SMTL ID : 5b3s.2 (1 other biounit)

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

HEA.1: 36 residues within 4Å: Chain A: A.24, G.27, 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, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: EDO.26 34 PLIP interactions: 34 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: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: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: CMO.6 38 PLIP interactions: 33 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:A.313, A:T.316, A:V.320, A:F.348, A:I.356, A:I.356, 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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.6

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.12, H2O.13, H2O.15

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

CMO.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: 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: P.12, Q.15, A.16, L.19, S.20 23 PLIP interactions: 5 interactions with chain D, 8 interactions with chain A, 5 interactions with chain M, 5 interactions with chain K Hydrophobic interactions: D:T.77, D:A.81, D:F.84, D:F.84, D:F.84, A:T.408, A:W.409, A:W.409, A:W.409, A:I.412, M:P.12, M:P.12, M:Q.15, M:A.16, M:L.19, K:F.4, K:F.4, K:F.4 Hydrogen bonds: A:T.408 Water bridges: A:N.406, A:N.406, K:F.4 Salt bridges: K:H.5 PGV.9: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152, V.155 Chain C: H.7, V.9, G.18, A.22, M.25, 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.36 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.152, A:V.155, 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 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55 Salt bridges: A:R.96 PGV.38: 26 residues within 4Å: Chain C: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, 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.39 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:I.60, C:F.84, C:F.91, C:F.201, C:I.208, C:I.208, C:T.211, 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

TGL.8: 17 residues within 4Å: Chain A: V.350, Y.379, F.418, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, F.32, S.35, S.36, L.39 Chain I: R.43 17 PLIP interactions: 1 interactions with chain I, 10 interactions with chain A, 6 interactions with chain B Salt bridges: I:R.43, B:H.24 Hydrophobic interactions: A:V.350, A:Y.379, A:F.418, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:F.430, B:F.32, B:F.32, B:L.39 Water bridges: B:G.8, B:F.9 TGL.50: 20 residues within 4Å: Chain A: W.334, G.343, F.414, A.415 Chain B: L.39, I.42, L.46, T.47, T.48, K.49 Chain D: R.70, T.72, E.74, W.75, V.78, M.83, I.86 Chain I: R.16 Ligands: EDO.70, DMU.73 18 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: D:E.74, D:W.75, D:V.78, D:I.86, B:L.39, B:I.42, B:L.46, B:T.47, B:K.49, A:W.334, A:W.334, A:W.334, A:F.414, A:F.414, A:A.415 Hydrogen bonds: D:W.75 Water bridges: D:E.74 Salt bridges: A:K.411 TGL.78: 23 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.113, F.393, F.400, I.472 Chain L: I.10, P.11, F.12, S.13, R.19, M.23, L.26, F.27, F.28 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:L.20, A:F.22, A:W.25, A:P.106, A:F.109, A:F.109, A:L.113, A:F.393, A:I.472, L:I.10, L:F.12, L:F.12, L:F.12, L:F.27, L:F.27, L:F.27, L:F.28, L:F.28

EDO.10: 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.11: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.57 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: T.484, V.485, D.486 Chain D: V.14 Chain M: I.1, T.2 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.8 Ligands: EDO.53 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: L.110 Ligands: EDO.44 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: H.503, E.506 Chain L: H.1 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: Y.19, M.71, P.72, I.75, G.76, L.105, S.157, L.195 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: Y.19, I.75, N.80, N.98, S.101, S.156, G.160, F.164 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: N.496, T.504, F.505, E.507 Chain F: W.73 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32 Ligand excluded by PLIP EDO.20: 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.61 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: V.485, D.486, L.487, T.488, T.489 Ligands: EDO.53 Ligand excluded by PLIP EDO.25: 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.26: 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.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.31: 2 residues within 4Å: Chain B: E.157 Ligands: EDO.43 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: Y.40 Chain I: A.24, V.27 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain B: L.135, F.206 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.31, EDO.47 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain A: L.7 Ligands: EDO.14, CHD.71 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: G.139, T.143, H.241 Chain G: W.16 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain C: H.1, H.68 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.43 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain C: N.123, P.124, L.125 Ligand excluded by PLIP EDO.51: 8 residues within 4Å: Chain A: L.495 Chain D: Y.8, A.9, L.10, P.11 Chain F: F.72, W.73 Ligands: EDO.53 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain D: P.11, D.23 Chain F: F.72, Q.80, R.81 Ligand excluded by PLIP EDO.53: 9 residues within 4Å: Chain A: T.488 Chain D: D.7, Y.8, L.10, P.11, S.12 Ligands: EDO.13, EDO.24, EDO.51 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain E: R.10, W.11, Y.14 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.11 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain F: A.1 Chain G: R.14, R.17 Ligands: PEK.37, CHD.62 Ligand excluded by PLIP EDO.60: 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.61: 5 residues within 4Å: Chain A: E.266 Chain F: N.66, S.67, T.68 Ligands: EDO.20 Ligand excluded by PLIP EDO.66: 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.67: 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.68: 5 residues within 4Å: Chain A: D.227 Chain B: G.177, R.178 Chain H: N.18, T.20 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain I: R.16, H.20 Ligands: TGL.50 Ligand excluded by PLIP EDO.79: 3 residues within 4Å: Chain C: P.11 Chain L: H.1, Y.2 Ligand excluded by PLIP

