SMTL ID : 7cp5.1

Bovine heart cytochrome c oxidase in a catalytic intermediate of E at 1.76 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

4 x HEA: HEME-A(Non-covalent)

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, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: TGL.77 36 PLIP interactions: 36 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:V.374, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:I.389, 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.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.8 40 PLIP interactions: 34 interactions with chain A, 5 interactions with chain B, 1 Ligand-Water interactions, 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: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 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240, A:H.240, A:H.376 Metal complexes: A:H.376, H2O.1 HEA.81: 34 residues within 4Å: Chain N: 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, 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: TGL.91 29 PLIP interactions: 29 interactions with chain N, Hydrophobic interactions: N:A.24, N:I.37, N:R.38, N:A.62, N:M.65, N:I.66, N:V.70, N:L.381, N:L.381, N:F.393, N:F.393, N:T.424 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:Y.371, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.82: 34 residues within 4Å: Chain N: 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 O: I.34, P.69, I.72, L.73 Ligands: PER.89 39 PLIP interactions: 5 interactions with chain O, 33 interactions with chain N, 1 Ligand-Water interactions, Hydrophobic interactions: O:I.34, O:I.34, O:P.69, O:I.72, O:L.73, N:W.236, N:V.243, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:T.316, N:V.320, N:F.348, N:I.356, N:I.356, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:T.316, N:D.369, N:D.369, N:R.438, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240, N:H.240, N:H.376 Metal complexes: N:H.376, H2O.62

2 x CU: COPPER (II) ION(Non-covalent)

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.7 CU.83: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: PER.89 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.69

2 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 MG.84: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.70, H2O.74, H2O.74

4 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:S.441 Water bridges: A:Q.43 NA.27: 3 residues within 4Å: Chain C: H.146, H.230, E.234 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.230, C:E.234 NA.85: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:Q.43 Water bridges: N:Q.43 NA.108: 3 residues within 4Å: Chain P: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.234

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

PGV.6: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16, L.19 13 PLIP interactions: 2 interactions with chain D, 3 interactions with chain M, 6 interactions with chain A, 2 interactions with chain K Hydrophobic interactions: D:A.81, D:F.84, M:P.12, M:Q.15, M:L.19, A:T.408, A:W.409, A:W.409, A:W.409, K:F.4, K:F.4 Hydrogen bonds: A:T.408 Water bridges: A:T.408 PGV.26: 30 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.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, F.91 Ligands: PEK.32 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.84, C:F.91, A:F.148, A:L.152, A:I.158, A:L.159, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.33: 22 residues within 4Å: Chain C: M.49, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, E.88, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: CDL.30 26 PLIP interactions: 24 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:W.56, C:I.60, C:F.84, C:I.208, C:I.208, 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.12, F:E.17 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.36: 6 residues within 4Å: Chain A: F.237 Chain C: T.93, W.97, Y.100, H.101 Ligands: CHD.29 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.237, C:T.93, C:W.97, C:W.97, C:W.97 Salt bridges: C:H.101 PGV.62: 5 residues within 4Å: Chain G: A.1 Chain P: T.93, W.97, H.101 Ligands: CHD.107 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: P:T.93, P:W.97, P:W.97, G:A.1 Salt bridges: P:H.101 PGV.86: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: T.77, A.81, F.84 Chain X: F.4, H.5 Chain Z: P.12, Q.15, A.16, L.19 11 PLIP interactions: 3 interactions with chain N, 2 interactions with chain Q, 2 interactions with chain X, 4 interactions with chain Z Hydrophobic interactions: N:T.408, N:W.409, N:I.412, Q:T.77, Q:F.84, X:F.4, X:F.4, Z:P.12, Z:P.12, Z:Q.15, Z:L.19 PGV.87: 29 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158 Chain P: 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, M.81, F.84, S.87, F.91 Ligands: PEK.112 18 PLIP interactions: 8 interactions with chain N, 10 interactions with chain P Hydrophobic interactions: N:F.148, N:L.152, N:I.158, P:A.22, P:T.26, P:T.51, P:W.55, P:W.55, P:W.55, P:W.56, P:F.84, P:F.91 Hydrogen bonds: N:R.96, N:R.96, N:M.97, P:W.55 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.113: 25 residues within 4Å: Chain P: M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, E.88, F.91, 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.110 25 PLIP interactions: 23 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:I.60, P:F.84, P:F.91, P:I.208, P:T.211, P:F.212, P:F.212 Hydrogen bonds: P:S.63, P:R.219, P:F.231, P:G.232 Water bridges: P:S.63, P:R.219, P:H.229, P:H.229, S:Q.12, S:E.17 Salt bridges: P:R.219, P:R.219, P:H.229

