SMTL ID : 7tih.1

Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: OH.18 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.1 CU.82: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: OH.99 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.32

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 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.8, H2O.8 MG.83: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 5 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 2 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.39, H2O.39

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

NA.3: 5 residues within 4Å: Chain A: E.40, G.45, T.46, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:D.442 NA.84: 4 residues within 4Å: Chain N: E.40, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:E.40

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: 17 residues within 4Å: Chain A: N.406, T.408, W.409, I.412, R.480 Chain D: T.80, A.84, F.87, F.88 Chain K: F.9, H.10 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16 15 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D, 3 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, D:T.80, D:F.87, D:F.88, K:F.9, K:F.9, M:Q.15 Hydrogen bonds: A:N.406 Water bridges: A:T.404, M:A.6, M:Q.15 Salt bridges: K:H.10 PGV.5: 27 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152, V.155, L.159 Chain C: H.9, V.11, 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, F.93 Ligands: PEK.61 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.152, A:V.155, A:L.159, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93 Hydrogen bonds: A:R.96, A:M.97, C:E.64 Salt bridges: A:R.96 PGV.31: 22 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, I.210, T.213, F.214, V.217, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.33, DMU.60 26 PLIP interactions: 25 interactions with chain C, 1 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:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:V.217 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:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.32: 12 residues within 4Å: Chain A: D.298, T.301 Chain C: W.99, Y.102, H.103, L.106, A.107 Chain P: W.258, W.259 Chain T: A.1, S.2 Ligands: CHD.30 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.298, A:T.301 Hydrophobic interactions: C:W.99, C:W.99 Salt bridges: C:H.103 PGV.98: 18 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, E.474, S.478, R.480 Chain Q: A.84, F.87 Chain X: F.9, H.10, V.17 Chain Z: A.6, T.10, P.12, Q.15, A.16 Ligands: EDO.144 11 PLIP interactions: 4 interactions with chain N, 2 interactions with chain Z, 2 interactions with chain Q, 3 interactions with chain X Hydrophobic interactions: N:W.409, N:I.412, Z:P.12, Z:Q.15, Q:A.84, Q:F.87, X:F.9, X:F.9, X:V.17 Water bridges: N:T.404 Salt bridges: N:R.480 PGV.104: 23 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155 Chain P: H.9, V.11, G.20, A.24, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, S.89 Ligands: PGV.108, PEK.132 10 PLIP interactions: 5 interactions with chain N, 5 interactions with chain P Hydrophobic interactions: N:V.155, P:A.24, P:W.57, P:W.57, P:W.57, P:W.58 Hydrogen bonds: N:R.96, N:R.96, N:M.97 Salt bridges: N:R.96 PGV.108: 22 residues within 4Å: Chain P: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, F.86, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.104 25 PLIP interactions: 24 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:I.62, P:F.86, P:I.210, P:I.210, P:I.210, P:T.213, 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:R.221, P:H.231, P:H.231, S:D.9 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.109: 11 residues within 4Å: Chain G: A.1, S.2 Chain N: F.237 Chain P: T.95, W.99, Y.102, H.103, A.107 Chain U: R.27 Ligands: PEK.103, CHD.106 8 PLIP interactions: 1 interactions with chain N, 5 interactions with chain P, 1 interactions with chain U, 1 interactions with chain O Hydrophobic interactions: N:F.237, P:T.95, P:W.99, P:W.99 Water bridges: P:H.103, U:R.27, O:R.178 Salt bridges: P:H.103

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

HEA.6: 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: OH.18 37 PLIP interactions: 32 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, 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:L.358, 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:P.69, B:I.72, 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 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240, A:H.240 Metal complexes: A:H.376, OH.18 HEA.7: 34 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, F.377, H.378, L.381, S.382, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:F.377, A:F.377, A:L.381, A:L.381, A:F.393, A:F.393, A:T.424, A:F.425, 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:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.86: 35 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 Ligands: OH.99 41 PLIP interactions: 35 interactions with chain N, 5 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:V.320, N:F.321, N:F.348, N:L.353, N:I.356, N:I.356, N:L.358, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, 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:H.291, N:D.369, N:R.438, N:R.438, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, OH.99 HEA.87: 33 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, V.374, F.377, H.378, L.381, S.382, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, M.468 Ligands: TGL.142 33 PLIP interactions: 33 interactions with chain N, Hydrophobic interactions: N:I.37, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:L.381, N:L.381, N:V.386, N:V.386, N:F.393, N:F.393, N:T.424, N:F.425 Hydrogen bonds: N:R.38, N:Y.54, N:Y.54, N:W.126, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:H.61, N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378

