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

Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.22 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: 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: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: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: PER.6 39 PLIP interactions: 34 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:I.356, A:I.356, A:L.358, A:V.373, 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, 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: PER.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.14, H2O.14, H2O.15

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

NA.5: 4 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.441

1 x PER: PEROXIDE ION(Non-covalent)

PER.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)

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

PGV.7: 34 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158, L.159, P.200 Chain C: H.9, V.11, G.20, A.24, T.28, L.31, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90, F.93 Ligands: PGV.38, PEK.44, DMU.54 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:F.148, A:L.152, A:I.158, A:L.159, A:P.200, C:A.24, C:T.28, C:L.31, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.57 Salt bridges: A:R.96 PGV.8: 18 residues within 4Å: Chain A: N.406, T.408, W.409, I.412, R.480 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16, L.19, S.20 19 PLIP interactions: 5 interactions with chain K, 5 interactions with chain M, 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: K:F.9, K:F.9, K:F.9, M:P.12, M:P.12, M:Q.15, M:L.19, A:T.408, A:W.409, A:I.412, D:T.80, D:A.84, D:F.87, D:F.87, D:F.87 Water bridges: K:F.9 Salt bridges: K:H.10 Hydrogen bonds: M:K.4, A:T.408 PGV.38: 27 residues within 4Å: Chain C: L.47, N.50, M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, E.90, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.7, CDL.39 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:L.47, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.43: 9 residues within 4Å: Chain A: F.237, D.298 Chain C: T.95, W.99, H.103, L.106, A.107 Chain H: N.24 Ligands: CHD.41 8 PLIP interactions: 1 interactions with chain H, 3 interactions with chain A, 4 interactions with chain C Water bridges: H:N.24, A:D.298, A:D.298 Hydrophobic interactions: A:F.237, C:T.95, C:W.99, C:W.99 Salt bridges: C:H.103 PGV.73: 3 residues within 4Å: Chain G: A.1, A.3 Ligands: CDL.72 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:A.1

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 28 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.102, P.106, F.109, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 Ligands: EDO.27, DMU.95 18 PLIP interactions: 7 interactions with chain L, 11 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29, A:T.17, A:L.20, A:F.22, A:F.22, A:W.25, A:W.25, A:F.102, A:F.109, A:L.113, A:I.472, A:I.472 TGL.29: 16 residues within 4Å: Chain A: F.346, V.350, T.354, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, F.32, S.35, S.36 Chain I: R.43 16 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.7, B:F.32, B:F.32, A:F.346, A:F.346, A:V.350, A:T.354, A:N.422, A:F.426, A:F.426, A:H.429, A:F.430 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.56: 21 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, F.418 Chain B: L.39, I.42, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, I.89 Chain I: R.16, H.20 Ligands: DMU.61 14 PLIP interactions: 6 interactions with chain A, 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, A:F.418, D:W.78, D:V.81, D:I.89, B:L.39, B:K.49 Hydrogen bonds: D:T.75, D:E.77, D:W.78