2 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.7: 14 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, L.68, P.69 Chain I: L.17 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:I.64, B:W.65, B:W.65, B:W.65, B:L.68, B:P.69, I:L.17, A:F.321, A:A.325 PSC.103: 15 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, M.45, H.52, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69 Ligands: DMU.102 12 PLIP interactions: 9 interactions with chain O, 3 interactions with chain N Hydrophobic interactions: O:I.41, O:I.41, O:M.56, O:W.65, O:W.65, O:L.68, O:P.69, N:F.321, N:F.321, N:A.325 Hydrogen bonds: O:D.57 Salt bridges: O:H.52

2 x PER: PEROXIDE ION(Non-covalent)

PER.8: 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) PER.89: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.82, CU.83 No protein-ligand interaction detected (PLIP)

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

EDO.9: 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.10: 7 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, R.56, H.94 Ligand excluded by PLIP EDO.11: 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.12: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.56 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: P.131, D.221, P.222 Ligand excluded by PLIP EDO.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: E.119, A.120 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: CHD.21 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: V.482, L.483, G.497, C.498 Chain D: S.5, Y.8 Ligand excluded by PLIP EDO.22: 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.23: 6 residues within 4Å: Chain B: M.146, E.147, M.148, V.214, P.215, L.216 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.38 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: G.139, T.143, H.241 Chain G: W.16 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.25, EDO.39 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.38 Ligand excluded by PLIP EDO.40: 10 residues within 4Å: Chain C: W.144, S.148, D.153, H.156 Chain F: A.1, S.2 Chain G: A.13, R.14, R.17 Ligands: EDO.57 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain C: F.249 Ligands: CDL.80 Ligand excluded by PLIP EDO.42: 1 residues within 4Å: Chain C: V.245 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain C: H.1, Q.2, H.68 Chain F: L.16 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain C: Q.66 Chain F: G.15 Chain J: Q.13 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain C: N.10, Q.66 Chain J: L.18, V.20, K.23 Ligands: EDO.67 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain A: T.488, L.495 Chain D: Y.8, A.9, L.10, S.12 Chain F: W.73 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain D: K.118, L.121, D.122, W.135, Y.137, N.140 Chain K: P.45 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain D: W.45, S.46, L.48, I.50, K.53 Ligands: EDO.54 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain E: Y.14, K.17, I.20, E.24 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain E: R.49, R.52, R.53 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain D: K.53 Chain E: L.89, N.90, G.93, I.94, S.95 Ligands: EDO.51 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.12 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain F: A.1 Chain G: R.14, R.17 Chain S: D.65 Ligands: EDO.40, CHD.61 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: 4 residues within 4Å: Chain C: F.223 Chain F: G.5, P.7 Chain J: N.3 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.63: 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.64: 6 residues within 4Å: Chain G: G.10, G.12, A.13, R.14, T.15 Chain N: Y.179 Ligand excluded by PLIP EDO.67: 6 