SMTL ID : 7thu.1

Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

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

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.83: 3 residues within 4Å: Chain N: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.9, H2O.9, H2O.12 MG.84: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.37, H2O.38, H2O.39

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

NA.3: 4 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:Q.43 Water bridges: A:Q.43 NA.85: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:S.441

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

PGV.4: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: T.10, P.12, Q.15 9 PLIP interactions: 2 interactions with chain K, 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: K:F.9, K:F.9, A:T.408, A:W.409, A:W.409, D:F.87, D:F.87 Hydrogen bonds: A:N.406, A:W.409 PGV.5: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, H.151, L.152, V.155 Chain C: H.9, V.11, G.20, A.24, 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 Ligands: PEK.32, PGV.34 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, A:L.152, A:V.155 Hydrogen bonds: C:E.64, A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.34: 25 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, 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: PGV.5, DMU.30, CDL.35 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: 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: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.87: 24 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, L.152 Chain P: H.9, V.11, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, S.89, E.90, F.93 Ligands: PEK.110 12 PLIP interactions: 7 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:A.24, P:T.28, P:W.57, P:W.57, P:W.57, P:W.58, P:F.93, N:L.152 Hydrogen bonds: N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.98: 9 residues within 4Å: Chain G: A.1 Chain N: W.288, D.298 Chain P: T.95, W.99, Y.102, H.103, A.107 Ligands: CHD.109 11 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O, 6 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: N:W.288, P:T.95, P:W.99, P:W.99, P:W.99, P:Y.102, G:A.1 Hydrogen bonds: N:D.298 Water bridges: N:D.298, O:R.178 Salt bridges: P:H.103 PGV.112: 20 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, 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 28 PLIP interactions: 26 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:I.210, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:T.66, P:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:H.231, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.131: 15 residues within 4Å: Chain A: W.288, G.296, M.297, D.298, Y.304 Chain B: R.178 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain T: A.1, S.2 Ligands: CHD.31, CDL.132 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain T, 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, T:A.1, C:T.95, C:W.99, C:W.99, C:W.99 Hydrogen bonds: A:D.298, A:D.298, B:R.178 Water bridges: A:T.301 PGV.148: 22 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, E.474, S.478, R.480 Chain Q: T.80, A.84, F.87, F.88 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.5, A.6, T.10, P.12, Q.15, A.16 Ligands: EDO.149 14 PLIP interactions: 4 interactions with chain Z, 6 interactions with chain N, 3 interactions with chain Q, 1 interactions with chain X Hydrophobic interactions: Z:P.12, Z:A.16, N:T.408, N:W.409, N:I.412, Q:A.84, Q:F.87, Q:F.88, X:F.9 Hydrogen bonds: Z:A.3 Water bridges: Z:A.6, N:T.404, N:T.404 Salt bridges: N:R.480

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

HEA.6: 31 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, 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, L.73 35 PLIP interactions: 31 interactions with chain A, 4 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:L.353, A:I.356, A:L.358, 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:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376 HEA.7: 36 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, F.393, M.417, V.421, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: 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:F.393, A:V.421, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:Y.371, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438 Salt bridges: A:R.438, A:R.439 Metal complexes: A:H.61, A:H.378 HEA.88: 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.321, 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 35 PLIP interactions: 30 interactions with chain N, 5 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:F.321, N:F.348, N:L.353, N:I.356, N:I.356, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, O:I.34, O:I.34, O:P.69, O:I.72, O:L.73 Hydrogen bonds: N:Y.244, N:Y.244, N:D.364 Water bridges: N:D.369, N:D.369, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 Metal complexes: N:H.376 HEA.89: 35 residues within 4Å: Chain N: 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, F.425, Q.428, R.438, R.439, Y.440, S.461, V.465, M.468 33 PLIP interactions: 33 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:F.377, N:L.381, N:L.381, N:V.386, N:F.393, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:Y.54, N:Y.54, N:W.126, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:H.61 Metal complexes: N:H.61, N:H.378

