SMTL ID : 9kuk.1

Bovine Heart Cytochrome c Oxidase in the Xenon-bound Fully Oxidized State under Aerobic Condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, 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, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 33 PLIP interactions: 33 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:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424 Hydrogen bonds: A:R.38, A:W.126, 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:F.425 pi-Cation interactions: A:H.378 Metal complexes: A:H.61, A:H.378 HEA.2: 32 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, I.72 Ligands: PER.6 36 PLIP interactions: 32 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:I.356, A:I.356, 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:I.34, B:P.69, B:I.72 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:D.369, A:D.369, A:R.438, A:R.438 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.77: 36 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, F.393, M.417, 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 N, Hydrophobic interactions: N:A.24, N:I.37, N:R.38, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:I.73, N:V.374, N:F.377, N:F.377, N:L.381, N:V.386, N:V.386, N:F.393, N:F.393, N:T.424 Hydrogen bonds: N:R.38, N:W.126, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:H.61, N:F.425 pi-Cation interactions: N:H.378 Metal complexes: N:H.61, N:H.378 HEA.78: 33 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, 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.82 38 PLIP interactions: 33 interactions with chain N, 5 interactions with chain O, 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:T.316, N:V.320, N:L.353, N:I.356, N:I.356, N:L.358, N:V.373, 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:W.126, N:Y.244, N:Y.244 Water bridges: 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 Metal complexes: N:H.376

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.79: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: PER.82 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.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.8, H2O.11, H2O.12 MG.80: 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.50, H2O.52, H2O.53

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

NA.5: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:S.441 Water bridges: A:Q.43 NA.81: 4 residues within 4Å: Chain N: E.40, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40, N:E.40

2 x PER: PEROXIDE ION(Non-covalent)

PER.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) PER.82: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.78, CU.79 No protein-ligand interaction detected (PLIP)

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.7: 17 residues within 4Å: Chain A: T.354, F.426, H.429, F.430, L.433, W.450 Chain B: M.5, L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 16 PLIP interactions: 5 interactions with chain A, 3 interactions with chain I, 8 interactions with chain B Hydrophobic interactions: A:T.354, A:F.426, A:H.429, A:F.430, A:F.430, B:L.7, B:V.31, B:F.32, B:F.32, B:L.39 Water bridges: I:R.43, I:R.43, B:L.7, B:H.24 Salt bridges: I:R.43, B:H.24 CDL.36: 19 residues within 4Å: Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, S.212, T.213, V.217, F.220, K.224, H.226 Chain J: K.8, F.12, T.27 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:Y.55, C:Y.55, C:W.58, C:F.220, C:K.224, J:T.27 Hydrogen bonds: C:Y.55 Water bridges: C:Y.55, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, C:H.226, J:K.8, J:K.8 CDL.71: 22 residues within 4Å: Chain A: F.2, I.3, L.7, T.17, L.18, L.21, F.22, W.25, W.103, L.113, F.393, F.400, S.401 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, F.28, F.29, S.31 25 PLIP interactions: 13 interactions with chain A, 12 interactions with chain L Hydrophobic interactions: A:F.2, A:L.7, A:T.17, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.103, A:L.113, A:F.393, A:F.400, L:I.11, L:F.13, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29 Water bridges: A:F.2, L:I.11 Hydrogen bonds: L:S.14 Salt bridges: L:R.20 CDL.109: 16 residues within 4Å: Chain P: M.51, M.54, Y.55, R.59, I.62, R.63, F.67, S.212, T.213, I.216, F.220, K.224, H.226 Chain W: K.8, F.12, T.27 16 PLIP interactions: 13 interactions with chain P, 3 interactions with chain W Hydrophobic interactions: P:Y.55, P:Y.55, P:Y.55, P:Y.55, P:I.216, P:I.216, P:K.224, W:T.27 Water bridges: P:R.59 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, P:H.226, W:K.8, W:K.8 CDL.142: 19 residues within 4Å: Chain N: F.346, V.419, N.422, M.423, F.426, H.429, F.430, L.433, W.450 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36, L.39 Chain V: R.43 18 PLIP interactions: 9 interactions with chain O, 6 interactions with chain N, 2 interactions with chain Q, 1 interactions with chain V Hydrophobic interactions: O:L.7, O:V.31, O:F.32, O:L.39, N:N.422, N:F.426, N:F.426, N:H.429, N:F.430, N:F.430 Hydrogen bonds: O:G.8 Water bridges: O:L.7, O:F.9, O:F.9, Q:Q.132, Q:Q.132 Salt bridges: O:H.24, V:R.43 CDL.144: 20 residues within 4Å: Chain N: F.2, I.3, L.7, T.17, L.18, L.20, L.21, F.22, W.25, P.106, L.110, L.113, F.400 Chain Y: I.11, P.12, F.13, S.14, R.20, F.28, F.29 24 PLIP interactions: 12 interactions with chain N, 12 interactions with chain Y Hydrophobic interactions: N:F.2, N:L.7, N:L.18, N:L.20, N:L.21, N:L.21, N:F.22, N:W.25, N:W.25, N:P.106, N:L.113, N:F.400, Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.29, Y:F.29 Hydrogen bonds: Y:S.14 Water bridges: Y:S.14, Y:R.20, Y:R.20 Salt bridges: Y:R.20

