SMTL ID : 7vuw.2 (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: 37 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 35 PLIP interactions: 35 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:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:V.465 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, 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 35 PLIP interactions: 30 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:I.356, A:I.356, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, 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.12, H2O.13, H2O.15

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:D.442 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)

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 18 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, H.24, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 18 PLIP interactions: 8 interactions with chain B, 2 interactions with chain I, 8 interactions with chain A Hydrophobic interactions: B:L.7, B:V.31, B:F.32, B:F.32, B:L.39, A:V.350, A:Y.379, A:F.426, A:F.426, A:F.426, A:F.426, A:F.430, A:F.430 Water bridges: B:G.8, B:F.9, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.82: 20 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, V.419 Chain B: L.39, I.42, L.46, T.47 Chain D: R.70, S.71, E.74, W.75, V.78, M.83, I.86 Chain I: R.16 Ligands: DMU.129 15 PLIP interactions: 7 interactions with chain A, 4 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:A.415, A:V.419, D:V.78, B:L.39, B:I.42, B:L.46, B:T.47 Salt bridges: A:K.411 Hydrogen bonds: D:T.72, D:E.74, D:W.75 TGL.133: 27 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.81, 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.29 19 PLIP interactions: 10 interactions with chain L, 9 interactions with chain A Hydrophobic interactions: L:I.10, L:P.11, L:F.12, L:F.12, L:F.12, L:L.26, L:F.27, L:F.27, L:F.27, L:F.28, A:T.17, A:W.25, A:W.25, A:W.81, A:F.109, A:L.113, A:F.393, A:F.400, A:I.472

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

PGV.8: 14 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: T.77, A.81, F.84 Chain K: F.4, H.5 Chain M: A.3, P.12, Q.15, A.16, L.19 15 PLIP interactions: 3 interactions with chain A, 6 interactions with chain M, 2 interactions with chain D, 4 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:I.412, M:P.12, M:P.12, M:A.16, M:L.19, D:T.77, D:F.84, K:F.4, K:F.4, K:F.4 Water bridges: M:A.3, M:A.3, K:F.4 PGV.9: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151, L.152, 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, F.91 Ligands: PEK.57 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.91, A:F.148, A:L.152, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:R.96, A:M.97 Water bridges: C:M.81, A:A.93 Salt bridges: A:R.96 PGV.59: 26 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, E.88, F.91, F.201, 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.61 25 PLIP interactions: 23 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:I.60, C:F.84, C:F.91, C:F.201, C:I.208, 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.60: 15 residues within 4Å: Chain A: F.237, D.298 Chain C: V.89, T.93, W.97, Y.100, H.101, A.105 Chain H: N.16, N.18 Ligands: EDO.22, EDO.23, EDO.34, CHD.55, EDO.78 11 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: C:V.89, C:T.93, C:W.97, C:W.97, C:W.97, A:F.237 Hydrogen bonds: A:D.298, H:N.16 Water bridges: A:D.298, A:D.298, H:N.18

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

DMU.10: 4 residues within 4Å: Chain K: V.25, A.28, T.29 Ligands: DMU.130 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:V.25, K:A.28, K:T.29 DMU.38: 8 residues within 4Å: Chain B: H.26, M.29, I.30, L.33, I.34, L.37, I.72 Chain I: K.36 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain I Hydrophobic interactions: B:L.33, B:I.34, B:L.37 Water bridges: B:H.26, B:H.26 Salt bridges: B:H.26 Hydrogen bonds: I:K.36, I:K.36, I:K.36 DMU.63: 11 residues within 4Å: Chain C: M.31, N.36, S.37, T.39, I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.64 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain J Hydrophobic interactions: C:I.43, J:L.38, J:Y.45, J:Y.45, J:Y.45 Hydrogen bonds: C:S.37, C:S.37 Water bridges: J:Y.45, J:Y.45 DMU.64: 12 residues within 4Å: Chain A: L.110, A.114 Chain C: S.27, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.63 6 PLIP interactions: 3 interactions with chain J, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: J:L.50, A:L.110, A:A.114, C:M.31 Hydrogen bonds: J:Y.45, J:Y.45 DMU.112: 7 residues within 4Å: Chain C: L.29, W.32, M.38, L.41 Chain G: W.62, G.63 Ligands: PEK.57 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:G.63 Hydrophobic interactions: C:L.29, C:W.32, C:L.41 DMU.129: 6 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: TGL.82 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain K Hydrophobic interactions: D:I.86, K:V.21, K:W.24, K:W.24, K:W.24, K:V.25 DMU.130: 6 residues within 4Å: Chain A: M.449, I.453 Chain K: A.28, T.29, W.35 Ligands: DMU.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain K Hydrophobic interactions: A:I.453 Water bridges: K:E.34, K:E.34 DMU.131: 8 residues within 4Å: Chain D: L.91, I.94, W.95, H.98 Chain K: Y.26, Q.30, I.31, G.32 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:L.91, D:W.95, D:H.98 Salt bridges: D:H.98 Hydrogen bonds: K:Y.26 Water bridges: K:G.32 DMU.132: 3 residues within 4Å: Chain K: T.18, F.19, A.22 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.19, K:F.19, K:A.22 DMU.141: 13 residues within 4Å: Chain A: L.35, F.459 Chain D: L.92, W.95, Y.99 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 11 PLIP interactions: 5 interactions with chain M, 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: M:L.27, M:L.27, M:A.30, M:L.34, D:L.92, D:W.95, A:L.35, A:F.459, A:F.459 Water bridges: M:H.36, D:Y.99

