SMTL ID : 7ypy.2 (1 other biounit)

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

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 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, 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:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:F.425 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:H.61, A:F.377, 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: 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, 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, A:H.376 Metal complexes: A:H.376

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

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.8, H2O.12, H2O.13

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.43

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)

PGV.7: 30 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, L.159 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, 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: PEK.38 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:F.148, A:L.152, A:L.159, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.86, C:F.93 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.57 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.33: 25 residues within 4Å: Chain C: N.50, M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, F.86, 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: CDL.34 27 PLIP interactions: 2 interactions with chain F, 25 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.65, C:R.221, C:H.231, C:H.231 Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, 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 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.47: 17 residues within 4Å: Chain A: N.406, T.408, W.409, I.412, R.480 Chain D: T.80, A.84, F.87, F.88 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 Ligands: CHD.70 9 PLIP interactions: 2 interactions with chain M, 1 interactions with chain A, 4 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: M:P.12, M:A.16, A:I.412, D:F.87, D:F.87, D:F.87, D:F.88, K:F.9 Water bridges: K:F.9

EDO.8: 6 residues within 4Å: Chain A: F.505, E.507, P.508 Chain F: R.56, I.57, W.73 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: Y.19, M.71, P.72, I.75, G.76, L.105, S.156, S.157 Ligand excluded by PLIP EDO.10: 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.11: 1 residues within 4Å: Chain A: F.2 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.53 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, V.485, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 Ligands: EDO.49 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligands: EDO.54 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: E.62 Ligands: CHD.27 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, L.96 Ligands: EDO.58 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: T.489 Chain F: I.70, P.83 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: L.33, V.57, A.60, S.116 Chain L: I.39, V.40 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: V.485, D.486, L.487, T.488, T.489 Ligands: EDO.49 Ligand excluded by PLIP EDO.22: 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.58 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: T.10, N.11, D.91, Y.502, H.503 Chain C: M.10, V.11 Ligands: EDO.79 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: E.266, P.267, G.269, Y.270 Chain F: S.67 Ligands: EDO.54 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: T.46 Chain B: F.206 Ligand excluded by PLIP EDO.30: 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.39: 9 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 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain C: Q.4, H.70 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.111 Chain H: W.68 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: P.73, A.74, K.77 Chain F: I.33 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: T.145, H.148, H.149 Chain G: T.11, W.16 Ligand excluded by PLIP EDO.49: 11 residues within 4Å: Chain A: T.484, T.488, L.495 Chain D: D.10, Y.11, L.13, P.14, S.15 Ligands: EDO.14, EDO.21, EDO.55 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain A: T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.12 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain A: E.266 Chain F: D.65, N.66, S.67, T.68 Ligands: EDO.15, EDO.24 Ligand excluded by PLIP EDO.55: 8 residues within 4Å: Chain A: L.495 Chain D: Y.11, A.12, L.13, P.14 Chain F: F.72, W.73 Ligands: EDO.49 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.57: 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.58: 7 residues within 4Å: Chain A: Y.510 Chain F: N.32, P.36, P.50, R.56 Ligands: EDO.18, EDO.22 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain F: E.11, Q.12, A.13, T.14, R.18 Chain J: Q.9 Ligands: EDO.69 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain C: P.73, H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.63: 4 residues within 4Å: Chain G: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.64: 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.65: 6 residues within 4Å: Chain C: W.34, F.35 Chain G: K.58, P.59, F.60, S.61 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain G: W.62, F.69 Ligands: DMU.45 Ligand excluded by PLIP EDO.68: 2 residues within 4Å: Chain I: R.16, H.20 Ligand excluded by PLIP EDO.69: 3 residues within 4Å: Chain J: K.10, Q.13 Ligands: EDO.59 Ligand excluded by PLIP EDO.78: 8 residues within 4Å: Chain A: V.118, E.119 Chain J: A.53, S.54, F.55, P.56 Chain L: K.46, K.47 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain C: P.13 Chain L: H.2, Y.3 Ligands: EDO.23 Ligand excluded by PLIP EDO.82: 6 residues within 4Å: Chain A: T.46, L.47 Chain D: V.103 Chain M: L.37, D.38, K.41 Ligand excluded by PLIP