26 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.8: 5 residues within 4Å: Chain A: I.169, M.189, F.282, F.285 Ligands: LFA.9 Ligand excluded by PLIP LFA.9: 12 residues within 4Å: Chain A: Y.179, W.186, W.275, M.278, S.279, F.282 Chain T: T.15, F.18, L.19, G.22, L.23 Ligands: LFA.8 Ligand excluded by PLIP LFA.31: 11 residues within 4Å: Chain A: W.275, S.279, I.311, I.314 Chain B: T.66, I.67 Chain T: G.22, L.23, P.26 Ligands: CHD.30, LFA.138 Ligand excluded by PLIP LFA.39: 7 residues within 4Å: Chain C: P.126, L.127, L.131, Y.253, W.258 Chain N: Y.304 Ligands: CHD.106 Ligand excluded by PLIP LFA.40: 3 residues within 4Å: Chain C: L.131, T.134 Chain G: C.31 Ligand excluded by PLIP LFA.41: 8 residues within 4Å: Chain A: F.237, W.288 Chain C: W.99, Y.102, H.103 Ligands: DMU.22, CHD.33, LFA.42 Ligand excluded by PLIP LFA.42: 5 residues within 4Å: Chain C: Y.102, L.106 Ligands: LFA.41, LFA.105, DMU.120 Ligand excluded by PLIP LFA.43: 9 residues within 4Å: Chain C: S.135, L.138, A.139, V.142 Chain G: T.15, W.16, A.24, S.27 Ligands: LFA.44 Ligand excluded by PLIP LFA.44: 8 residues within 4Å: Chain C: G.141, V.142, T.145, H.149, H.243 Chain G: W.16 Ligands: LFA.43, DMU.48 Ligand excluded by PLIP LFA.45: 11 residues within 4Å: Chain C: V.91, T.95, F.98, W.240, H.243, F.244, V.247, V.248, F.251 Ligands: LFA.46, DMU.48 Ligand excluded by PLIP LFA.46: 5 residues within 4Å: Chain C: I.84, I.87, I.88, W.240 Ligands: LFA.45 Ligand excluded by PLIP LFA.57: 5 residues within 4Å: Ligands: DMU.47, CHD.106, LFA.114, LFA.115, DMU.141 Ligand excluded by PLIP LFA.69: 10 residues within 4Å: Chain G: F.18, L.19, G.22, L.23 Chain N: Y.179, W.186, W.275, M.278, F.282 Ligands: LFA.83 Ligand excluded by PLIP LFA.75: 10 residues within 4Å: Chain G: G.22, L.23, P.26 Chain N: W.275, S.279, I.311 Chain O: T.66, I.67 Ligands: CHD.66, LFA.97 Ligand excluded by PLIP LFA.83: 6 residues within 4Å: Chain N: M.189, V.193, L.197, F.282, F.285 Ligands: LFA.69 Ligand excluded by PLIP LFA.97: 5 residues within 4Å: Chain G: R.17, F.21 Chain O: Q.59 Ligands: CHD.66, LFA.75 Ligand excluded by PLIP LFA.105: 5 residues within 4Å: Chain P: W.258 Ligands: DMU.22, CHD.33, LFA.42, DMU.120 Ligand excluded by PLIP LFA.112: 7 residues within 4Å: Chain A: Y.304 Chain P: P.126, L.127, L.131, Y.253, W.258 Ligands: CHD.33 Ligand excluded by PLIP LFA.113: 2 residues within 4Å: Chain P: T.134 Chain T: C.31 Ligand excluded by PLIP LFA.114: 8 residues within 4Å: Chain N: F.237, W.288 Chain P: T.95, W.99, A.107 Ligands: LFA.57, CHD.106, DMU.141 Ligand excluded by PLIP LFA.115: 4 residues within 4Å: Chain P: Y.102, L.106 Ligands: DMU.47, LFA.57 Ligand excluded by PLIP LFA.116: 6 residues within 4Å: Chain P: S.135, L.138, A.139 Chain T: W.16, S.27 Ligands: LFA.117 Ligand excluded by PLIP LFA.117: 8 residues within 4Å: Chain P: L.138, G.141, V.142, T.145, H.149 Chain T: W.16 Ligands: LFA.116, DMU.121 Ligand excluded by PLIP LFA.118: 9 residues within 4Å: Chain P: V.91, T.95, F.98, W.240, F.244, V.247, V.248 Ligands: LFA.119, DMU.121 Ligand excluded by PLIP LFA.119: 5 residues within 4Å: Chain P: I.84, I.87, W.240 Ligands: LFA.118, DMU.122 Ligand excluded by PLIP LFA.138: 6 residues within 4Å: Chain T: R.17, F.21, L.25, P.26 Ligands: CHD.30, LFA.31 Ligand excluded by PLIP