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

EDO.11: 8 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.8 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: L.7 Ligands: EDO.25 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: P.174, A.175, S.177 Ligands: EDO.20 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, E.62 Ligands: EDO.40 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.102 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain A: P.174, T.509, Y.510, V.511 Chain F: N.32, L.34, P.36, R.56 Ligands: EDO.105 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: C.498, P.499 Chain D: Y.8 Chain L: P.6 Ligands: EDO.135 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: K.172, P.173, P.174, M.176 Ligands: EDO.15, EDO.28 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: Y.19, M.71, P.72, I.75, G.76, L.105, S.157, L.195 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: I.229, H.233 Chain C: H.101 Ligands: CHD.55, PGV.60 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Ligands: CHD.55, PGV.60 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: L.33, A.60, S.116 Chain L: I.38, V.39 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: L.110 Ligands: EDO.14 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: Q.52, A.137, H.138, A.139 Ligand excluded by PLIP EDO.27: 1 residues within 4Å: Chain G: R.56 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: N.170, K.172, P.173, P.174 Chain C: Y.6 Ligands: EDO.20 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: F.2 Ligands: TGL.133 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: H.503, E.506 Chain C: H.1 Chain L: H.1 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain A: E.266, P.267, G.269, Y.270 Chain F: S.67 Ligands: EDO.50, EDO.101 Ligand excluded by PLIP EDO.32: 9 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 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, S.84 Ligands: EDO.101 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: W.288, Y.304 Ligands: PGV.60 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain A: T.10, N.11, D.91, Y.502, H.503 Chain C: V.9 Ligands: EDO.140 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: T.125, L.135, F.206 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain B: Q.59 Ligands: EDO.16 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.77, EDO.118 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: S.36, L.39, S.43 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: Y.40 Chain I: A.24, V.27, S.28 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: 4 residues within 4Å: Chain B: D.88, I.90 Chain H: F.10, P.15 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain B: S.117, F.118, D.119 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain B: S.14, P.15, I.16, L.168, T.183, L.184, M.185 Ligands: EDO.51 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: T.55, M.56, D.57, A.58 Ligands: EDO.31, EDO.101 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain B: M.87, L.170, T.182, T.183 Ligands: EDO.49 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.51, K.55 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain B: E.132, R.141 Chain D: R.119 Chain I: G.67, I.68 Ligand excluded by PLIP EDO.54: 9 residues within 4Å: Chain A: D.445, A.446 Chain B: M.1, A.2, Y.3, P.4, L.133 Chain D: Q.116, M.120 Ligand excluded by PLIP EDO.65: 8 residues within 4Å: Chain C: W.144, S.148, H.156 Chain F: A.1, S.2 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain C: G.139, H.241 Chain G: W.16 Ligand excluded by PLIP EDO.67: 2 residues within 4Å: Chain C: H.241, V.245 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain C: H.241 Ligands: PEK.56, EDO.73, EDO.80 Ligand excluded by PLIP EDO.69: 3 residues within 4Å: Chain C: I.85, I.86 Ligands: PEK.56 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain C: H.147 Chain G: T.11, W.16 Ligands: EDO.80 Ligand excluded by PLIP EDO.71: 2 residues within 4Å: Chain C: F.249 Ligands: CDL.111 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain C: P.71, Q.74, K.75, R.78 Ligand excluded by PLIP EDO.73: 4 residues within 4Å: Chain C: E.234, W.238 Ligands: PEK.56, EDO.68 Ligand excluded by PLIP EDO.74: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain C: M.150, S.227, N.228 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain C: Q.2, H.68 Ligands: EDO.107 Ligand excluded by PLIP EDO.77: 7 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.42, EDO.118 Ligand excluded by PLIP EDO.78: 4 residues within 4Å: Chain C: T.93, W.97 Ligands: PEK.56, PGV.60 Ligand excluded by PLIP EDO.79: 3 residues within 4Å: Chain A: E.119 Chain C: H.34, F.35 Ligand excluded by PLIP EDO.80: 6 residues within 4Å: Chain C: T.143, H.146, H.147, H.241 