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

EDO.8: 8 residues within 4Å: Chain A: L.483, T.484, V.485, W.494, G.497, C.498 Chain D: Y.11 Ligands: EDO.13 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: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.62 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: W.334, S.335, P.336, D.407, K.411 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: V.482, L.483, G.497, C.498 Chain D: S.8, Y.11 Ligands: EDO.8 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: E.266, P.267, G.269, Y.270 Chain F: S.67 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: G.269, M.271, G.272 Chain B: A.58, E.62 Ligands: CHD.22 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, H.94 Ligand excluded by PLIP EDO.19: 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.20: 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.23: 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.24: 4 residues within 4Å: Chain A: L.136, A.137 Chain B: D.158, V.159 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: M.146, E.147, P.215, L.216 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: H.22, F.23, H.26, P.79, R.82 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: S.94, L.95, Y.113, M.148, F.219 Chain H: Q.12 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: K.217, Y.218, K.221 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: N.92, P.93 Chain H: Q.12, T.13, A.14, P.15 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain C: W.146, S.150, H.158 Chain F: A.1 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain C: H.243, V.247 Ligands: EDO.39 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain C: H.243 Ligands: EDO.38, PEK.44, DMU.64 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain C: I.45, T.48 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.46: 7 residues within 4Å: Chain D: W.48, S.49, L.51, S.52, I.53, K.56 Ligands: EDO.56 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain D: P.25, D.26, V.27, A.28, K.63 Chain E: R.30 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain D: E.144, W.145 Chain K: T.49 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain D: A.28, V.30, K.31, L.33, L.62 Ligand excluded by PLIP EDO.50: 2 residues within 4Å: Chain D: H.101 Chain K: I.36 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: K.121, L.124, D.125, W.138, N.143 Ligand excluded by PLIP EDO.52: 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.54: 4 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligands: EDO.59 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain D: K.56 Chain E: L.93, N.94, G.97, I.98, S.99 Ligands: EDO.46 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain E: Y.82, P.83, E.102 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain C: H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain E: E.28 Chain F: R.81 Ligands: EDO.54 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.10 Ligand excluded by PLIP EDO.63: 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: 3 residues within 4Å: Chain G: W.62, F.69 Ligands: DMU.30 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain G: P.59, D.64, G.65, N.66 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain G: D.7 Chain P: Y.81 Ligands: DMU.64 Ligand excluded by PLIP EDO.70: 2 residues within 4Å: Chain I: R.16, H.20 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain I: Y.54, D.55, K.58, D.59, E.62 Ligand excluded by PLIP EDO.72: 7 residues within 4Å: Chain C: Y.55, R.59, R.63 Chain J: T.27, D.28, L.31 Ligands: CDL.35 Ligand excluded by PLIP EDO.74: 1 residues within 4Å: Ligands: DMU.42 Ligand excluded by PLIP EDO.75: 4 residues within 4Å: Chain A: A.114 Chain C: S.29 Chain J: S.46, L.50 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain A: V.118, E.119 Chain J: A.53, S.54, F.55, P.56 Chain L: K.46 Ligand excluded by PLIP EDO.77: 1 residues within 4Å: Chain K: A.33 Ligand excluded by PLIP EDO.78: 1 residues within 4Å: Chain K: Y.31 Ligand excluded by PLIP EDO.80: 1 residues within 4Å: Chain L: F.38 Ligand excluded by PLIP EDO.82: 4 