SMTL ID : 7w3e.2 (1 other biounit)

Bovine cytochrome c oxidese in CN-bound fully reduced state at 50 K

HEA.1: 35 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, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425, 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, 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: 30 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, V.320, G.352, 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 34 PLIP interactions: 5 interactions with chain B, 29 interactions with chain A, Hydrophobic interactions: B:I.34, B:I.34, B:P.69, B:I.72, B:L.73, 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:I.356, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381 Hydrogen bonds: A:W.126 Water bridges: A:Y.244, A:T.316, A:D.369, A:D.369 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240, A:H.240 Metal complexes: A:H.376

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

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.13, H2O.13, H2O.14

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:Q.43 Water bridges: A:Q.43 NA.25: 3 residues within 4Å: Chain C: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.234

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)

PGV.7: 32 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, V.155, P.200 Chain C: H.7, V.9, G.18, S.21, 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.27 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:F.148, A:L.152, A:V.155, A:P.200, C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.91 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55 Water bridges: A:A.93, C:M.81 Salt bridges: A:R.96 PGV.29: 24 residues within 4Å: Chain C: M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, E.88, L.204, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 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.84, C:L.204, 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.11, F:E.16 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.30: 10 residues within 4Å: Chain A: F.237, W.288 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.18 Ligands: CHD.24 7 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: A:F.237, A:W.288, C:T.93, C:W.97, C:W.97 Water bridges: B:R.178, H:N.18 PGV.40: 15 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.77, A.81, F.84 Chain K: F.4, H.5 Chain M: P.5, P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 4 interactions with chain K, 5 interactions with chain M, 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: K:F.4, K:F.4, M:P.12, M:Q.15, M:A.16, M:L.19, D:A.81, D:F.84, D:F.84, D:F.84, A:W.409 Water bridges: K:F.4, M:A.6, A:T.404 Salt bridges: K:H.5

EDO.8: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.44 Ligand excluded by PLIP EDO.9: 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.10: 7 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.29, N.31, P.49, R.55 Ligands: EDO.48 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, W.104 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.14: 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.15: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.69, P.82, S.83 Ligand excluded by PLIP EDO.20: 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.21: 3 residues within 4Å: Chain B: T.125, L.135, F.206 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: Q.103, W.104, Y.105, Y.121, N.203 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: E.157 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.23 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain C: Q.2, H.68 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain A: L.495 Chain D: Y.8, A.9, L.10, P.11 Chain F: F.71, W.72 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain E: Y.13, K.16, I.19, E.23 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.66, T.67, V.68, W.70 Ligands: EDO.8 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain A: Y.510 Chain F: P.35, K.36, T.38, N.46, L.47 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain F: F.71, Q.79, R.80, P.82 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain C: P.71, H.229 Chain F: D.8, E.16 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain A: Y.510 Chain F: N.31, P.35, P.49, R.55 Ligands: EDO.10 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain F: A.23, Q.27, D.28, I.32, L.33 Ligand excluded by PLIP EDO.50: 1 residues within 4Å: Chain F: H.93 Ligand excluded by PLIP EDO.53: 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.54: 4 residues within 4Å: Chain G: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.55: 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.62: 3 residues within 4Å: Chain C: P.11 Chain L: H.1, Y.2 Ligand excluded by PLIP

TGL.16: 16 residues within 4Å: Chain A: T.354, 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, L.39 Chain I: R.43 15 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:T.354, A:N.422, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, B:L.7, B:V.31, B:F.32, B:F.32 Water bridges: B:G.8, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.17: 20 residues within 4Å: Chain A: W.334, L.342, F.346, K.411, F.414, A.415 Chain B: L.39, I.42, S.43, L.46, T.47 Chain D: R.70, T.72, E.74, W.75, V.78, M.83, I.86 Chain I: R.16, H.20 21 PLIP interactions: 4 interactions with chain B, 8 interactions with chain D, 8 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.39, B:I.42, B:L.46, B:T.47, D:W.75, D:V.78, D:V.78, D:I.86, A:W.334, A:W.334, A:L.342, A:F.346, A:K.411, A:F.414, A:F.414, I:R.16 Hydrogen bonds: D:T.72, D:E.74, D:W.75 Water bridges: D:T.72 Salt bridges: A:K.411

CUA.18: 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.19: 19 residues within 4Å: Chain A: F.268, F.321, A.325, H.328 Chain B: I.41, H.52, M.56, D.57, E.60, V.61, W.65, L.68, P.69 Chain E: D.3, F.6, L.36 Chain I: R.10, A.14, L.17 16 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A, 2 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: B:I.41, B:M.56, B:V.61, B:W.65, B:L.68, B:L.68, B:P.69, A:F.268, A:F.321, A:F.321, A:A.325, I:L.17 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, E:D.3 pi-Cation interactions: E:F.6

CHD.24: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Ligands: PGV.30 10 PLIP interactions: 7 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.298, A:D.300, A:T.301 Salt bridges: A:H.233, C:H.101 CHD.32: 6 residues within 4Å: Chain C: R.154, Q.159, F.162, F.217, L.221 Chain J: F.1 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:F.162, C:F.162, C:F.162, C:F.217, C:L.221, J:F.1 Water bridges: C:Q.159 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.57: 7 residues within 4Å: Chain A: L.7, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:M.36, J:T.37 Hydrogen bonds: J:Y.32, J:Y.32, J:R.33

