F.237, A:F.237, C:T.93, C:W.97, C:W.97, C:L.104 Hydrogen bonds: H:N.18 Salt bridges: C:H.101

142 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 6 residues within 4Å: Chain A: D.221, P.222, A.223 Ligands: EDO.33, EDO.43, EDO.72 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain A: F.2 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligands: EDO.172 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.124 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, E.62 Ligands: CHD.42 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: L.33, A.60, S.116 Chain L: I.38, V.39 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: Y.304 Ligands: PGV.67 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: Q.52, A.137, H.138, A.139 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, R.56, H.94 Ligand excluded by PLIP EDO.19: 10 residues within 4Å: Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain L: N.9 Ligands: EDO.165 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: F.505, E.507, P.508, T.509 Chain F: R.56, I.57, W.73 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: P.501, H.503, E.506 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: G.45, T.46 Ligands: EDO.27, EDO.47, EDO.58, EDO.96, EDO.168 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: W.103 Ligands: EDO.79, TGL.156 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: F.418, N.422, M.423 Ligands: TGL.38 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: H.328 Chain I: A.14, L.17 Ligands: PSC.41 Ligand excluded by PLIP EDO.27: 10 residues within 4Å: Chain A: Q.43, P.44, G.45, T.46, L.47 Chain D: P.103, I.104, P.105 Ligands: EDO.23, EDO.96 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: P.106, P.107, L.110 Chain C: L.20 Ligands: EDO.79 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: Y.19, M.71, P.72, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: N.170, K.172, P.173, P.174, M.176 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: W.334, S.335, D.407, K.411 Ligands: EDO.172 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: V.485, D.486, L.487, T.488, T.489 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: P.131, D.221, P.222 Ligands: EDO.9 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain A: T.404, D.407 Chain M: I.1, A.3 Ligands: PGV.7, EDO.172 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: L.483, V.485, W.494, G.497, C.498 Chain D: Y.8 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain A: M.390, H.413, M.417, A.464, V.465, M.468 Ligands: HEA.1 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.9, EDO.72, EDO.138 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain B: P.15, E.18, M.185, S.187 Chain I: Y.51 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: T.125, L.135 Ligands: EDO.23, EDO.58 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: M.87, L.170, T.182, T.183 Ligands: EDO.59 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain B: Y.3, Q.6, L.7, G.8, F.9 Ligands: TGL.38, EDO.98 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: N.92, P.93 Chain H: Q.6, T.7, A.8, P.9 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain B: W.104, M.122, N.203, F.206 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain B: T.111, D.112, Y.113, E.114, D.115 Chain H: R.52, K.55 Ligand excluded by PLIP EDO.53: 8 residues within 4Å: Chain B: S.94, L.95, Y.113, M.148, L.216, F.219 Chain H: Q.6 Ligands: EDO.54 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain B: Y.113, F.219, E.220, S.223 Ligands: EDO.53 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain B: S.36, L.39, Y.40 Ligands: TGL.38 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain B: T.63, T.66, I.67 Ligands: CHD.42 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain B: Y.40, S.43, T.47 Ligands: TGL.39 Ligand excluded by PLIP EDO.58: 6 residues within 4Å: Chain B: T.125, R.134 Chain D: P.105 Ligands: EDO.23, EDO.47, EDO.96 Ligand excluded by PLIP EDO.59: 8 residues within 4Å: Chain B: S.14, P.15, I.16, L.168, T.183, L.184, M.185 Ligands: EDO.48 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain B: E.147 Ligands: EDO.61 Ligand excluded by PLIP EDO.61: 5 residues within 4Å: Chain B: M.146, E.147, P.215, L.216 Ligands: EDO.60 Ligand excluded by PLIP EDO.72: 8 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.9, EDO.43, EDO.87, EDO.138 Ligand excluded by PLIP EDO.73: 3 residues within 4Å: Chain C: S.103, W.114, W.257 Ligand excluded by PLIP EDO.74: 5 residues within 4Å: Chain C: L.136, G.139, T.143 Chain G: W.16 