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

EDO.8: 6 residues within 4Å: Chain A: L.483, V.485, W.494, G.497, C.498 Chain D: Y.11 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: P.182, H.256, T.259, K.265, T.490, N.491 Ligands: EDO.59 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.335, D.407, K.411 Ligands: TGL.43 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: G.269, Y.270, M.271, G.272 Chain B: A.58, E.62 Ligands: CHD.131 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: K.265, T.489 Chain F: P.83 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.16: 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.17: 4 residues within 4Å: Chain A: L.48, G.49, D.50 Chain M: K.41 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: 5 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, D.158, V.159 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: M.146, E.147, P.215, L.216 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: F.23, H.26, P.79, R.82 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: S.94, L.95, D.112, Y.113, M.148 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: K.217, Y.218, K.221 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: N.92, P.93 Chain H: Q.12, T.13, P.15 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain G: A.13, R.14 Ligands: PEK.62 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: H.243 Ligands: EDO.37, DMU.40 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: H.243 Ligands: EDO.36, PEK.42 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain C: M.44, T.48 Chain J: L.38 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: V.30, Q.37, E.58, R.61, L.62 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain D: W.48, S.49, L.51, S.52, I.53, K.56 Ligands: EDO.53 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: D.26, A.28, K.63 Chain E: R.30 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain D: E.144, W.145 Chain K: T.49, P.50 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain D: A.28, V.30, K.31, K.41, L.62, K.63 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain D: Y.22 Chain E: W.27, R.30, K.31, N.34 Chain F: P.83 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligands: EDO.55 Ligand excluded by PLIP EDO.52: 2 residues within 4Å: Chain E: R.53, R.57 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain D: K.56 Chain E: N.94, G.97, I.98, S.99 Ligands: EDO.45 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain E: Y.82, P.83, R.90, T.100, E.102 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain E: E.28 Chain F: R.81 Ligands: EDO.51 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain F: D.9, E.17 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.59: 8 residues within 4Å: Chain A: Q.180, 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.64: 2 residues within 4Å: Chain G: F.69 Ligands: DMU.60 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain G: P.59, D.64, G.65, N.66 Ligand excluded by PLIP EDO.66: 2 residues within 4Å: Chain G: D.7 Chain P: L.85 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain G: D.7, G.9 Chain P: Y.81 Ligands: DMU.40 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain B: T.47 Chain I: R.16, H.20 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain D: K.127 Chain I: Y.54, D.55, D.59, E.62 Ligand excluded by PLIP EDO.73: 2 residues within 4Å: Chain J: W.52 Ligands: DMU.41 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain C: S.29, M.33 Chain J: S.46, L.50 Ligand excluded by PLIP EDO.75: 4 residues within 4Å: Chain C: N.12 Chain J: G.17, L.18, P.19 