residues within 4Å: Chain A: L.47 Chain D: V.103 Chain M: D.38, K.41 Ligand excluded by PLIP EDO.90: 7 residues within 4Å: Chain N: Y.260, Y.261, H.395, P.398, V.485, W.494 Chain Z: I.1 Ligand excluded by PLIP EDO.91: 6 residues within 4Å: Chain N: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.126 Ligand excluded by PLIP EDO.92: 8 residues within 4Å: Chain N: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain Q: Y.11 Ligand excluded by PLIP EDO.93: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.94: 1 residues within 4Å: Chain N: L.110 Ligand excluded by PLIP EDO.95: 10 residues within 4Å: Chain N: P.173, P.174, T.509, Y.510, V.511 Chain S: N.32, L.34, P.36 Ligands: EDO.124, EDO.130 Ligand excluded by PLIP EDO.96: 9 residues within 4Å: Chain N: E.266, P.267, F.268, G.269, Y.270 Chain S: S.67, T.68 Ligands: EDO.127, EDO.129 Ligand excluded by PLIP EDO.97: 6 residues within 4Å: Chain N: G.269, Y.270, M.271, G.272 Chain O: E.62 Ligands: PEK.33 Ligand excluded by PLIP EDO.99: 4 residues within 4Å: Chain N: C.498 Chain Q: Y.11 Chain Y: G.6, P.7 Ligand excluded by PLIP EDO.100: 3 residues within 4Å: Chain N: K.265, T.489 Chain S: I.70 Ligand excluded by PLIP EDO.101: 5 residues within 4Å: Chain N: E.507 Chain P: T.5 Chain S: P.30, N.32, P.50 Ligand excluded by PLIP EDO.102: 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.127 Ligand excluded by PLIP EDO.105: 6 residues within 4Å: Chain O: E.19, H.22, F.23, P.79, R.82, I.83 Ligand excluded by PLIP EDO.106: 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.115: 1 residues within 4Å: Chain P: S.179 Ligand excluded by PLIP EDO.116: 3 residues within 4Å: Chain P: Q.68, H.70 Chain W: Q.13 Ligand excluded by PLIP EDO.117: 8 residues within 4Å: Chain P: W.146, S.150, D.155, H.158 Chain S: A.1 Chain T: A.13, R.14, R.17 Ligand excluded by PLIP EDO.119: 7 residues within 4Å: Chain N: L.495 Chain Q: Y.11, A.12, L.13, P.14 Chain S: F.72, W.73 Ligand excluded by PLIP EDO.120: 4 residues within 4Å: Chain Q: V.27, A.28, K.63 Chain R: R.30 Ligand excluded by PLIP EDO.121: 5 residues within 4Å: Chain Q: K.121, L.124, D.125, W.138 Chain X: P.50 Ligand excluded by PLIP EDO.122: 3 residues within 4Å: Chain R: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.123: 4 residues within 4Å: Chain R: V.16, N.20, D.49, R.53 Ligand excluded by PLIP EDO.124: 9 residues within 4Å: Chain N: G.88, P.90, P.173, P.174, P.508 Chain P: H.6, Y.8 Chain S: N.32 Ligands: EDO.95 Ligand excluded by PLIP EDO.126: 6 residues within 4Å: Chain N: T.490 Chain S: S.67, T.68, V.69, W.71 Ligands: EDO.91 Ligand excluded by PLIP EDO.127: 8 residues within 4Å: Chain N: E.266 Chain S: D.65, N.66, S.67, T.68 Ligands: EDO.96, EDO.102, EDO.129 Ligand excluded by PLIP EDO.128: 4 residues within 4Å: Chain S: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.129: 8 residues within 4Å: Chain G: R.14 Chain N: Y.270, M.271 Chain S: D.65, S.67 Ligands: PEK.33, EDO.96, EDO.127 Ligand excluded by PLIP EDO.130: 6 residues within 4Å: Chain S: D.29, N.32, L.34, A.35, P.36 Ligands: EDO.95 Ligand excluded by PLIP EDO.133: 4 residues within 4Å: Chain T: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.135: 6 residues within 4Å: Chain P: G.120 Chain T: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.136: 6 residues within 4Å: Chain N: D.227 Chain O: G.177, R.178 Chain P: T.109 Chain U: N.24, T.26 Ligand excluded by PLIP EDO.138: 5 residues within 4Å: Chain V: N.53, Y.54, D.55, E.62 Ligands: EDO.139 Ligand excluded by PLIP EDO.139: 4 residues within 4Å: Chain V: F.50, N.53, Y.54 Ligands: EDO.138 Ligand excluded by PLIP EDO.140: 7 residues within 4Å: Chain O: E.132, R.141, L.191 Chain Q: R.122 Chain V: G.67, I.68 Chain X: W.53 Ligand excluded by PLIP EDO.141: 5 residues within 4Å: Chain P: F.225 Chain S: G.5, V.6, P.7 Chain W: N.3 Ligand excluded by PLIP EDO.143: 3 residues within 4Å: Chain P: N.12, P.13 Chain W: P.19 Ligand excluded by PLIP EDO.144: 4 residues within 4Å: Chain P: M.33 Chain W: C.49, W.52 Ligands: DMU.108 Ligand excluded by PLIP EDO.149: 2 residues within 4Å: Chain Z: T.10 Ligands: PGV.148 Ligand excluded by PLIP