Ligands: EDO.84 Ligand excluded by PLIP EDO.75: 2 residues within 4Å: Chain C: F.249 Ligands: CDL.131 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain C: L.125, Y.251, W.256 Ligands: CDL.131 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain C: H.241 Ligands: PEK.63, EDO.83 Ligand excluded by PLIP EDO.78: 5 residues within 4Å: Chain C: N.10, Q.66, H.68 Ligands: EDO.85, EDO.149 Ligand excluded by PLIP EDO.79: 3 residues within 4Å: Chain A: W.103 Ligands: EDO.24, EDO.28 Ligand excluded by PLIP EDO.80: 4 residues within 4Å: Chain C: T.93, W.97 Ligands: PEK.63, PGV.67 Ligand excluded by PLIP EDO.81: 3 residues within 4Å: Chain C: H.147 Chain G: T.11, W.16 Ligand excluded by PLIP EDO.82: 5 residues within 4Å: Chain C: H.1, Q.2, H.68 Chain F: L.16 Ligands: EDO.85 Ligand excluded by PLIP EDO.83: 4 residues within 4Å: Chain C: E.234, W.238 Ligands: PEK.63, EDO.77 Ligand excluded by PLIP EDO.84: 3 residues within 4Å: Chain C: D.244, V.245 Ligands: EDO.74 Ligand excluded by PLIP EDO.85: 5 residues within 4Å: Chain C: Q.66, H.68 Chain J: Q.13 Ligands: EDO.78, EDO.82 Ligand excluded by PLIP EDO.86: 3 residues within 4Å: Chain C: P.71, A.72 Chain F: I.33 Ligand excluded by PLIP EDO.87: 6 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.72, EDO.138 Ligand excluded by PLIP EDO.88: 4 residues within 4Å: Chain D: I.94, H.98, Y.99 Ligands: EDO.94 Ligand excluded by PLIP EDO.89: 4 residues within 4Å: Chain A: I.332, W.334 Chain D: R.70 Ligands: TGL.39 Ligand excluded by PLIP EDO.90: 6 residues within 4Å: Chain B: P.130 Chain D: E.109, E.111, W.112, K.115 Ligands: EDO.91 Ligand excluded by PLIP EDO.91: 3 residues within 4Å: Chain D: E.111, K.115 Ligands: EDO.90 Ligand excluded by PLIP EDO.92: 6 residues within 4Å: Chain D: P.22, D.23, V.24, A.25, K.60 Chain E: R.26 Ligand excluded by PLIP EDO.93: 6 residues within 4Å: Chain D: K.118, L.121, D.122, W.135 Chain K: P.45 Ligands: EDO.106 Ligand excluded by PLIP EDO.94: 2 residues within 4Å: Chain D: L.91 Ligands: EDO.88 Ligand excluded by PLIP EDO.95: 8 residues within 4Å: Chain D: K.124, P.127, S.132, A.133, Y.137 Chain I: F.50 Ligands: EDO.143, EDO.146 Ligand excluded by PLIP EDO.96: 6 residues within 4Å: Chain D: P.103, I.104, P.105 Ligands: EDO.23, EDO.27, EDO.58 Ligand excluded by PLIP EDO.97: 6 residues within 4Å: Chain D: F.84, F.85, F.88 Chain M: S.20, F.23 Ligands: EDO.171 Ligand excluded by PLIP EDO.98: 5 residues within 4Å: Chain D: Q.129, K.134 Chain I: R.43 Ligands: TGL.38, EDO.49 Ligand excluded by PLIP EDO.99: 3 residues within 4Å: Chain D: R.58, E.67 Ligands: EDO.100 Ligand excluded by PLIP EDO.100: 1 residues within 4Å: Ligands: EDO.99 Ligand excluded by PLIP EDO.101: 3 residues within 4Å: Chain D: D.15, R.16, M.68 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain D: L.37, D.51, E.52, E.55 Ligands: EDO.105 Ligand excluded by PLIP EDO.103: 6 residues within 4Å: Chain D: A.25, V.27, K.28, L.30, K.38, L.59 Ligand excluded by PLIP EDO.104: 4 residues within 4Å: Chain D: K.42, A.43, S.44 Chain E: R.52 Ligand excluded by PLIP EDO.105: 4 residues within 4Å: Chain D: S.33, Q.34, E.55 Ligands: EDO.102 Ligand excluded by PLIP EDO.106: 5 residues within 4Å: Chain D: D.122, K.124, Y.137 Chain I: E.62 Ligands: EDO.93 Ligand excluded by PLIP EDO.107: 5 residues within 4Å: Chain D: Y.13, V.14, D.15, K.62 Chain M: T.2 Ligand excluded by PLIP EDO.108: 3 residues within 4Å: Chain D: K.134 Chain K: S.38, V.40 Ligand excluded by PLIP EDO.109: 4 residues within 4Å: Chain E: Y.14, K.17, I.20, E.24 Ligand excluded by PLIP EDO.110: 3 residues within 4Å: Chain E: R.49, R.52, R.53 Ligand excluded by PLIP EDO.111: 5 residues within 4Å: Chain D: K.53 Chain E: N.90, G.93, I.94, S.95 Ligand excluded by PLIP EDO.112: 5 residues within 4Å: Chain E: D.19, I.20, D.21, L.54 Ligands: EDO.113 Ligand excluded by PLIP EDO.113: 5 residues within 4Å: Chain E: K.17, D.19, D.21, E.24 Ligands: EDO.112 Ligand excluded by PLIP EDO.114: 4 residues within 4Å: Chain E: R.10, W.11, Y.14 Ligands: EDO.121 Ligand excluded by PLIP EDO.115: 4 residues within 4Å: Chain E: Y.78, P.79, I.82, E.98 Ligand excluded by PLIP EDO.116: 2 residues within 4Å: Chain E: E.98, E.99 Ligand excluded by PLIP EDO.117: 7 residues within 4Å: Chain D: Y.19, D.23 Chain E: W.23, R.26, K.27, N.30 Chain F: P.83 Ligand excluded by PLIP EDO.118: 6 residues within 4Å: Chain B: T.51 Chain D: R.17, D.18 Chain E: V.66, D.69, K.70 Ligand excluded by PLIP EDO.119: 3 residues within 4Å: Chain E: R.53, L.54, N.55 Ligand excluded by PLIP EDO.120: 3 residues within 4Å: Chain E: N.16, P.18, R.53 Ligand