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: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.78: 1 residues within 4Å: Chain K: Y.31 Ligand excluded by PLIP EDO.80: 2 residues within 4Å: Chain L: S.31, F.38 Ligand excluded by PLIP EDO.81: 5 residues within 4Å: Chain A: T.46, L.47 Chain D: V.103 Chain M: D.38, K.41 Ligand excluded by PLIP EDO.88: 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.89: 6 residues within 4Å: Chain N: P.182, H.256, T.259, T.490, N.491 Ligands: EDO.127 Ligand excluded by PLIP EDO.90: 9 residues within 4Å: Chain N: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain Q: K.7, Y.11 Ligand excluded by PLIP EDO.91: 8 residues within 4Å: Chain N: G.88, P.173, P.174, P.508 Chain P: H.6, Y.8 Chain S: N.32 Ligands: EDO.93 Ligand excluded by PLIP EDO.92: 1 residues within 4Å: Chain N: P.106 Ligand excluded by PLIP EDO.93: 10 residues within 4Å: Chain N: P.174, P.508, T.509, Y.510, V.511 Chain S: N.32, L.34, P.36, R.56 Ligands: EDO.91 Ligand excluded by PLIP EDO.94: 6 residues within 4Å: Chain N: G.269, M.271, G.272 Chain O: A.58, E.62 Ligands: PEK.62 Ligand excluded by PLIP EDO.95: 7 residues within 4Å: Chain N: G.226, D.227 Chain O: G.177, R.178 Chain P: T.109 Chain U: N.24, T.26 Ligand excluded by PLIP EDO.96: 3 residues within 4Å: Chain N: K.265, T.489 Chain S: S.84 Ligand excluded by PLIP EDO.97: 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.128 Ligand excluded by PLIP EDO.101: 6 residues within 4Å: Chain O: E.19, H.22, F.23, P.79, R.82, I.83 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain O: E.132, R.141 Chain Q: R.122 Chain V: G.67, I.68 Ligand excluded by PLIP EDO.112: 1 residues within 4Å: Chain P: L.175 Ligand excluded by PLIP EDO.113: 3 residues within 4Å: Chain P: Q.68 Chain S: G.15 Chain W: Q.13 Ligand excluded by PLIP EDO.114: 7 residues within 4Å: Chain N: E.507 Chain P: T.5 Chain S: P.30, N.32, P.50, R.56, L.96 Ligand excluded by PLIP EDO.115: 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.116: 4 residues within 4Å: Chain P: N.12, P.13 Chain W: G.17, P.19 Ligand excluded by PLIP EDO.118: 8 residues within 4Å: Chain N: L.495 Chain Q: Y.11, A.12, L.13, P.14 Chain S: F.72, W.73 Ligands: EDO.121 Ligand excluded by PLIP EDO.119: 5 residues within 4Å: Chain Q: P.25, V.27, A.28, K.63 Chain R: R.30 Ligand excluded by PLIP EDO.120: 4 residues within 4Å: Chain N: C.498 Chain Q: K.7 Chain Y: G.6, P.7 Ligand excluded by PLIP EDO.121: 4 residues within 4Å: Chain Q: D.26 Chain S: R.81, P.83 Ligands: EDO.118 Ligand excluded by PLIP EDO.124: 3 residues within 4Å: Chain R: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.125: 4 residues within 4Å: Chain R: V.16, N.20, D.49, R.53 Ligand excluded by PLIP EDO.127: 6 residues within 4Å: Chain N: T.490 Chain S: S.67, T.68, V.69, W.71 Ligands: EDO.89 Ligand excluded by PLIP EDO.128: 6 residues within 4Å: Chain N: E.266 Chain S: N.66, S.67, T.68 Ligands: EDO.97, EDO.129 Ligand excluded by PLIP EDO.129: 4 residues within 4Å: Chain G: R.14 Chain S: D.65, S.67 Ligands: EDO.128 Ligand excluded by PLIP EDO.130: 3 residues within 4Å: Chain S: D.29, L.34, P.36 Ligand excluded by PLIP EDO.134: 4 residues within 4Å: Chain T: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.137: 4 residues within 4Å: Chain V: Y.54, D.55, E.62 Ligands: EDO.138 Ligand excluded by PLIP EDO.138: 4 residues within 4Å: Chain V: F.50, N.53, Y.54 Ligands: EDO.137 Ligand excluded by PLIP EDO.139: 4 residues within 4Å: Chain P: F.225 Chain S: G.5, P.7 Chain W: N.3 Ligand excluded by PLIP EDO.141: 3 residues within 4Å: Chain P: M.33 Chain W: C.49 Ligands: DMU.105 Ligand excluded by PLIP EDO.144: 3 residues within 4Å: Chain Z: P.9, T.10 Ligands: PGV.98 Ligand excluded by PLIP