Ligands: EDO.68, EDO.70 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain C: R.154, F.223 Chain F: G.5 Ligands: CHD.62 Ligand excluded by PLIP EDO.83: 3 residues within 4Å: Chain D: D.122, Y.137 Chain I: E.62 Ligand excluded by PLIP EDO.84: 3 residues within 4Å: Chain D: E.141, W.142 Chain K: G.41 Ligand excluded by PLIP EDO.85: 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.86: 4 residues within 4Å: Chain D: K.118, D.122, W.135 Chain K: P.45 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain D: P.127, I.128 Chain I: A.46, F.50 Ligand excluded by PLIP EDO.88: 4 residues within 4Å: Chain D: Y.13, V.14, D.15 Ligands: EDO.89 Ligand excluded by PLIP EDO.89: 4 residues within 4Å: Chain D: Y.13, A.25, H.26 Ligands: EDO.88 Ligand excluded by PLIP EDO.90: 7 residues within 4Å: Chain A: L.495 Chain D: Y.8, A.9, L.10, P.11 Chain F: F.72, W.73 Ligand excluded by PLIP EDO.91: 5 residues within 4Å: Chain E: R.10, W.11, Y.14 Ligands: EDO.92, EDO.95 Ligand excluded by PLIP EDO.92: 6 residues within 4Å: Chain E: W.11, Y.14, K.27, T.31 Ligands: EDO.91, EDO.95 Ligand excluded by PLIP EDO.93: 4 residues within 4Å: Chain E: R.49, R.52, R.53, L.92 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain D: Y.19 Chain E: W.23, R.26, K.27, N.30 Ligand excluded by PLIP EDO.95: 7 residues within 4Å: Chain E: W.11, K.27, T.31, Y.35 Chain F: S.84 Ligands: EDO.91, EDO.92 Ligand excluded by PLIP EDO.96: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.98: 4 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 Ligands: EDO.104 Ligand excluded by PLIP EDO.99: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.100: 7 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 Ligands: EDO.110 Ligand excluded by PLIP EDO.101: 7 residues within 4Å: Chain A: E.266 Chain F: N.66, S.67, T.68 Ligands: EDO.31, EDO.33, EDO.50 Ligand excluded by PLIP EDO.102: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.17 Ligand excluded by PLIP EDO.103: 5 residues within 4Å: Chain F: A.24, Q.28, D.29, I.33, L.34 Ligand excluded by PLIP EDO.104: 4 residues within 4Å: Chain C: N.228 Chain F: D.9, M.21 Ligands: EDO.98 Ligand excluded by PLIP EDO.105: 7 residues within 4Å: Chain A: Y.510 Chain F: N.32, P.36, P.50, R.56 Ligands: EDO.18, EDO.106 Ligand excluded by PLIP EDO.106: 7 residues within 4Å: Chain C: T.3 Chain F: P.30, N.32, P.50, R.56, H.94 Ligands: EDO.105 Ligand excluded by PLIP EDO.107: 4 residues within 4Å: Chain F: G.15, L.16, E.19 Ligands: EDO.76 Ligand excluded by PLIP EDO.108: 3 residues within 4Å: Chain F: T.53, K.55, W.73 Ligand excluded by PLIP EDO.109: 2 residues within 4Å: Chain F: P.30, Y.31 Ligand excluded by PLIP EDO.110: 3 residues within 4Å: Chain F: P.36, K.37 Ligands: EDO.100 Ligand excluded by PLIP EDO.113: 2 residues within 4Å: Chain G: A.1, A.3 Ligand excluded by PLIP EDO.114: 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.115: 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.116: 3 residues within 4Å: Chain G: P.49, Y.50, H.51 Ligand excluded by PLIP EDO.117: 3 residues within 4Å: Chain G: R.56, N.66, P.79 Ligand excluded by PLIP EDO.118: 4 residues within 4Å: Chain H: W.62, T.65 Ligands: EDO.42, EDO.77 Ligand excluded by PLIP EDO.119: 6 residues within 4Å: Chain B: D.115 Chain H: K.55, I.60, V.63, S.64 Ligands: EDO.120 Ligand excluded by PLIP EDO.120: 4 residues within 4Å: Chain H: S.64, D.67, D.68 Ligands: EDO.119 Ligand excluded by PLIP EDO.122: 6 residues within 4Å: Chain I: N.53, Y.54, D.55, K.58, E.62 Ligands: EDO.123 Ligand excluded by PLIP EDO.123: 3 residues within 4Å: Chain I: F.50, Y.54 Ligands: EDO.122 Ligand excluded by PLIP EDO.124: 1 residues within 4Å: Chain I: A.32 Ligand excluded by PLIP EDO.125: 5 residues within 4Å: Chain C: N.10, P.11 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.126: 4 residues within 4Å: Chain F: T.14 Chain J: Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.127: 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.128: 7 residues within 4Å: Chain C: Y.53, R.57, R.61 Chain J: T.27, D.28, L.31 Ligands: CDL.61 Ligand excluded by PLIP EDO.135: 3 residues within 4Å: Chain A: P.501 Chain L: E.4 Ligands: EDO.19 Ligand excluded by PLIP EDO.136: 2 residues within 4Å: Chain A: L.113 Chain L: I.38 Ligand excluded by PLIP EDO.137: 4 residues within 4Å: Chain L: G.29, S.30, A.33 Chain M: P.29 Ligand excluded by PLIP EDO.138: 5 residues within 4Å: Chain A: M.1, F.2, R.5 Chain L: Y.2, E.3 Ligand excluded by PLIP EDO.139: 6 residues within 4Å: Chain L: E.3, G.7, K.8, I.10, F.12, S.13 Ligand excluded by PLIP EDO.140: 5 residues within 4Å: Chain A: Y.502 Chain C: P.11 Chain L: H.1, Y.2 Ligands: EDO.35 Ligand excluded by PLIP EDO.142: 3 residues within 4Å: Chain M: V.21, L.24, S.25 Ligand excluded by PLIP