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

EDO.10: 6 residues within 4Å: Chain A: D.221, P.222, A.223 Ligands: EDO.20, EDO.36, EDO.47 Ligand excluded by PLIP EDO.11: 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.10 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: Y.19, M.71, P.72, I.75, G.76, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: Q.52, A.137, H.138 Chain B: W.104, G.201, S.202 Ligand excluded by PLIP EDO.14: 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.15: 5 residues within 4Å: Chain A: V.485, D.486, L.487, T.488, T.489 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: T.489 Chain F: I.70, P.83 Ligand excluded by PLIP EDO.17: 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.18: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.69 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: P.131, D.221, P.222 Ligands: EDO.10 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, E.62 Ligand excluded by PLIP EDO.22: 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.23: 4 residues within 4Å: Chain A: E.119, A.120 Ligands: EDO.84, EDO.92 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: V.482, L.483, G.497, C.498 Chain D: S.8, Y.11 Ligand excluded by PLIP EDO.25: 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.26: 8 residues within 4Å: Chain A: Y.19, N.80, M.92, N.98, S.101, G.160, N.163, F.164 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain A: F.2 Ligands: TGL.9 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: W.104, Y.121, M.122, N.203, F.206 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.35: 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.36: 4 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.10, EDO.47 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: P.15, E.18, S.187 Chain I: Y.51 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.111 Chain H: W.68 Ligands: EDO.10, EDO.36, EDO.52 Ligand excluded by PLIP EDO.48: 10 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain F: A.1, S.2 Chain G: A.13, R.14, R.17 Ligands: EDO.70 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain C: H.3, Q.4, H.70 Chain F: L.16 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain C: N.12, Q.68 Chain J: L.18, V.20, K.23 Ligands: EDO.80 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain C: Q.68 Chain F: G.15 Chain J: Q.13 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain B: G.177 Chain C: E.111 Chain H: W.68, W.72 Ligands: EDO.47 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain B: P.130 Chain D: E.114, W.115, K.118 Ligand excluded by PLIP EDO.58: 2 residues within 4Å: Chain D: Y.11 Chain F: K.55 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Chain F: P.83 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain A: T.488, L.495 Chain D: Y.11, A.12, L.13, S.15 Chain F: W.73 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain D: K.56 Chain E: L.93, N.94, G.97, I.98, S.99 Ligand excluded by PLIP EDO.66: 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.67: 3 residues within 4Å: Chain C: H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain C: F.225 Chain F: G.5, P.7 Chain J: N.3 Ligand excluded by PLIP EDO.69: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.18 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain F: A.1 Chain G: R.14, R.17 Ligands: PEK.42, EDO.48 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain C: F.35 Chain G: K.58, P.59, S.61 Ligand excluded by PLIP EDO.75: 6 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain G: A.46, F.47, Y.82 Ligand excluded by PLIP EDO.77: 5 residues within 4Å: Chain A: D.227 Chain B: G.177, R.178 Chain H: N.24, T.26 Ligand excluded by PLIP EDO.80: 6 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligands: EDO.50 Ligand excluded by PLIP EDO.81: 3 residues within 4Å: Chain J: Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.82: 1 residues within 4Å: Chain J: A.6 Ligand excluded by PLIP EDO.83: 4 residues within 4Å: Chain A: F.8 Chain J: H.21, L.22, Y.32 Ligand excluded by PLIP EDO.84: 8 residues within 4Å: Chain A: V.118, E.119 Chain J: A.53, S.54, F.55, P.56 Chain L: K.46 Ligands: EDO.23 Ligand excluded by PLIP EDO.91: 6 residues within 4Å: Chain A: F.2 Chain L: G.8, K.9, I.11, F.13, S.14 Ligand excluded by PLIP EDO.92: 6 residues within 4Å: Chain A: E.119, A.120 Chain L: Q.43, K.46, K.47 Ligands: EDO.23 Ligand excluded by PLIP EDO.93: 3 residues within 4Å: Chain L: S.31, F.38 Ligands: DMU.95 Ligand excluded by PLIP EDO.97: 5 residues within 4Å: Chain A: T.46, L.47 Chain D: V.103 Chain M: D.38, K.41 Ligand excluded by PLIP EDO.98: 2 residues within 4Å: Chain M: H.36 Ligands: DMU.96 Ligand excluded by PLIP

15 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-functional Binders)(Non-covalent)