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.15: 15 residues within 4Å: Chain A: F.346, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, H.24, L.28, V.31, S.35, L.39 Chain I: R.43 13 PLIP interactions: 1 interactions with chain I, 4 interactions with chain B, 8 interactions with chain A Salt bridges: I:R.43, B:H.24 Hydrophobic interactions: B:L.7, B:V.31, A:F.346, A:F.346, A:F.426, A:H.429, A:F.430, A:F.430, A:L.433, A:W.450 Water bridges: B:F.9 TGL.45: 15 residues within 4Å: Chain A: I.332, W.334, F.414 Chain B: L.39, I.42, L.46, T.47, T.48 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86 10 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:F.414, D:E.77, D:W.78, B:L.39, B:I.42 Hydrogen bonds: D:T.75 Water bridges: D:T.75 TGL.79: 19 residues within 4Å: Chain A: F.2, I.3, L.7, L.18, L.21, F.22, W.25, P.106, F.109, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.25, F.28, F.29 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:F.2, A:F.2, A:I.3, A:L.7, A:L.18, A:W.25, A:W.25, A:F.109, A:F.400, A:I.472, L:I.11, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29 Hydrogen bonds: L:S.14 Salt bridges: L:R.20 TGL.86: 16 residues within 4Å: Chain N: F.346, Y.379, N.422, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35, L.39 Chain V: R.43 9 PLIP interactions: 4 interactions with chain O, 4 interactions with chain N, 1 interactions with chain V Hydrophobic interactions: O:V.31, O:F.32, N:F.346, N:F.346, N:F.426, N:H.429 Water bridges: O:F.9 Salt bridges: O:H.24, V:R.43 TGL.118: 14 residues within 4Å: Chain N: W.334, F.414, A.415 Chain O: L.39, S.43, L.46, T.47, K.49 Chain Q: T.75, E.77, W.78, M.86 Chain V: R.16, H.20 8 PLIP interactions: 5 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: N:W.334, N:W.334, N:F.414, N:F.414, N:A.415, Q:W.78 Hydrogen bonds: Q:T.75 Water bridges: Q:E.77 TGL.145: 20 residues within 4Å: Chain N: F.2, T.17, L.20, L.21, W.25, P.106, F.109, L.110, L.113, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29 18 PLIP interactions: 9 interactions with chain N, 9 interactions with chain Y Hydrophobic interactions: N:F.2, N:T.17, N:L.20, N:L.21, N:W.25, N:F.109, N:L.113, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29

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

CUA.21: 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.103: 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

10 x CHD: CHOLIC ACID(Non-covalent)