2 x OH: HYDROXIDE ION(Non-covalent)

OH.18: 5 residues within 4Å: Chain A: H.240, V.243, H.376 Ligands: CU.1, HEA.6 No protein-ligand interaction detected (PLIP) OH.99: 5 residues within 4Å: Chain N: H.240, V.243, H.376 Ligands: CU.82, HEA.86 No protein-ligand interaction detected (PLIP)

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

CUA.19: 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.100: 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 TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.20: 17 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 D: Q.132, K.137 Chain I: R.43 16 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B, 1 interactions with chain I, 1 interactions with chain D Hydrophobic interactions: A:F.346, A:V.350, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, B:V.31, B:F.32, B:F.32, B:L.39, D:Q.132 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.43: 18 residues within 4Å: Chain A: W.334, M.339, G.343, F.414, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81 Ligands: EDO.11 12 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: B:L.39, B:I.42, B:K.49, D:E.77, D:W.78, D:V.81, A:W.334, A:W.334, A:F.414, A:F.414, A:F.418 Hydrogen bonds: D:T.75 TGL.79: 17 residues within 4Å: Chain A: T.17, L.18, L.21, W.25, P.106, L.113, F.393, F.397, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, F.28, F.29 18 PLIP interactions: 10 interactions with chain L, 8 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29, A:L.18, A:W.25, A:W.25, A:L.113, A:F.393, A:F.393, A:F.397, A:I.472 Hydrogen bonds: L:S.14 Salt bridges: L:R.20 TGL.85: 18 residues within 4Å: Chain N: F.346, V.350, 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, S.36, L.39 Chain V: R.43 16 PLIP interactions: 8 interactions with chain O, 7 interactions with chain N, 1 interactions with chain V Hydrophobic interactions: O:L.7, O:V.31, O:F.32, O:F.32, O:L.39, N:F.346, N:V.350, N:F.426, N:F.426, N:H.429, N:F.430, N:L.433 Water bridges: O:G.8, O:F.9 Salt bridges: O:H.24, V:R.43 TGL.117: 14 residues within 4Å: Chain N: W.334, K.411, F.414, A.415 Chain O: L.39, I.42, K.49 Chain Q: S.74, T.75, E.77, W.78, V.81 Chain V: R.16, H.20 8 PLIP interactions: 2 interactions with chain O, 3 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: O:L.39, O:I.42, N:W.334, N:F.414, N:A.415, Q:W.78, Q:V.81 Water bridges: Q:E.77 TGL.142: 26 residues within 4Å: Chain N: F.2, W.6, L.7, T.17, L.18, L.20, L.21, W.25, P.106, F.109, L.112, L.113, F.393, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29, I.39 Ligands: HEA.87 22 PLIP interactions: 13 interactions with chain N, 9 interactions with chain Y Hydrophobic interactions: N:F.2, N:T.17, N:L.18, N:L.20, N:W.25, N:F.109, N:F.109, N:F.109, N:L.112, N:L.113, N:F.393, 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.29, Y:F.29, Y:I.39

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.21: 18 residues within 4Å: Chain A: F.268, F.321, A.325, H.328 Chain B: H.52, M.56, D.57, E.60, V.61, W.65 Chain E: E.6, D.8, F.11, D.40, L.41 Chain I: R.10, A.14, L.17 13 PLIP interactions: 4 interactions with chain E, 4 interactions with chain B, 3 interactions with chain I, 2 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:M.56, B:V.61, I:A.14, A:F.268, A:A.325 PSC.123: 20 residues within 4Å: Chain N: F.268, F.321, L.324, H.328 Chain O: L.37, I.41, M.45, H.52, M.56, D.57, W.65 Chain R: E.6, T.7, D.8, F.11, D.40, L.41 Chain V: R.10, A.14, L.17 13 PLIP interactions: 5 interactions with chain N, 2 interactions with chain R, 2 interactions with chain V, 4 interactions with chain O Hydrophobic interactions: N:F.268, N:F.321, N:F.321, N:L.324, N:L.324, V:A.14, V:L.17, O:I.41, O:M.56, O:W.65 Water bridges: R:D.40 Salt bridges: R:D.8, O:H.52

10 x CHD: CHOLIC ACID(Non-covalent)

CHD.30: 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.32, CDL.133 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.99 Hydrogen bonds: A:T.301, A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.34: 4 residues within 4Å: Chain C: R.156, F.164, L.223 Chain J: F.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:L.223, J:F.1 Water bridges: C:Q.161 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.67: 10 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, W.275 Chain O: E.62, T.63 Ligands: PEK.62 10 PLIP interactions: 4 interactions with chain N, 2 interactions with chain O, 4 interactions with chain G Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275 Hydrogen bonds: O:E.62, O:E.62 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.72: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:M.36, J:L.40 Hydrogen bonds: J:Y.32, J:R.33, J:R.33 CHD.106: 10 residues within 4Å: Chain C: L.127 Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.39, PGV.109 10 PLIP interactions: 7 interactions with chain N, 2 interactions with chain P, 1 interactions with chain C Hydrophobic interactions: N:W.288, N:Y.304, C:L.127 Hydrogen bonds: N:D.300, N:D.300, N:T.301, P:W.99 Water bridges: N:T.301 Salt bridges: N:H.233, P:H.103 CHD.111: 5 residues within 4Å: Chain P: R.156, Q.161, F.164, L.223 Chain W: F.1 7 PLIP interactions: 6 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164, P:F.164, P:L.223, W:F.1 Water bridges: P:Q.161 Salt bridges: P:R.156 CHD.131: 12 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: EDO.13, PEK.107 13 PLIP interactions: 3 interactions with chain B, 6 interactions with chain T, 4 interactions with chain A Hydrogen bonds: B:E.62, B:T.63 Water bridges: B:T.63, T:R.14, T:R.17, T:R.17 Hydrophobic interactions: T:F.18, A:M.271, A:W.275, A:W.275, A:W.275 Salt bridges: T:R.14, T:R.17 CHD.135: 10 residues within 4Å: Chain P: T.145, H.148, H.149 Chain T: H.8, G.9, G.10, T.11, G.12, W.16 Ligands: PEK.103 3 PLIP interactions: 1 interactions with chain T, 2 interactions with chain P Hydrophobic interactions: T:W.16 Salt bridges: P:H.148, P:H.149 CHD.140: 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:L.40 Hydrogen bonds: W:R.33, W:R.33 CHD.143: 9 residues within 4Å: Chain N: L.113, M.117 Chain W: F.55 Chain Y: A.35, 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