residues within 4Å: Chain C: N.10, P.11 Chain J: G.17, L.18, P.19 Ligands: EDO.45 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain F: T.14 Chain J: Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.78: 4 residues within 4Å: Chain L: G.7, K.8, I.10, F.12 Ligand excluded by PLIP EDO.92: 6 residues within 4Å: Chain N: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.127 Ligand excluded by PLIP EDO.93: 9 residues within 4Å: Chain N: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain Q: Y.8 Ligands: EDO.125 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain N: K.265, T.489 Chain S: I.70, P.83, S.84 Ligand excluded by PLIP EDO.95: 5 residues within 4Å: Chain N: E.507 Chain P: T.3 Chain S: P.30, N.32, P.50 Ligand excluded by PLIP EDO.96: 7 residues within 4Å: Chain N: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain Z: I.1 Ligand excluded by PLIP EDO.97: 3 residues within 4Å: Chain N: P.131, D.221, P.222 Ligand excluded by PLIP EDO.98: 8 residues within 4Å: Chain N: K.265, E.266 Chain O: T.55 Chain S: N.66, T.68, I.70, S.84 Ligands: EDO.131 Ligand excluded by PLIP EDO.99: 6 residues within 4Å: Chain N: V.485, D.486, L.487, T.488, T.489 Ligands: EDO.125 Ligand excluded by PLIP EDO.100: 3 residues within 4Å: Chain N: L.136, A.137 Chain O: Q.103 Ligand excluded by PLIP EDO.104: 7 residues within 4Å: Chain N: Y.447 Chain O: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.105: 6 residues within 4Å: Chain N: D.227 Chain O: G.177, R.178 Chain P: T.107 Chain U: N.18, T.20 Ligand excluded by PLIP EDO.106: 2 residues within 4Å: Chain O: M.122, F.206 Ligand excluded by PLIP EDO.116: 4 residues within 4Å: Chain P: T.143, H.146, H.147 Chain T: T.11 Ligand excluded by PLIP EDO.117: 4 residues within 4Å: Chain P: L.136, G.139, T.143 Ligands: CDL.132 Ligand excluded by PLIP EDO.118: 1 residues within 4Å: Chain P: H.241 Ligand excluded by PLIP EDO.119: 5 residues within 4Å: Chain N: P.222, A.223 Chain O: G.177 Chain P: E.109 Chain U: W.62 Ligand excluded by PLIP EDO.120: 8 residues within 4Å: Chain P: W.144, S.148, H.156 Chain S: A.1, S.2 Chain T: A.13, R.14, R.17 Ligand excluded by PLIP EDO.121: 3 residues within 4Å: Chain P: Q.2, H.68 Chain S: L.16 Ligand excluded by PLIP EDO.122: 5 residues within 4Å: Chain P: N.10, P.11 Chain W: G.17, P.19 Ligands: EDO.144 Ligand excluded by PLIP EDO.123: 2 residues within 4Å: Chain P: N.123, L.125 Ligand excluded by PLIP EDO.125: 8 residues within 4Å: Chain N: T.488, L.495 Chain Q: Y.8, L.10, P.11, S.12 Ligands: EDO.93, EDO.99 Ligand excluded by PLIP EDO.127: 7 residues within 4Å: Chain N: T.489, T.490 Chain S: S.67, T.68, V.69, W.71 Ligands: EDO.92 Ligand excluded by PLIP EDO.128: 6 residues within 4Å: Chain N: Y.510 Chain S: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.129: 4 residues within 4Å: Chain Q: D.23 Chain S: F.72, Q.80, R.81 Ligand excluded by PLIP EDO.130: 3 residues within 4Å: Chain P: H.229 Chain S: D.9, E.17 Ligand excluded by PLIP EDO.131: 5 residues within 4Å: Chain N: E.266 Chain S: N.66, S.67, T.68 Ligands: EDO.98 Ligand excluded by PLIP EDO.133: 6 residues within 4Å: Chain P: G.118 Chain T: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.134: 5 residues within 4Å: Chain P: F.33 Chain T: K.58, P.59, F.60, S.61 Ligand excluded by PLIP EDO.135: 4 residues within 4Å: Chain T: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.138: 4 residues within 4Å: Chain S: T.14 Chain W: Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.144: 5 residues within 4Å: Chain N: Y.502 Chain P: P.11 Chain Y: H.1, Y.2 Ligands: EDO.122 Ligand excluded by PLIP EDO.145: 7 residues within 4Å: Chain N: V.118, E.119 Chain W: A.53, S.54, F.55, P.56 Chain Y: K.45 Ligand excluded by PLIP