CHD.22: 12 residues within 4Å: Chain A: M.271, 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.111 11 PLIP interactions: 4 interactions with chain T, 4 interactions with chain A, 3 interactions with chain B Water bridges: T:R.17, T:R.17, B:T.63 Salt bridges: T:R.14, T:R.17 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 Hydrogen bonds: B:E.62, B:T.63 CHD.31: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Chain P: L.127 Ligands: PGV.131, CDL.132 8 PLIP interactions: 2 interactions with chain C, 1 interactions with chain P, 5 interactions with chain A Hydrogen bonds: C:W.99, A:T.301, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: P:L.127, A:W.288, A:Y.304 CHD.36: 7 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Water bridges: C:Q.161 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.67: 12 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.33 11 PLIP interactions: 3 interactions with chain O, 4 interactions with chain N, 4 interactions with chain G Hydrogen bonds: O:E.62, O:E.62, O:T.63 Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.73: 4 residues within 4Å: Chain J: Y.32, R.33, T.37, L.40 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:L.40 Hydrogen bonds: J:Y.32, J:R.33, J:R.33 CHD.109: 9 residues within 4Å: Chain C: L.127 Chain N: H.233, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.41, PGV.98 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: N:Y.304, P:W.99 Hydrogen bonds: N:T.301, P:W.99 Water bridges: N:T.301 Salt bridges: N:H.233, P:H.103 CHD.114: 6 residues within 4Å: Chain P: R.156, Q.161, F.164, F.219, L.223 Chain W: F.1 8 PLIP interactions: 6 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164, P:F.164, P:F.219, P:L.223, W:F.1 Salt bridges: P:R.156 Hydrogen bonds: W:F.1 CHD.134: 10 residues within 4Å: Chain P: T.145, H.148, H.149 Chain T: H.8, G.9, G.10, G.12, T.15, W.16 Ligands: PEK.107 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain P Hydrophobic interactions: T:W.16 Hydrogen bonds: T:H.8 Salt bridges: P:H.149 CHD.142: 4 residues within 4Å: Chain W: Y.32, R.33, T.37, L.40 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:R.33 Hydrogen bonds: W:R.33, W:R.33 CHD.146: 7 residues within 4Å: Chain N: M.117 Chain W: F.55 Chain Y: F.38, I.39, R.41, H.42, L.45 3 PLIP interactions: 3 interactions with chain Y Hydrophobic interactions: Y:H.42, Y:L.45 Hydrogen bonds: Y:H.42

6 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.30: 7 residues within 4Å: Chain C: W.34, M.40 Chain G: W.62, G.63, F.69 Ligands: PGV.34, EDO.65 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:G.63, C:W.34 Hydrophobic interactions: C:W.34 DMU.42: 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: EDO.74 8 PLIP interactions: 3 interactions with chain J, 5 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45, C:I.45 Hydrogen bonds: C:S.39, C:T.41 Water bridges: C:S.39, C:T.41 DMU.64: 13 residues within 4Å: Chain C: G.141, T.145, H.149, H.243 Chain G: H.8, G.9, G.10, G.12, T.15, W.16 Ligands: EDO.39, CDL.41, EDO.68 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:H.8, G:G.10, G:G.10 Water bridges: G:G.12, C:H.149 Salt bridges: C:H.149, C:H.149 DMU.81: 11 residues within 4Å: Chain A: L.35, F.459, L.462 Chain D: W.98, Y.102 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A, 2 interactions with chain M Hydrophobic interactions: D:W.98, D:W.98, A:L.35, A:L.462, M:L.27, M:L.27 Water bridges: D:Y.102, D:Y.102 DMU.108: 9 residues within 4Å: Chain P: N.38, S.39, T.41, I.45 Chain W: L.38, G.41, G.42, Y.45 Ligands: EDO.144 10 PLIP interactions: 6 interactions with chain P, 4 interactions with chain W Hydrophobic interactions: P:I.45, W:L.38, W:Y.45, W:Y.45 Hydrogen bonds: P:N.38, P:S.39, P:S.39, P:T.41, P:T.41, W:Y.45 DMU.147: 11 residues within 4Å: Chain N: F.459 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 6 interactions with chain Z, 3 interactions with chain Q Hydrophobic interactions: Z:L.27, Z:L.27, Z:L.34, Q:L.95, Q:W.98, Q:W.98 Hydrogen bonds: Z:W.32, Z:Y.35 Water bridges: Z:H.36