excluded by PLIP EDO.121: 5 residues within 4Å: Chain E: W.11, Y.14, K.27, T.31 Ligands: EDO.114 Ligand excluded by PLIP EDO.123: 4 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 Ligands: EDO.129 Ligand excluded by PLIP EDO.124: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.13 Ligand excluded by PLIP EDO.125: 6 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.126: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.127: 6 residues within 4Å: Chain F: T.8, D.9, E.10, M.21, R.25 Ligands: EDO.129 Ligand excluded by PLIP EDO.128: 6 residues within 4Å: Chain F: V.20, A.24, Q.28, D.29, I.33, L.34 Ligand excluded by PLIP EDO.129: 5 residues within 4Å: Chain C: N.228 Chain F: D.9, M.21 Ligands: EDO.123, EDO.127 Ligand excluded by PLIP EDO.130: 8 residues within 4Å: Chain A: P.174, T.509, Y.510, V.511 Chain F: N.32, L.34, P.36, R.56 Ligand excluded by PLIP EDO.133: 6 residues within 4Å: Chain C: G.118 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.134: 6 residues within 4Å: Chain C: W.32, F.33 Chain G: K.58, P.59, F.60, S.61 Ligand excluded by PLIP EDO.135: 2 residues within 4Å: Chain G: A.1, A.3 Ligand excluded by PLIP EDO.136: 5 residues within 4Å: Chain C: T.117 Chain G: Y.50 Chain H: F.75, P.76, G.77 Ligand excluded by PLIP EDO.137: 6 residues within 4Å: Chain H: F.14, P.15, N.16, N.18, R.21 Ligands: PGV.67 Ligand excluded by PLIP EDO.138: 5 residues within 4Å: Chain H: S.61, T.65 Ligands: EDO.43, EDO.72, EDO.87 Ligand excluded by PLIP EDO.139: 7 residues within 4Å: Chain A: D.227 Chain B: G.177, R.178 Chain C: T.107 Chain H: N.18, T.20 Ligands: PGV.67 Ligand excluded by PLIP EDO.141: 2 residues within 4Å: Chain I: Q.70, S.71 Ligand excluded by PLIP EDO.142: 5 residues within 4Å: Chain I: Y.54, D.55, D.59, E.62 Ligands: EDO.146 Ligand excluded by PLIP EDO.143: 6 residues within 4Å: Chain D: P.127, I.128 Chain I: A.46, D.49, F.50 Ligands: EDO.95 Ligand excluded by PLIP EDO.144: 7 residues within 4Å: Chain B: L.50 Chain E: P.73, H.74 Chain I: L.12, R.15, R.16 Ligands: TGL.39 Ligand excluded by PLIP EDO.145: 4 residues within 4Å: Chain B: R.141 Chain I: G.67, I.68, F.69 Ligand excluded by PLIP EDO.146: 4 residues within 4Å: Chain I: F.50, Y.54 Ligands: EDO.95, EDO.142 Ligand excluded by PLIP EDO.148: 1 residues within 4Å: Chain J: F.55 Ligand excluded by PLIP EDO.149: 6 residues within 4Å: Chain C: N.10, P.11 Chain J: G.17, L.18, P.19 Ligands: EDO.78 Ligand excluded by PLIP EDO.150: 7 residues within 4Å: Chain C: Y.53, R.57, R.61 Chain J: T.27, D.28, L.31 Ligands: CDL.68 Ligand excluded by PLIP EDO.151: 3 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: W.24 Ligand excluded by PLIP EDO.152: 3 residues within 4Å: Chain K: W.24, A.28 Ligands: EDO.153 Ligand excluded by PLIP EDO.153: 2 residues within 4Å: Chain K: W.35 Ligands: EDO.152 Ligand excluded by PLIP EDO.154: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.155: 5 residues within 4Å: Chain D: W.142 Chain K: G.41, R.42, V.43, T.44 Ligand excluded by PLIP EDO.157: 6 residues within 4Å: Chain L: G.7, K.8, I.10, F.12, S.13 Ligands: EDO.164 Ligand excluded by PLIP EDO.158: 3 residues within 4Å: Chain A: M.117 Chain L: F.37 Ligands: EDO.161 Ligand excluded by PLIP EDO.159: 3 residues within 4Å: Chain L: S.30, F.37 Ligands: TGL.156 Ligand excluded by PLIP EDO.160: 3 residues within 4Å: Chain L: T.25, A.33 Chain M: S.25 Ligand excluded by PLIP EDO.161: 3 residues within 4Å: Chain L: R.40, H.41 Ligands: EDO.158 Ligand excluded by PLIP EDO.162: 3 residues within 4Å: Chain C: P.11 Chain L: H.1, Y.2 Ligand excluded by PLIP EDO.163: 5 residues within 4Å: Chain A: M.1, F.2, R.5 Chain L: Y.2, E.3 Ligand excluded by PLIP EDO.164: 4 residues within 4Å: Chain L: K.8, S.13, E.15 Ligands: EDO.157 Ligand excluded by PLIP EDO.165: 9 residues within 4Å: Chain A: R.5, P.499, P.500, Y.502 Chain L: E.3, E.4, G.5, N.9 Ligands: EDO.19 Ligand excluded by PLIP EDO.166: 7 residues within 4Å: Chain A: V.118, E.119 Chain J: A.53, S.54, F.55, P.56 Chain L: K.45 Ligand excluded by PLIP EDO.168: 4 residues within 4Å: Chain A: T.46 Chain M: K.41 Ligands: EDO.23, EDO.170 Ligand excluded by PLIP EDO.169: 4 residues within 4Å: Chain M: P.9, S.11, P.12 Ligands: PGV.7 Ligand excluded by PLIP EDO.170: 6 residues within 4Å: Chain A: T.46, L.47 Chain D: V.100 Chain M: D.38, K.41 Ligands: EDO.168 Ligand excluded by PLIP EDO.171: 2 residues within 4Å: Chain M: S.20 Ligands: EDO.97 Ligand excluded by PLIP EDO.172: 8 residues within 4Å: Chain A: Y.261, K.333, S.335, D.407 Chain M: I.1 Ligands: EDO.11, EDO.31, EDO.35 Ligand excluded by PLIP