PEK.26: 8 residues within 4Å: Chain C: I.82, V.89, T.93, F.96, W.238, V.245, V.246, F.249 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.82, C:V.89, C:F.96, C:F.96, C:W.238, C:W.238, C:V.245, C:V.246 PEK.27: 28 residues within 4Å: Chain A: H.151, V.155, A.203, L.210, L.215 Chain C: W.32, F.33, T.172, Q.175, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203, I.207 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 22 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A, 9 interactions with chain G Hydrophobic interactions: C:W.32, C:F.33, C:Q.175, C:I.186, C:F.201, C:F.201, C:F.201, C:I.207, A:V.155, A:A.203, A:L.210, A:L.215, G:W.62, G:F.69 Hydrogen bonds: C:I.186, G:T.68, G:F.70, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.28: 8 residues within 4Å: Chain C: I.163, T.166, L.167, Y.170 Chain G: R.17, F.21, L.25 Ligands: CDL.52 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:T.166, C:L.167, C:Y.170, C:Y.170, C:Y.170, G:F.21, G:L.25 PEK.51: 2 residues within 4Å: Chain G: G.6 Ligands: CDL.52 No protein-ligand interaction detected (PLIP)

CDL.31: 19 residues within 4Å: Chain C: T.46, M.49, L.50, Y.53, W.56, R.57, I.60, R.61, V.169, T.172, I.207, S.210, T.211, I.214, V.215, F.218, K.222 Chain J: F.12, L.31 19 PLIP interactions: 2 interactions with chain J, 17 interactions with chain C Hydrophobic interactions: J:L.31, J:L.31, C:T.46, C:M.49, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:I.60, C:V.169, C:T.172, C:I.207, C:I.214, C:V.215, C:F.218 Hydrogen bonds: C:Y.53 Water bridges: C:R.57 Salt bridges: C:R.61 CDL.52: 14 residues within 4Å: Chain C: N.123, L.125, L.129, L.136, V.140 Chain G: L.23, S.27, L.30, L.33, N.34, L.37, H.38 Ligands: PEK.28, PEK.51 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: C:L.136, G:L.23, G:L.30, G:L.30, G:N.34, G:L.37 Hydrogen bonds: C:N.123, G:N.34 Salt bridges: G:H.38 CDL.61: 21 residues within 4Å: Chain A: F.2, I.3, W.6, L.7, T.17, L.18, L.20, L.21, F.22, W.25, P.106, F.400 Chain L: I.10, P.11, F.12, S.13, R.19, M.24, F.27, F.28, A.34 24 PLIP interactions: 12 interactions with chain L, 12 interactions with chain A Hydrophobic interactions: 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, L:A.34, A:F.2, A:F.2, A:W.6, A:L.7, A:L.18, A:L.20, A:L.21, A:W.25, A:W.25, A:W.25 Hydrogen bonds: L:S.13 Salt bridges: L:R.19 Water bridges: A:F.2, A:I.3

DMU.33: 12 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.34, DMU.35 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain J Hydrophobic interactions: C:T.39, J:L.38, J:Y.45, J:Y.45, J:Y.45 Hydrogen bonds: C:N.36, C:N.36, C:S.37, C:S.37, C:S.37, J:Y.45 DMU.34: 6 residues within 4Å: Chain C: N.36, S.37, M.38, T.39 Ligands: DMU.33, DMU.39 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:T.39 Hydrogen bonds: C:N.36, C:S.37, C:M.38, C:T.39, G:S.61 DMU.35: 12 residues within 4Å: Chain A: L.110, A.114, L.145 Chain C: S.27, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, W.52 Ligands: DMU.33 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 2 interactions with chain J Hydrophobic interactions: C:M.31, C:F.35, C:F.35, A:L.110, A:A.114, A:L.145 Hydrogen bonds: J:Y.45, J:Y.45 DMU.38: 6 residues within 4Å: Chain C: W.114, P.115, V.252, W.256, W.257, S.259 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.252, C:W.256, C:W.256 Hydrogen bonds: C:W.114, C:W.257 Water bridges: C:W.114, C:S.259, C:S.259 DMU.39: 7 residues within 4Å: Chain C: L.29, W.32, M.38 Chain G: W.62, G.63, F.69 Ligands: DMU.34 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.29, C:W.32, C:W.32, G:F.69 Hydrogen bonds: G:G.63 DMU.58: 6 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: DMU.59 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:W.24, K:W.24, K:W.24, K:V.25, D:I.86 Water bridges: K:A.22 DMU.59: 6 residues within 4Å: Chain K: W.24, V.25, A.28, Q.30 Ligands: DMU.58, DMU.60 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:W.24, K:V.25, K:A.28 DMU.60: 5 residues within 4Å: Chain A: I.453 Chain K: A.28, T.29, W.35 Ligands: DMU.59 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain K Hydrophobic interactions: A:I.453, K:T.29, K:W.35, K:W.35, K:W.35 DMU.63: 13 residues within 4Å: Chain A: L.35, F.459, L.462 Chain D: L.92, W.95, Y.99 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 11 PLIP interactions: 3 interactions with chain M, 5 interactions with chain D, 3 interactions with chain A