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

CUA.36: 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.37: 16 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: I.41, M.45, H.52, T.55, M.56, D.57, V.61, I.64, W.65, P.69 Chain E: H.1, D.36 Chain I: A.14 11 PLIP interactions: 2 interactions with chain A, 2 interactions with chain I, 7 interactions with chain B Hydrophobic interactions: A:F.321, A:A.325, I:A.14, B:I.41, B:M.56, B:I.64, B:P.69 Water bridges: I:A.14 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, B:H.52

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.55: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Ligands: EDO.22, EDO.23, PGV.60 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.62: 8 residues within 4Å: Chain C: R.154, L.158, Q.159, F.162, F.217, L.221 Chain J: F.1 Ligands: EDO.81 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.158, 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.134: 7 residues within 4Å: Chain L: W.18, L.21, A.22 Chain M: K.13, E.14, I.17, V.21 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: L:L.21, M:K.13, M:E.14 Hydrogen bonds: M:E.14

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.56: 16 residues within 4Å: Chain C: K.75, R.78, Y.79, I.82, V.89, T.93, F.96, W.238, F.242, V.245, V.246, F.249 Ligands: EDO.68, EDO.69, EDO.73, EDO.78 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.82, C:V.89, C:F.96, C:W.238, C:V.245, C:V.246, C:F.249 Hydrogen bonds: C:K.75, C:K.75, C:Y.79 Salt bridges: C:K.75 PEK.57: 25 residues within 4Å: Chain A: H.151, V.155, T.207, L.210, L.215 Chain C: W.32, F.33, 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.9, DMU.112 14 PLIP interactions: 7 interactions with chain G, 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: G:F.69, C:W.32, C:F.33, C:Y.179, C:F.201, A:V.155, A:L.210 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.186 Water bridges: G:F.69, G:F.69 PEK.58: 11 residues within 4Å: Chain C: K.155, H.156, Q.159, T.166, Y.170 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, P.26 13 PLIP interactions: 6 interactions with chain G, 6 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:L.25, G:L.25, G:P.26, C:Y.170, C:Y.170, C:Y.170 Hydrogen bonds: G:R.17, C:K.155, C:H.156, F:A.1 Salt bridges: G:R.17, G:R.17 Water bridges: C:Q.159

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.61: 23 residues within 4Å: Chain C: M.49, L.50, M.52, Y.53, W.56, R.57, I.60, R.61, F.65, 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 Ligands: PGV.59, EDO.128 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:M.49, C:L.50, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:T.172, C:I.207, C:I.207, C:I.214, C:V.215, C:F.218 Hydrogen bonds: C:Y.53 Water bridges: C:R.61, J:G.24 Salt bridges: C:R.61, C:K.222, C:K.222, C:H.224 CDL.111: 18 residues within 4Å: Chain C: N.123, L.125, L.129, T.132, S.133, L.136, V.140, L.248, Y.251, V.252 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: EDO.71 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: C:L.129, C:T.132, C:L.136, C:L.136, C:V.140, C:L.248, C:Y.251, C:V.252, G:L.23, G:L.30, G:L.30, G:N.34 Hydrogen bonds: C:N.123 Water bridges: G:N.34 Salt bridges: G:H.38, G:H.38

1 x ZN: ZINC ION(Non-covalent)

ZN.97: 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)

PO4.121: 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, H:Q.25 Water bridges: H:R.21, H:R.21, H:R.32, 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
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
Z

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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