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.33: 21 residues within 4Å: Chain C: M.44, M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27 Ligands: PGV.31 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:V.171, C:T.213, C:F.220 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226 Water bridges: J:K.8, J:T.27 CDL.39: 21 residues within 4Å: Chain C: N.125, P.126, L.127, L.131, L.138, Y.253, W.258 Chain G: S.27, L.30, N.34, L.37, H.38 Chain N: F.282, D.300, S.307, I.311 Chain O: L.78, L.81, Y.85 Ligands: DMU.40, CHD.106 18 PLIP interactions: 10 interactions with chain C, 3 interactions with chain O, 4 interactions with chain G, 1 interactions with chain N Hydrophobic interactions: C:P.126, C:L.127, C:L.127, C:L.131, C:L.138, C:Y.253, C:W.258, C:W.258, C:W.258, O:L.78, O:L.81, O:Y.85, G:L.30, G:L.37, N:F.282 Hydrogen bonds: C:N.125 Salt bridges: G:H.38, G:H.38 CDL.110: 20 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 13 PLIP interactions: 12 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:M.51, P:L.52, P:Y.55, P:Y.55, P:W.58, P:I.62, P:F.220, P:F.220 Hydrogen bonds: P:Y.55 Salt bridges: P:R.63, P:K.224, P:H.226 Water bridges: W:D.28 CDL.133: 25 residues within 4Å: Chain A: S.279, F.282, I.286, D.300, Y.304, S.307, I.311 Chain B: I.74, L.78, R.82, Y.85 Chain P: N.125, L.127, T.134, L.138, V.142 Chain T: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.30, PEK.107 17 PLIP interactions: 4 interactions with chain P, 7 interactions with chain A, 2 interactions with chain B, 4 interactions with chain T Hydrophobic interactions: P:T.134, P:L.138, P:V.142, A:F.282, A:I.286, A:Y.304, A:I.311, A:I.311, B:I.74, B:L.78, T:L.23, T:L.30 Hydrogen bonds: P:N.125, A:D.300, A:D.300 Water bridges: T:N.34 Salt bridges: T:H.38

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

DMU.40: 11 residues within 4Å: Chain C: G.141, T.145, H.149 Chain G: G.9, G.10, G.12, T.15, W.16 Ligands: EDO.36, CDL.39, EDO.68 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:G.10, G:G.12 Salt bridges: C:H.149 DMU.41: 9 residues within 4Å: Chain C: N.38, S.39, T.41 Chain J: L.38, G.41, G.42, Y.45 Ligands: DMU.60, EDO.73 8 PLIP interactions: 4 interactions with chain J, 4 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45 Hydrogen bonds: J:Y.45, C:T.41 Water bridges: C:S.39, C:M.40, C:T.41 DMU.50: 12 residues within 4Å: Chain A: L.462 Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 11 PLIP interactions: 6 interactions with chain D, 3 interactions with chain M, 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: D:W.98, D:W.98, D:W.98, M:L.27, M:A.30, M:L.34, L:F.37, A:L.462 Hydrogen bonds: D:Y.102, D:Y.102, D:Y.102 DMU.60: 10 residues within 4Å: Chain C: W.34, N.38, M.40 Chain G: W.62, G.63, F.69 Ligands: PGV.31, DMU.41, PEK.61, EDO.64 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.34 Hydrogen bonds: C:N.38, G:G.63 DMU.105: 8 residues within 4Å: Chain P: N.38, S.39, T.41 Chain W: L.38, G.41, G.42, Y.45 Ligands: EDO.141 7 PLIP interactions: 3 interactions with chain P, 4 interactions with chain W Hydrogen bonds: P:N.38, P:S.39, P:S.39, W:Y.45 Hydrophobic interactions: W:L.38, W:Y.45, W:Y.45 DMU.122: 13 residues within 4Å: Chain N: L.35, F.459, L.462 Chain Q: W.98, Y.102 Chain Z: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 11 PLIP interactions: 5 interactions with chain Q, 3 interactions with chain Z, 3 interactions with chain N Hydrophobic interactions: Q:W.98, Q:W.98, Q:W.98, Z:L.27, Z:A.30, Z:L.34, N:L.35, N:F.459, N:L.462 Hydrogen bonds: Q:Y.102, Q:Y.102