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.19: 15 residues within 4Å: Chain A: F.346, V.350, 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: R.43 16 PLIP interactions: 8 interactions with chain B, 2 interactions with chain I, 6 interactions with chain A Hydrophobic interactions: B:L.7, B:L.28, B:V.31, B:F.32, B:F.32, A:F.346, A:V.350, A:F.426, A:H.429, 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.47: 19 residues within 4Å: Chain A: W.334, L.342, G.343, F.414, A.415, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.70, S.71, T.72, E.74, W.75 Chain I: R.16, H.20 12 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, B:K.49, A:W.334, A:W.334, A:W.334, A:F.414, A:F.418, D:W.75 Hydrogen bonds: D:T.72, D:E.74, D:W.75 TGL.77: 26 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.102, P.106, 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, F.27, F.28, S.30 Ligands: HEA.1 20 PLIP interactions: 12 interactions with chain A, 8 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:F.102, 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.28, L:F.28 TGL.88: 19 residues within 4Å: Chain N: F.346, T.354, Y.379, F.418, V.419, N.422, M.423, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, L.28, V.31, F.32, S.35 Chain V: K.42, R.43 13 PLIP interactions: 6 interactions with chain O, 6 interactions with chain N, 1 interactions with chain V Hydrophobic interactions: O:L.7, O:V.31, O:F.32, O:F.32, N:T.354, N:F.418, N:F.426, N:F.426, N:F.426, N:F.430 Water bridges: O:G.8 Salt bridges: O:H.24, V:R.43 TGL.90: 17 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, F.414, A.415, V.419 Chain O: L.39, I.42, L.46, T.47 Chain Q: E.74, W.75, V.78, V.79, M.83, I.86 13 PLIP interactions: 4 interactions with chain O, 5 interactions with chain Q, 4 interactions with chain N Hydrophobic interactions: O:L.39, O:I.42, O:L.46, O:T.47, Q:E.74, Q:W.75, Q:V.78, Q:V.79, Q:I.86, N:W.334, N:W.334, N:W.334, N:V.419 TGL.91: 24 residues within 4Å: Chain N: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, F.109, L.110, L.113, F.393, F.400, S.401, I.472 Chain Y: N.9, I.10, P.11, F.12, M.23, F.27, F.28, I.38 Ligands: HEA.81 21 PLIP interactions: 8 interactions with chain Y, 13 interactions with chain N Hydrophobic interactions: Y:I.10, Y:F.12, Y:F.12, Y:F.27, Y:F.27, Y:F.28, Y:F.28, Y:I.38, N:L.18, N:L.20, N:L.20, N:F.22, N:W.25, N:W.25, N:W.25, N:W.81, N:F.109, N:F.109, N:L.113, N:I.472, N:I.472

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

CUA.20: 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 CUA.101: 6 residues within 4Å: Chain O: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.196, O:E.198, O:C.200, O:C.200, O:H.204

6 x CHD: CHOLIC ACID(Non-covalent)

CHD.21: 13 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: EDO.16, PEK.114 13 PLIP interactions: 7 interactions with chain T, 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: T:F.21, A:M.271, A:W.275, A:W.275, A:W.275 Water bridges: T:R.14, T:R.17, T:R.17, T:R.17 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:E.62, B:T.63 CHD.29: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.97, H.101 Chain P: L.125 Ligands: PGV.36 12 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C, 1 interactions with chain P Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.97, P:L.125 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.61: 13 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: E.62, T.63, T.66 Ligands: PEK.34, EDO.57 14 PLIP interactions: 4 interactions with chain N, 4 interactions with chain O, 6 interactions with chain G Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, O:T.66, G:F.18, G:F.21 Hydrogen bonds: O:E.62, O:T.63 Water bridges: O:T.63, G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.76: 5 residues within 4Å: Chain L: W.18, L.21 Chain M: E.14, I.17, V.21 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: L:W.18, M:I.17, M:V.21 Water bridges: M:E.14 CHD.107: 10 residues within 4Å: Chain C: L.125 Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.97, H.101 Ligands: PGV.62, CDL.80 11 PLIP interactions: 7 interactions with chain N, 3 interactions with chain P, 1 interactions with chain C Hydrophobic interactions: N:W.288, N:Y.304, P:W.97, C:L.125 Hydrogen bonds: N:T.301, P:W.97 Water bridges: N:D.298, N:D.300, N:T.301 Salt bridges: N:H.233, P:H.101 CHD.143: 5 residues within 4Å: Chain Y: W.18, L.21, A.22 Chain Z: E.14, I.17 6 PLIP interactions: 3 interactions with chain Z, 3 interactions with chain Y Hydrophobic interactions: Z:I.17, Y:W.18, Y:W.18 Hydrogen bonds: Z:E.14, Y:A.22 Water bridges: Z:S.11