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.38: 21 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 Ligands: EDO.25, EDO.49, EDO.55, EDO.98 19 PLIP interactions: 7 interactions with chain B, 10 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:L.7, B:L.28, B:V.31, B:F.32, B:F.32, B:L.39, A:F.346, A:V.350, A:F.426, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430 Salt bridges: B:H.24, I:R.43 Water bridges: I:R.43 TGL.39: 24 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, V.419 Chain B: L.39, I.42, L.46, T.47, K.49 Chain D: R.70, S.71, E.74, W.75, V.78, M.83, I.86 Chain I: R.16 Ligands: EDO.57, EDO.89, EDO.144 14 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: B:L.39, B:I.42, B:K.49, D:V.78, D:I.86, A:W.334, A:W.334, A:W.334, A:L.342, A:K.411, A:A.415, A:V.419 Water bridges: D:W.75 Salt bridges: A:K.411 TGL.156: 28 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.109, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: N.9, I.10, P.11, F.12, S.13, R.19, M.23, M.24, L.26, F.27, F.28, S.30 Ligands: EDO.24, EDO.159 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:T.17, A:L.20, A:F.22, A:W.25, A:W.25, A:W.25, A:F.109, A:F.400, A:I.472, L:I.10, L:P.11, L:F.12, L:L.26, L:F.27, L:F.27, L:F.28, L:F.28