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.42: 14 residues within 4Å: Chain C: Y.81, I.84, L.85, V.91, T.95, F.98, Y.102, W.240, H.243, F.244, V.247, F.251 Chain T: A.3 Ligands: EDO.37 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain T Hydrophobic interactions: C:Y.81, C:L.85, C:V.91, C:F.98, C:H.243, C:V.247, C:F.251, T:A.3 PEK.61: 25 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, 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, DMU.60 16 PLIP interactions: 7 interactions with chain G, 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: G:F.69, A:V.155, A:A.203, A:L.210, A:L.215, C:W.34, C:I.188, C:F.203, C:I.209 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.188 Water bridges: G:F.69, G:F.69 PEK.62: 14 residues within 4Å: Chain C: K.157, H.158, T.168, Y.172 Chain F: A.1 Chain G: R.14, R.17, F.21 Chain O: Q.59, T.66 Chain S: D.65 Ligands: EDO.35, CHD.67, EDO.94 11 PLIP interactions: 4 interactions with chain C, 1 interactions with chain F, 5 interactions with chain G, 1 interactions with chain O Hydrophobic interactions: C:T.168, C:Y.172, G:F.21, O:T.66 Salt bridges: C:K.157, C:H.158, G:R.14, G:R.17 Hydrogen bonds: F:A.1, G:R.17, G:R.17 PEK.103: 14 residues within 4Å: Chain G: A.1 Chain P: I.87, V.91, T.95, F.98, H.148, E.236, W.240, H.243, F.244, V.247, F.251 Ligands: PGV.109, CHD.135 13 PLIP interactions: 12 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: P:I.87, P:V.91, P:F.98, P:W.240, P:H.243, P:V.247, P:F.251, P:F.251, P:F.251, P:F.251, G:A.1 Hydrogen bonds: P:E.236 Salt bridges: P:H.243 PEK.107: 13 residues within 4Å: Chain B: Q.59, T.66, I.67 Chain F: D.65 Chain P: K.157, H.158, Q.161, T.168 Chain S: A.1 Chain T: R.17, F.21 Ligands: CHD.131, CDL.133 16 PLIP interactions: 3 interactions with chain B, 4 interactions with chain P, 1 interactions with chain F, 7 interactions with chain T, 1 interactions with chain S Hydrophobic interactions: B:T.66, B:I.67, P:T.168, T:F.21 Hydrogen bonds: B:Q.59, F:D.65, T:R.17, S:A.1 Water bridges: P:K.157, T:R.17, T:R.17 Salt bridges: P:K.157, P:H.158, T:R.17, T:R.17, T:R.17 PEK.132: 23 residues within 4Å: Chain N: H.151, V.155, A.203, T.207, L.215 Chain P: L.31, W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.104 15 PLIP interactions: 6 interactions with chain T, 7 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: T:F.69, P:L.31, P:W.34, P:I.188, P:F.203, P:F.203, N:V.155, N:A.203 Hydrogen bonds: T:T.68, T:F.70, T:N.76, P:Y.181, P:I.188 Water bridges: T:F.69, T:F.69

2 x ZN: ZINC ION(Non-covalent)

ZN.57: 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: 5 residues within 4Å: Chain S: C.60, C.62, C.82, C.85, T.87 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)(Non-functional Binders)

SAC.69: 1 residues within 4Å: Chain I: T.2 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:T.2, I:T.2, I:T.2 SAC.136: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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