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

DMU.28: 5 residues within 4Å: Chain C: W.32, M.38 Chain G: W.62, F.69 Ligands: PEK.32 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:F.69, C:W.32, C:W.32 DMU.35: 11 residues within 4Å: Chain A: L.110, L.145 Chain C: S.27, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 10 PLIP interactions: 2 interactions with chain A, 5 interactions with chain J, 3 interactions with chain C Hydrophobic interactions: A:L.110, A:L.145, J:L.50, C:M.31, C:F.35, C:F.35 Hydrogen bonds: J:Y.45, J:Y.45, J:Y.48, J:Y.48 DMU.46: 4 residues within 4Å: Chain D: L.91, I.94, H.98 Ligands: DMU.79 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.91, D:I.94 DMU.48: 2 residues within 4Å: Chain D: W.75, V.79 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.75, D:W.75 DMU.66: 6 residues within 4Å: Chain C: I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45 Hydrogen bonds: J:Y.45 DMU.69: 5 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24 Ligands: DMU.70 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:V.21, K:W.24, K:W.24, K:W.24, D:I.86 DMU.70: 5 residues within 4Å: Chain K: W.24, A.28, T.29 Ligands: DMU.69, DMU.73 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:W.24, K:A.28, K:T.29 DMU.71: 2 residues within 4Å: Chain K: A.28, W.35 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:W.35 DMU.72: 4 residues within 4Å: Chain D: L.91 Chain K: S.15, F.19 Ligands: DMU.74 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:F.19, K:F.19, D:L.91 DMU.73: 1 residues within 4Å: Ligands: DMU.70 No protein-ligand interaction detected (PLIP) DMU.74: 3 residues within 4Å: Chain D: L.91 Chain K: Y.26 Ligands: DMU.72 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: D:L.91, K:Y.26, K:Y.26, K:Y.26 DMU.75: 9 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: A.34, F.37, I.38, R.40, H.41, L.44, K.45 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:I.38, L:H.41 Hydrogen bonds: L:R.40, L:R.40, L:H.41, L:L.44 Salt bridges: L:R.40, L:H.41 DMU.79: 12 residues within 4Å: Chain D: W.95, Y.99 Chain L: F.36 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 Ligands: DMU.46 9 PLIP interactions: 4 interactions with chain M, 1 interactions with chain L, 4 interactions with chain D Hydrophobic interactions: M:A.30, M:L.34, L:F.36, D:W.95 Hydrogen bonds: M:W.32 Water bridges: M:H.36, D:Y.99, D:Y.99, D:Y.99 DMU.102: 9 residues within 4Å: Chain O: H.26, M.29, I.30, L.33, I.34, L.37, I.72, L.75 Ligands: PSC.103 7 PLIP interactions: 7 interactions with chain O Hydrophobic interactions: O:I.30, O:L.33, O:I.34, O:L.37, O:I.72, O:L.75 Hydrogen bonds: O:H.26 DMU.109: 6 residues within 4Å: Chain P: L.29, W.32, M.38 Chain T: G.63, F.69 Ligands: PEK.112 3 PLIP interactions: 3 interactions with chain P Hydrophobic interactions: P:L.29, P:W.32, P:W.32 DMU.115: 9 residues within 4Å: Chain N: L.110, A.114 Chain P: S.27, T.30, M.31, F.35 Chain W: S.46, C.49, W.52 5 PLIP interactions: 2 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: N:L.110, N:A.114, P:T.30, P:F.35, P:F.35 DMU.124: 3 residues within 4Å: Chain Q: L.91, W.95, H.98 No protein-ligand interaction detected (PLIP) DMU.137: 6 residues within 4Å: Chain P: I.43 Chain W: T.37, L.38, G.41, G.42, Y.45 5 PLIP interactions: 1 interactions with chain P, 4 interactions with chain W Hydrophobic interactions: P:I.43, W:Y.45, W:Y.45 Hydrogen bonds: W:Y.45, W:Y.45 DMU.139: 5 residues within 4Å: Chain N: M.423 Chain Q: I.86 Chain X: W.24, V.25 Ligands: DMU.141 4 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain X Hydrophobic interactions: Q:I.86, X:W.24, X:W.24, X:V.25 DMU.140: 4 residues within 4Å: Chain N: I.453 Chain X: A.28, T.29, W.35 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain X Hydrophobic interactions: N:I.453, X:T.29, X:W.35, X:W.35 DMU.141: 3 residues within 4Å: Chain X: A.28, T.29 Ligands: DMU.139 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:A.28, X:T.29 DMU.142: 2 residues within 4Å: Chain X: F.19, A.22 3 PLIP interactions: 3 interactions with chain X Hydrophobic interactions: X:F.19, X:F.19, X:A.22 DMU.146: 12 residues within 4Å: Chain N: F.459 Chain Q: L.92, W.95, Y.99 Chain Z: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 10 PLIP interactions: 4 interactions with chain Z, 2 interactions with chain N, 4 interactions with chain Q Hydrophobic interactions: Z:L.27, Z:L.27, Z:A.30, N:F.459, N:F.459, Q:L.92, Q:W.95, Q:W.95 Water bridges: Z:H.36, Q:Y.99