DMU.28: 3 residues within 4Å: Ligands: DMU.85, DMU.86, DMU.88 No protein-ligand interaction detected (PLIP) DMU.45: 10 residues within 4Å: Chain A: L.110 Chain C: M.33, F.37 Chain J: S.46, Y.48, C.49, L.50, W.52, A.53 Ligands: DMU.53 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: C:M.33, C:F.37, J:L.50, J:A.53, A:L.110 Hydrogen bonds: J:Y.45, J:Y.45 DMU.53: 10 residues within 4Å: Chain C: N.38, S.39, T.41, I.45 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.45 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:I.45, J:Y.45, J:Y.45 Hydrogen bonds: C:N.38, C:S.39, C:S.39, J:Y.45 DMU.54: 7 residues within 4Å: Chain C: W.34, M.40 Chain G: W.62, G.63, F.69 Ligands: PGV.7, PEK.44 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:G.63 Water bridges: G:W.62, G:D.64, G:F.69, G:F.69 Hydrophobic interactions: C:W.34, C:W.34 DMU.55: 3 residues within 4Å: Chain C: L.250, F.251 Ligands: PEK.46 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.250, C:F.251 DMU.61: 3 residues within 4Å: Chain D: S.74, W.78 Ligands: TGL.56 9 PLIP interactions: 1 interactions with chain K, 8 interactions with chain D Water bridges: K:D.11, D:S.74, D:N.76, D:N.76, D:N.76 Hydrophobic interactions: D:W.78, D:W.78, D:W.78 Hydrogen bonds: D:S.74 DMU.79: 10 residues within 4Å: Chain B: H.26, M.29, I.30, L.33, I.34, L.37, I.72, L.75 Chain I: K.36 Ligands: PSC.32 9 PLIP interactions: 2 interactions with chain I, 7 interactions with chain B Hydrogen bonds: I:K.36, I:E.41, B:H.26 Hydrophobic interactions: B:I.30, B:L.33, B:I.34, B:L.37, B:L.75 Salt bridges: B:H.26 DMU.85: 8 residues within 4Å: Chain A: M.423 Chain D: I.89 Chain K: V.26, W.29, V.30 Ligands: DMU.28, DMU.88, DMU.90 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:V.26, K:W.29, K:W.29, K:W.29, K:W.29, K:V.30, D:I.89 DMU.86: 7 residues within 4Å: Chain K: A.33, T.34, Q.35, W.40 Ligands: DMU.28, DMU.87, DMU.88 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:W.40, K:W.40 Hydrogen bonds: K:Q.35 Water bridges: K:I.38 DMU.87: 9 residues within 4Å: Chain D: L.94, L.95, I.97, H.101 Chain K: Y.31, Q.35, I.36, G.37 Ligands: DMU.86 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: D:L.94, D:L.95, D:I.97, D:H.101 Water bridges: D:K.100, K:Q.35, K:G.37 Salt bridges: D:H.101 Hydrogen bonds: K:Y.31 DMU.88: 10 residues within 4Å: Chain K: W.29, V.30, A.33, T.34, Q.35, W.40 Ligands: DMU.28, DMU.85, DMU.86, DMU.90 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:W.29, K:V.30, K:A.33, K:W.40 DMU.89: 7 residues within 4Å: Chain K: N.15, A.19, S.20, T.23, F.24, A.27 Ligands: DMU.90 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:F.24, K:F.24, K:F.24, K:A.27 Hydrogen bonds: K:N.15, K:S.20, K:T.23 Water bridges: K:A.19 DMU.90: 6 residues within 4Å: Chain K: T.23, A.27, Y.31 Ligands: DMU.85, DMU.88, DMU.89 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:A.27, K:Y.31, K:Y.31, K:Y.31 Hydrogen bonds: K:T.23, K:T.23 DMU.95: 11 residues within 4Å: Chain A: W.25, M.117 Chain J: F.55 Chain L: S.31, A.35, F.38, R.41, H.42, L.45 Ligands: TGL.9, EDO.93 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: L:A.35, A:W.25 Hydrogen bonds: L:R.41, L:H.42 Water bridges: L:H.42, L:H.42 Salt bridges: L:R.41, L:H.42 DMU.96: 12 residues within 4Å: Chain A: F.459 Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 Ligands: EDO.98 7 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A, 4 interactions with chain D, 1 interactions with chain M Hydrophobic interactions: L:F.37, A:F.459, D:W.98, D:W.98, M:A.30 Water bridges: D:Y.102, D:Y.102