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.32: 22 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.215 Chain C: Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, I.209 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.5 15 PLIP interactions: 5 interactions with chain C, 6 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: C:I.188, C:F.203, C:I.209, G:F.69, A:V.155, A:A.203, A:T.207, A:L.215 Hydrogen bonds: C:Y.181, C:I.188, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.33: 19 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain F: A.1 Chain G: R.14, R.17, F.21, L.25, A.29 Chain N: M.271 Chain O: Q.59, T.66, I.67 Chain S: D.65 Ligands: CHD.67, EDO.97, EDO.129 16 PLIP interactions: 8 interactions with chain G, 4 interactions with chain C, 1 interactions with chain F, 3 interactions with chain O Hydrophobic interactions: G:F.21, G:F.21, G:L.25, G:A.29, C:T.168, C:Y.172, O:T.66, O:I.67, O:I.67 Salt bridges: G:R.14, G:R.17, G:R.17, G:R.17, C:K.157, C:H.158 Hydrogen bonds: F:A.1 PEK.44: 14 residues within 4Å: Chain C: R.80, Y.81, I.84, L.85, I.88, V.91, T.95, F.98, Y.102, W.240, F.244, V.247, V.254 Ligands: EDO.39 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.81, C:L.85, C:I.88, C:V.91, C:F.98, C:F.98, C:F.98, C:V.247, C:V.254 Hydrogen bonds: C:R.80 Water bridges: C:E.236, C:E.236 PEK.107: 12 residues within 4Å: Chain P: I.87, V.91, T.95, F.98, H.148, W.240, H.243, F.244, V.247, V.248, F.251 Ligands: CHD.134 11 PLIP interactions: 11 interactions with chain P Hydrophobic interactions: P:I.87, P:V.91, P:F.98, P:W.240, P:H.243, P:F.244, P:V.247, P:V.248 Hydrogen bonds: P:H.149 Salt bridges: P:H.148, P:H.243 PEK.110: 18 residues within 4Å: Chain N: H.151, V.155, A.203 Chain P: Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, F.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.87 12 PLIP interactions: 4 interactions with chain P, 6 interactions with chain T, 2 interactions with chain N Hydrophobic interactions: P:I.188, P:F.203, P:F.203, T:W.62, T:F.69, N:V.155, N:A.203 Hydrogen bonds: P:I.188, T:T.68, T:F.70, T:N.76, T:N.76 PEK.111: 16 residues within 4Å: Chain A: I.311 Chain B: Q.59, T.66 Chain F: D.65 Chain P: K.157, H.158, Q.161, I.165, T.168 Chain S: A.1 Chain T: R.14, R.17, F.21, P.26 Ligands: CHD.22, CDL.132 12 PLIP interactions: 2 interactions with chain F, 4 interactions with chain T, 4 interactions with chain P, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: F:D.65, F:D.65, T:R.17 Salt bridges: T:R.17, T:R.17, T:R.17, P:K.157, P:H.158 Hydrophobic interactions: P:I.165, P:T.168, B:T.66, A:I.311