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.30: 16 residues within 4Å: Chain C: M.49, L.50, Y.53, W.56, R.57, I.60, V.169, T.172, L.173, I.207, S.210, T.211, I.214, V.215, F.218 Ligands: PGV.33 16 PLIP interactions: 16 interactions with chain C 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:V.169, C:T.172, C:L.173, C:I.207, C:I.214, C:I.214, C:F.218 Hydrogen bonds: C:Y.53 CDL.80: 22 residues within 4Å: Chain C: T.132, S.133, V.140, V.252 Chain G: L.23, S.27, L.30, N.34, H.38 Chain N: F.282, L.283, I.286, Y.304, S.307, I.311 Chain O: A.70, L.73, A.77, L.81 Ligands: PEK.34, EDO.41, CHD.107 15 PLIP interactions: 1 interactions with chain C, 3 interactions with chain O, 4 interactions with chain G, 7 interactions with chain N Hydrophobic interactions: C:T.132, O:L.73, O:A.77, O:L.81, G:L.23, G:L.23, G:L.30, G:L.30, N:F.282, N:F.282, N:L.283, N:I.286, N:Y.304, N:I.311, N:I.311 CDL.110: 15 residues within 4Å: Chain P: M.49, L.50, M.52, Y.53, W.56, R.57, I.60, T.172, I.207, T.211, I.214, V.215, F.218 Chain W: L.31 Ligands: PGV.113 18 PLIP interactions: 18 interactions with chain P Hydrophobic interactions: P:L.50, P:Y.53, P:Y.53, P:Y.53, P:Y.53, P:W.56, P:W.56, P:R.57, P:R.57, P:T.172, P:I.207, P:T.211, P:I.214, P:V.215, P:F.218, P:F.218, P:F.218 Hydrogen bonds: P:Y.53 CDL.132: 26 residues within 4Å: Chain A: F.282, L.283, I.286, Y.304, S.307, I.311, I.314 Chain B: A.70, I.74, A.77, L.81 Chain P: L.125, L.129, T.132, S.133, L.136, V.140 Chain T: L.23, A.24, S.27, L.30, C.31, N.34, H.38 Ligands: PEK.114, EDO.117 18 PLIP interactions: 7 interactions with chain A, 3 interactions with chain P, 4 interactions with chain B, 4 interactions with chain T Hydrophobic interactions: A:F.282, A:F.282, A:L.283, A:I.286, A:Y.304, A:I.311, A:I.314, P:L.129, P:T.132, P:L.136, B:I.74, B:I.74, B:A.77, B:L.81, T:L.23, T:L.23, T:L.30, T:L.30