TGL.25: 18 residues within 4Å: Chain A: T.354, F.418, N.422, M.423, 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: K.42, R.43 13 PLIP interactions: 1 interactions with chain I, 6 interactions with chain A, 6 interactions with chain B Salt bridges: I:R.43, B:H.24 Hydrophobic interactions: A:T.354, A:F.418, A:N.422, A:F.426, A:F.426, A:F.430, B:V.31, B:F.32, B:L.39 Water bridges: B:G.8, B:F.9 TGL.48: 17 residues within 4Å: Chain A: W.334, M.339, G.343, F.414, A.415, V.419 Chain B: L.39, I.42, L.46 Chain D: R.73, T.75, E.77, W.78, V.81, V.82, M.86, I.89 16 PLIP interactions: 8 interactions with chain D, 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:E.77, D:W.78, D:W.78, D:V.81, D:V.82, A:W.334, A:W.334, A:W.334, A:A.415, A:V.419, B:L.39, B:L.46 Hydrogen bonds: D:T.75, D:E.77, D:W.78 Salt bridges: A:K.411 TGL.77: 28 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, P.106, F.109, L.110, L.112, 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, L.27, F.28, F.29, I.39 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.21, A:F.22, A:F.22, A:W.25, A:W.25, A:P.106, A:F.109, A:F.109, A:L.112, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.28, L:I.39

CUA.26: 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

CHD.27: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Ligands: EDO.16 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.62, B:T.63 Water bridges: B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.35: 8 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:F.164, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.37: 7 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.103 CHD.70: 7 residues within 4Å: Chain K: A.16, A.19, S.20, T.23, F.24 Ligands: PGV.47, DMU.75 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:A.16, K:A.19, K:T.23 Hydrogen bonds: K:T.23 CHD.80: 5 residues within 4Å: Chain L: W.19, L.22, A.23 Chain M: E.14, I.17 6 PLIP interactions: 2 interactions with chain L, 4 interactions with chain M Hydrophobic interactions: L:W.19, M:E.14, M:I.17, M:I.17 Hydrogen bonds: L:A.23, M:E.14

PSC.28: 22 residues within 4Å: Chain A: F.268, F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, T.55, M.56, D.57, E.60, V.61, I.64, W.65, P.69 Chain E: E.6, D.8, F.11 Chain I: R.10, A.14, L.17 14 PLIP interactions: 9 interactions with chain B, 1 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:V.61, B:I.64, B:W.65, B:P.69, A:F.268, A:F.321, A:L.324, A:A.325 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, E:D.8

DMU.31: 7 residues within 4Å: Chain B: H.26, M.29, I.30, L.33, I.34, L.75 Chain I: K.36 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: B:I.34, B:L.75 Salt bridges: B:H.26, I:K.36 Hydrogen bonds: I:K.36 DMU.36: 13 residues within 4Å: Chain A: L.110, A.114, L.145 Chain C: S.29, M.33, F.37 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.46 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain J, 3 interactions with chain A Hydrophobic interactions: C:M.33, C:F.37, J:L.50, A:L.110, A:A.114, A:L.145 Hydrogen bonds: J:Y.45, J:Y.45 DMU.45: 9 residues within 4Å: Chain C: W.34, N.38, M.40 Chain G: S.61, W.62, G.63, F.69 Ligands: DMU.46, EDO.66 10 PLIP interactions: 3 interactions with chain G, 7 interactions with chain C Hydrophobic interactions: G:F.69, G:F.69, C:W.34, C:W.34 Hydrogen bonds: G:G.63, C:W.34, C:N.38, C:N.38, C:N.38 Water bridges: C:M.40 DMU.46: 11 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.36, DMU.45 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain J Hydrogen bonds: C:N.38, C:S.39, C:S.39, J:Y.45 Hydrophobic interactions: J:Y.45, J:Y.45 DMU.71: 7 residues within 4Å: Chain A: M.423 Chain D: I.89 Chain K: V.26, W.29, V.30 Ligands: DMU.74, DMU.75 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: D:I.89, K:W.29, K:W.29, K:W.29 DMU.72: 9 residues within 4Å: Chain B: M.5 Chain K: A.33, T.34, G.37, I.38, E.39, W.40 Ligands: DMU.73, DMU.76 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:W.40, K:W.40 Hydrogen bonds: K:G.37, K:E.39 Water bridges: K:W.40 DMU.73: 9 residues within 4Å: Chain D: L.94, I.97, W.98, H.101 Chain K: Y.31, Q.35, I.36, G.37 Ligands: DMU.72 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain K Hydrophobic interactions: D:L.94, D:W.98 Water bridges: D:K.100, D:K.100, K:T.34, K:Q.35, K:G.37 Salt bridges: D:H.101 Hydrogen bonds: K:Y.31 DMU.74: 6 residues within 4Å: Chain K: V.30, A.33, T.34 Ligands: DMU.71, DMU.75, DMU.76 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:A.33, K:T.34 DMU.75: 6 residues within 4Å: Chain K: T.23, F.24, A.27 Ligands: CHD.70, DMU.71, DMU.74 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.24, K:F.24, K:A.27 DMU.76: 2 residues within 4Å: Ligands: DMU.72, DMU.74 No protein-ligand interaction detected (PLIP) DMU.81: 13 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 10 PLIP interactions: 6 interactions with chain M, 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: M:L.27, M:A.30, M:L.34, A:L.35, A:F.459, D:L.95, D:W.98 Water bridges: M:W.32, M:H.36, M:H.36