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.35: 25 residues within 4Å: Chain C: M.44, T.48, M.51, L.52, Y.55, R.59, I.62, R.63, F.67, G.170, V.171, T.174, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27 Ligands: PGV.34, EDO.72 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:R.59, C:I.62, C:V.171, C:T.174, C:T.213, C:I.216 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, C:H.226, J:K.8 CDL.41: 24 residues within 4Å: Chain C: N.125, P.126, L.127, L.131, L.138, Y.253, W.258 Chain G: W.16, L.23, S.27, N.34, H.38, R.42 Chain N: I.286, D.300, Y.304, S.307, I.311 Chain O: A.77, L.78, L.81, Y.85 Ligands: DMU.64, CHD.109 18 PLIP interactions: 2 interactions with chain N, 2 interactions with chain O, 6 interactions with chain G, 8 interactions with chain C Hydrophobic interactions: N:Y.304, N:I.311, O:L.78, O:L.81, G:W.16, G:L.23, C:P.126, C:L.127, C:L.138, C:Y.253, C:W.258, C:W.258, C:W.258 Hydrogen bonds: G:N.34, G:H.38, C:N.125 Salt bridges: G:H.38, G:H.38 CDL.113: 21 residues within 4Å: Chain P: M.44, T.48, M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, F.12, T.27, L.31 22 PLIP interactions: 18 interactions with chain P, 4 interactions with chain W Hydrophobic interactions: P:M.51, P:Y.55, P:W.58, P:R.59, P:I.62, P:T.213, P:I.216, P:V.217, P:F.220, P:F.220, P:F.220, W:L.31 Hydrogen bonds: P:Y.55 Water bridges: P:R.59, W:K.8, W:K.8 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, P:H.226, W:K.8 CDL.132: 31 residues within 4Å: Chain A: S.279, F.282, D.300, Y.304, S.307, I.311 Chain B: A.70, I.74, A.77, L.78, L.81, R.82, Y.85 Chain P: N.125, L.127, L.131, S.135, L.138, V.142, Y.253, V.254 Chain T: G.22, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.31, PEK.111, PGV.131 19 PLIP interactions: 5 interactions with chain B, 7 interactions with chain P, 3 interactions with chain A, 4 interactions with chain T Hydrophobic interactions: B:A.70, B:I.74, B:A.77, B:L.78, B:R.82, P:L.131, P:L.131, P:L.138, P:V.142, P:Y.253, P:V.254, A:F.282, A:I.311, T:L.30, T:N.34, T:L.37 Hydrogen bonds: P:N.125, A:D.300 Salt bridges: T:H.38

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.53: 15 residues within 4Å: Chain A: F.321, H.328 Chain B: H.52, M.56, D.57, E.60, W.65 Chain E: E.6, D.8, F.11, D.40 Chain I: R.10, G.11, A.14, L.17 11 PLIP interactions: 4 interactions with chain E, 3 interactions with chain B, 3 interactions with chain I, 1 interactions with chain A Hydrogen bonds: E:D.40, I:G.11, I:A.14 Water bridges: E:D.40, E:D.40 Salt bridges: E:D.8, B:H.52, B:H.52 Hydrophobic interactions: B:W.65, I:A.14, A:F.321 PSC.104: 17 residues within 4Å: Chain N: F.268, F.321, H.328 Chain O: H.52, T.55, M.56, D.57, V.61, W.65 Chain R: E.6, D.8, F.11, D.40, L.41 Chain V: R.10, A.14, L.17 8 PLIP interactions: 2 interactions with chain R, 2 interactions with chain O, 2 interactions with chain N, 2 interactions with chain V Salt bridges: R:D.8, O:H.52 pi-Cation interactions: R:F.11 Hydrogen bonds: O:D.57 Hydrophobic interactions: N:F.268, N:F.321, V:A.14 Water bridges: V:A.14

2 x ZN: ZINC ION(Non-covalent)

ZN.60: 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.125: 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 SAC: N-ACETYL-SERINE(Non-covalent)

SAC.69: 1 residues within 4Å: Chain I: T.2 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.2 SAC.137: 1 residues within 4Å: Chain V: T.2 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:T.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishigami, I. et al., Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase. J.Biol.Chem. (2022)

Release Date

2022-03-30

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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