6 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.31: 10 residues within 4Å: Chain C: Y.79, L.83, V.89, T.93, F.96, W.238, F.242, V.245, F.249 Chain T: S.2 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.79, C:L.83, C:V.89, C:F.96, C:F.96, C:W.238, C:W.238, C:V.245, C:F.249, C:F.249 PEK.32: 28 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: L.29, W.32, T.172, Q.175, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.26, DMU.28 20 PLIP interactions: 8 interactions with chain C, 8 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: C:L.29, C:W.32, C:T.172, C:Q.175, C:I.186, C:F.201, C:F.201, G:W.62, G:F.69, A:V.155, A:A.203, A:L.210, A:L.215 Hydrogen bonds: C:I.186, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.34: 10 residues within 4Å: Chain C: Q.159, I.163, T.166, Y.170 Chain G: F.21, G.22 Chain N: W.275, S.279 Ligands: CHD.61, CDL.80 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain N, 1 interactions with chain G Hydrophobic interactions: C:I.163, C:T.166, C:Y.170, C:Y.170, C:Y.170, N:W.275, G:F.21 PEK.111: 9 residues within 4Å: Chain P: R.78, I.82, V.89, T.93, F.96, W.238, F.242, V.245, F.249 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:I.82, P:V.89, P:F.96, P:F.96, P:W.238, P:V.245 PEK.112: 27 residues within 4Å: Chain N: H.151, V.155, A.203, T.207, L.210, L.215 Chain P: W.32, F.33, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.87, DMU.109 20 PLIP interactions: 8 interactions with chain P, 8 interactions with chain T, 4 interactions with chain N Hydrophobic interactions: P:W.32, P:F.33, P:A.176, P:I.186, P:F.201, P:F.201, P:F.201, T:W.62, T:F.69, N:V.155, N:A.203, N:L.210, N:L.215 Hydrogen bonds: P:I.186, T:T.68, T:F.70, T:N.76, T:N.76 Water bridges: T:F.69, T:F.69 PEK.114: 11 residues within 4Å: Chain A: W.275, I.311 Chain B: T.66 Chain P: I.163, T.166, Y.170 Chain T: F.21, L.25, W.36 Ligands: CHD.21, CDL.132 8 PLIP interactions: 2 interactions with chain A, 2 interactions with chain T, 3 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: A:W.275, A:I.311, T:L.25, T:W.36, P:Y.170, P:Y.170, P:Y.170, B:T.66

2 x ZN: ZINC ION(Non-covalent)

ZN.55: 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 ZN.126: 4 residues within 4Å: Chain S: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.65: 4 residues within 4Å: Chain H: R.21, Q.25, L.28, R.32 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:Q.25, H:Q.25, H:Q.25 Water bridges: H:R.21, H:R.21 Salt bridges: H:R.21, H:R.32 PO4.136: 4 residues within 4Å: Chain U: R.21, Q.25, L.28, R.32 6 PLIP interactions: 6 interactions with chain U Hydrogen bonds: U:Q.25, U:Q.25 Water bridges: U:R.21, U:R.21 Salt bridges: U:R.21, U:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates. J.Biol.Chem. (2021)

Release Date

2021-07-21

Peptides

Cytochrome c oxidase subunit 1: AN
Cytochrome c oxidase subunit 2: BO
Cytochrome c oxidase subunit 3: CP
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: DQ
Cytochrome c oxidase subunit 5A, mitochondrial: ER
Cytochrome c oxidase subunit 5B, mitochondrial: FS
Cytochrome c oxidase subunit 6A2, mitochondrial: GT
Cytochrome c oxidase subunit 6B1: HU
Cytochrome c oxidase subunit 6C: IV
Cytochrome c oxidase subunit 7A1, mitochondrial: JW
Cytochrome c oxidase subunit 7B, mitochondrial: KX
Cytochrome c oxidase subunit 7C, mitochondrial: LY
Cytochrome c oxidase subunit 8B, mitochondrial: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
N

B
B

O
O

C
C

P
P

D
D

Q
Q

E
E

R
R

F
F

S
S

G
G

T
T

H
H

U
U

I
I

V
V

J
J

W
W

K
K

X
X

L
L

Y
Y

M
M

Z
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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