CUA.27: 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

PSC.28: 13 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, P.69 Chain I: L.17 12 PLIP interactions: 2 interactions with chain I, 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: I:L.17, B:I.41, B:I.41, B:V.61, B:I.64, B:P.69, A:F.321, A:F.321, A:A.325 Water bridges: I:A.14 Hydrogen bonds: B:D.57 Salt bridges: B:H.52

DMU.29: 9 residues within 4Å: Chain B: H.26, M.29, I.30, L.33, I.34, I.72, L.75, L.78, P.79 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.30, B:L.33, B:I.34 Hydrogen bonds: B:L.75 DMU.40: 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.42 8 PLIP interactions: 4 interactions with chain J, 4 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45, C:I.43 Hydrogen bonds: J:Y.45, C:N.36, C:S.37, C:S.37 DMU.42: 11 residues within 4Å: Chain A: L.110 Chain C: S.27, T.30, M.31, F.35 Chain J: S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.40 8 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: C:T.30, C:M.31, C:F.35, C:F.35, A:L.110, J:L.50 Water bridges: J:Y.45, J:Y.45 DMU.49: 7 residues within 4Å: Chain C: W.114, P.115, V.252, W.256, W.257, S.259 Ligands: CDL.64 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.252, C:W.256, C:W.256 Hydrogen bonds: C:W.257, C:S.259, C:S.259 Water bridges: C:W.114, C:W.114 DMU.65: 7 residues within 4Å: Chain C: L.29, W.32, M.38 Chain G: W.62, G.63, F.69 Ligands: PEK.36 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.29, C:W.32, G:F.69 Hydrogen bonds: G:G.63 DMU.72: 7 residues within 4Å: Chain D: L.91, W.95, H.98 Chain K: Y.26, Q.30, I.31, G.32 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain K Hydrophobic interactions: D:W.95 Salt bridges: D:H.98 Hydrogen bonds: K:Y.26, K:Q.30 Water bridges: K:Q.30, K:G.32 DMU.73: 8 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: TGL.50, DMU.75, DMU.76 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: D:I.86, K:W.24, K:W.24, K:V.25 DMU.74: 6 residues within 4Å: Chain A: I.453 Chain K: A.28, T.29, I.33, W.35 Ligands: DMU.75 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:W.35, A:I.453 Hydrogen bonds: K:I.33 Water bridges: K:Q.30, K:G.32 DMU.75: 6 residues within 4Å: Chain K: W.24, V.25, A.28 Ligands: DMU.73, DMU.74, DMU.76 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:W.24, K:A.28 DMU.76: 5 residues within 4Å: Chain K: T.18, F.19, A.22 Ligands: DMU.73, DMU.75 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:F.19, K:F.19 DMU.80: 11 residues within 4Å: Chain A: L.35, F.459 Chain D: W.95, Y.99 Chain L: F.36 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain L, 2 interactions with chain M, 1 interactions with chain A Hydrophobic interactions: D:W.95, L:F.36, M:L.27, A:L.35 Water bridges: D:Y.99, M:H.36

CHD.34: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.97, H.101 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.101 CHD.41: 5 residues within 4Å: Chain C: R.154, F.162, F.217, L.221 Chain J: F.1 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:F.162, C:F.162, C:F.217, C:L.221 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.62: 7 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.37, EDO.59 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 CHD.71: 8 residues within 4Å: Chain A: I.3, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 Ligands: EDO.44 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:Y.32, J:M.36, J:T.37 Hydrogen bonds: J:Y.32, J:Y.32, J:R.33 CHD.77: 7 residues within 4Å: Chain L: W.18, L.21, A.22 Chain M: K.13, E.14, I.17, V.21 9 PLIP interactions: 4 interactions with chain L, 5 interactions with chain M Hydrophobic interactions: L:W.18, L:W.18, M:K.13, M:E.14, M:I.17, M:I.17 Hydrogen bonds: L:A.22, M:E.14 Water bridges: L:N.16

PEK.35: 13 residues within 4Å: Chain A: V.193 Chain C: K.75, R.78, Y.79, I.82, L.83, V.89, T.93, F.96, W.238, F.242, V.245, F.249 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.82, C:I.82, C:L.83, C:V.89, C:V.89, C:F.96, C:F.96, C:W.238, C:V.245, C:F.249, C:F.249