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.40: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.41: 20 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, W.65, P.69 Chain E: D.4, F.7, D.36, L.37 Chain I: R.10, A.14, L.17 Ligands: EDO.26 13 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 3 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:W.65, B:P.69, A:F.321, A:F.321, A:L.324, I:L.17 Salt bridges: B:H.52 Hydrogen bonds: I:R.10, E:D.4 Water bridges: I:A.14

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.42: 8 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Ligands: EDO.14, EDO.56 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.62, B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.62: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Ligands: PGV.67 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:D.300, A:T.301 Salt bridges: A:H.233, C:H.101 CHD.69: 5 residues within 4Å: Chain C: R.154, F.162, F.217, L.221 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:F.162, C:F.162, C:F.162, C:F.217, C:L.221 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.132: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.65 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.21 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17

3 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.63: 13 residues within 4Å: Chain C: K.75, R.78, Y.79, I.82, V.89, T.93, F.96, W.238, V.245, F.249 Ligands: EDO.77, EDO.80, EDO.83 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.79, C:I.82, C:V.89, C:V.89, C:F.96, C:W.238, C:W.238, C:W.238, C:V.245, C:F.249, C:F.249 Salt bridges: C:K.75 PEK.64: 27 residues within 4Å: Chain A: H.151, A.203, T.207, L.210, L.215 Chain C: L.29, W.32, F.33, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8, DMU.70 19 PLIP interactions: 7 interactions with chain G, 9 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: G:F.69, C:L.29, C:W.32, C:W.32, C:F.33, C:I.186, C:F.201, C:F.201, A:A.203, A:L.210, A:L.215 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:A.182, C:I.186 Water bridges: G:F.69, G:F.69 PEK.65: 13 residues within 4Å: Chain C: K.155, H.156, Q.159, I.163, T.166, Y.170 Chain F: A.1 Chain G: R.17, F.21, G.22, L.23, W.36 Ligands: CHD.132 13 PLIP interactions: 7 interactions with chain C, 5 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:I.163, C:Y.170, C:Y.170, C:Y.170, G:F.21, G:L.23 Hydrogen bonds: C:K.155, C:K.155, C:Q.159, F:A.1 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.17

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.68: 26 residues within 4Å: Chain C: T.46, M.49, L.50, M.52, Y.53, W.56, R.57, I.60, R.61, F.65, V.169, T.172, I.207, S.210, T.211, I.214, V.215, F.218, R.219, K.222, H.224 Chain J: K.8, T.27, L.31 Ligands: PGV.66, EDO.150 31 PLIP interactions: 27 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:T.46, C:L.50, C:Y.53, C:Y.53, C:Y.53, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:V.169, C:T.172, C:I.207, C:T.211, C:I.214, C:I.214, C:V.215, C:F.218, J:L.31 Hydrogen bonds: C:Y.53 Water bridges: C:R.61, J:K.8 Salt bridges: C:R.61, C:K.222, C:K.222, C:K.222, C:K.222, C:H.224, J:K.8, J:K.8 CDL.131: 18 residues within 4Å: Chain C: N.123, L.125, L.129, S.133, V.140, L.248, Y.251, V.252, W.256 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: EDO.75, EDO.76 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: C:L.129, C:V.140, C:L.248, C:Y.251, C:V.252, C:W.256, G:L.23, G:L.30, G:L.30, G:L.37 Hydrogen bonds: C:N.123, G:N.34 Salt bridges: G:H.38

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.70: 6 residues within 4Å: Chain C: W.32, M.38 Chain G: S.61, W.62, F.69 Ligands: PEK.64 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.32 Hydrogen bonds: G:S.61 DMU.71: 10 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.147 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:I.43, J:Y.45, J:Y.45 Hydrogen bonds: C:N.36, C:S.37, C:S.37, J:Y.45 DMU.147: 7 residues within 4Å: Chain C: M.31, F.35 Chain J: Y.45, Y.48, C.49, W.52 Ligands: DMU.71 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Y.45, J:Y.45 DMU.167: 11 residues within 4Å: Chain A: F.459 Chain D: W.95, Y.99 Chain L: F.36 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 10 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A, 3 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: D:W.95, D:W.95, A:F.459, M:L.27, M:A.30, L:F.36 Water bridges: D:Y.99, D:Y.99, D:Y.99, M:H.36

1 x ZN: ZINC ION(Non-covalent)

ZN.122: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.140: 4 residues within 4Å: Chain H: R.21, Q.25, L.28, R.32 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:Q.25 Water bridges: H:R.21, H:R.21, H:R.21, H:R.21, H:R.32 Salt bridges: H:R.21, H:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J.Biol.Chem. (2023)

Release Date

2022-11-16

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2, mitochondrial: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B, mitochondrial: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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