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

CUA.30: 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

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.31: 6 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, B:T.66 Hydrogen bonds: B:E.62, B:T.63 Water bridges: B:Q.59, B:T.63 CHD.40: 6 residues within 4Å: Chain C: R.156, L.160, F.164, F.219, L.223 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.41: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.43 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.103 CHD.94: 4 residues within 4Å: Chain L: W.19 Chain M: E.14, I.17, V.21 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain M Hydrophobic interactions: L:W.19, M:I.17 Water bridges: M:E.14

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.32: 24 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: I.41, H.52, T.55, M.56, D.57, V.61, I.64, W.65, P.69, I.72 Chain E: E.6, D.8, F.11, D.40, L.41 Chain I: R.10, G.11, A.14, L.17 Ligands: DMU.79 18 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, 3 interactions with chain I, 3 interactions with chain E Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:V.61, B:I.64, B:W.65, B:P.69, B:I.72, A:F.321, A:L.324, A:A.325, I:L.17 Salt bridges: B:H.52, E:D.8 Hydrogen bonds: I:G.11 Water bridges: I:A.14, E:D.40 pi-Cation interactions: E:F.11

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.39: 26 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, G.170, V.171, T.174, I.209, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, L.31, V.34 Ligands: PGV.38 24 PLIP interactions: 20 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:V.171, C:I.209, C:I.216, C:I.216, C:F.220, C:F.220, J:V.34 Hydrogen bonds: C:Y.55 Water bridges: C:R.59, C:R.63, J:K.8, J:G.24 Salt bridges: C:R.63, C:K.224, C:H.226, J:K.8 CDL.72: 17 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, S.135, V.142, V.254, W.258 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.42, PGV.73 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain G Hydrophobic interactions: C:L.131, C:T.134, C:V.254, C:W.258, G:L.30, G:L.30, G:L.37 Hydrogen bonds: C:N.125 Water bridges: G:N.34 Salt bridges: G:H.38

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.42: 11 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22 Ligands: EDO.70, CDL.72 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:T.168, C:Y.172 Hydrogen bonds: C:K.157, C:K.157, G:R.17 Water bridges: C:Q.161 Salt bridges: G:R.17 PEK.44: 22 residues within 4Å: Chain A: H.151, L.215 Chain C: L.31, W.34, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7, DMU.54 16 PLIP interactions: 8 interactions with chain G, 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: G:W.62, G:F.69, C:L.31, C:W.34, C:I.188, C:F.203, C:F.203, A:L.215 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:A.184, C:I.188 Water bridges: G:F.69, G:F.69 PEK.46: 15 residues within 4Å: Chain A: V.193, L.197 Chain C: K.77, Y.81, I.84, L.85, V.91, L.92, T.95, F.98, W.240, F.244, V.247, F.251 Ligands: DMU.55 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.81, C:Y.81, C:I.84, C:I.84, C:L.85, C:V.91, C:V.91, C:L.92, C:F.98, C:F.98, C:W.240, C:W.240, C:V.247, C:F.251, C:F.251, A:V.193, A:L.197 Hydrogen bonds: C:K.77 Salt bridges: C:K.77

1 x ZN: ZINC ION(Non-covalent)

ZN.65: 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)

PO4.78: 4 residues within 4Å: Chain H: R.27, Q.31, L.34, R.38 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:Q.31, H:Q.31, H:Q.31 Water bridges: H:R.27, H:R.27 Salt bridges: H:R.27, H:R.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yano, N. et al., The Mg2+-containing water cluster of mammalian cytochrome c oxidase collects four pumping proton equivalents in each catalytic cycle. J. Biol. Chem. (2016)

Release Date

2022-09-21

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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