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

DMU.10: 3 residues within 4Å: Chain A: W.334, M.339 Ligands: DMU.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.334 DMU.11: 13 residues within 4Å: Chain A: N.406, T.408, W.409, I.412, R.480 Chain D: A.84, F.87 Chain K: F.9, H.10 Chain M: K.4, P.5, A.6 Ligands: DMU.74 13 PLIP interactions: 7 interactions with chain A, 1 interactions with chain M, 4 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, D:A.84, D:F.87, K:F.9 Hydrogen bonds: A:N.406, A:T.408, A:R.480, M:A.6 Water bridges: D:E.77, D:E.77 DMU.22: 14 residues within 4Å: Chain A: D.298 Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: F.20, P.21, N.22, N.24, R.27 Ligands: CHD.33, LFA.41, LFA.105 11 PLIP interactions: 3 interactions with chain H, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: H:N.22, A:D.298 Water bridges: H:N.24, H:N.24, A:T.301, A:T.301, A:T.301 Hydrophobic interactions: C:W.99, C:W.99, C:W.99, C:L.106 DMU.23: 12 residues within 4Å: Chain A: I.286, A.303, Y.304, S.307, A.308, I.311 Chain B: L.81, Y.85 Chain T: N.34, H.38 Ligands: DMU.32, DMU.139 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.286, A:Y.304, A:I.311 Hydrogen bonds: B:Y.85, B:Y.85 DMU.26: 4 residues within 4Å: Chain B: H.26, I.30, I.34, I.72 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.30, B:I.34, B:I.72 DMU.27: 3 residues within 4Å: Chain A: F.321 Chain B: L.37 Ligands: DMU.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.321, B:L.37 DMU.28: 10 residues within 4Å: Chain A: L.324, A.325, H.328 Chain B: H.52, M.56, D.57, W.65 Chain E: D.40 Chain I: A.14 Ligands: DMU.27 10 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E, 2 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:W.65, A:L.324, A:A.325 Hydrogen bonds: B:D.57, E:D.40, E:D.40 Water bridges: B:H.52, I:G.11, I:A.14 Salt bridges: B:H.52 DMU.32: 9 residues within 4Å: Chain B: A.77, L.78, L.81, R.82, Y.85 Chain T: L.37, H.38 Ligands: DMU.23, DMU.139 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain B Hydrophobic interactions: T:L.37, B:L.78, B:L.81 Salt bridges: T:H.38 DMU.38: 3 residues within 4Å: Chain C: W.34, M.40 Chain G: F.69 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.34, G:F.69 DMU.47: 8 residues within 4Å: Chain C: W.116, P.117, V.254, W.258, W.259, S.261 Ligands: LFA.57, LFA.115 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.254, C:W.258 Hydrogen bonds: C:W.116 DMU.48: 5 residues within 4Å: Chain C: L.138, D.246, V.247 Ligands: LFA.44, LFA.45 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.138, C:V.247 DMU.49: 1 residues within 4Å: Chain C: F.251 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.251 DMU.50: 10 residues within 4Å: Chain C: N.38, S.39, T.41, I.45 Chain J: T.37, G.41, G.42, Y.45 Ligands: DMU.51, DMU.55 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:I.45, J:Y.45 Hydrogen bonds: C:N.38, C:N.38, C:S.39, C:S.39, C:S.39, C:T.41, J:Y.45 DMU.51: 7 residues within 4Å: Chain C: N.38, S.39, M.40, T.41 Chain G: S.61, W.62 Ligands: DMU.50 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:S.61, C:S.39, C:M.40 DMU.55: 12 residues within 4Å: Chain A: L.110, L.145 Chain C: M.33, F.37 Chain J: S.46, Y.48, C.49, L.50, W.52, A.53 Ligands: DMU.50, XE.56 7 PLIP interactions: 2 interactions with chain J, 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: J:L.50, J:A.53, A:L.110, A:L.145, C:M.33, C:F.37, C:F.37 DMU.58: 15 residues within 4Å: Chain A: I.332, W.334, M.339, K.411, F.414, A.415, F.418 Chain D: R.73, S.74, T.75, N.76, E.77, W.78, V.81 Ligands: DMU.10 17 PLIP interactions: 8 interactions with chain A, 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:F.414, A:A.415, A:F.418, D:V.81 Hydrogen bonds: A:W.334, A:K.411, D:R.73, D:T.75, D:T.75, D:T.75, D:W.78 Water bridges: A:I.332, A:W.334, D:M.71, D:N.72, B:L.46 Salt bridges: A:K.411 DMU.67: 10 residues within 4Å: Chain C: N.125, L.127, L.131 Chain G: C.31, N.34, H.38 Chain N: D.300 Chain O: Y.85 Ligands: DMU.76, DMU.98 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain N, 2 interactions with chain G Hydrophobic interactions: C:L.127, C:L.131, N:D.300 Hydrogen bonds: C:N.125, C:N.125, G:H.38 Salt bridges: G:H.38 DMU.70: 4 residues within 4Å: Chain J: G.41, L.44, Y.45, Y.48 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:L.44 DMU.72: 6 residues within 4Å: Chain L: W.19, L.22, A.23, T.26 Chain M: I.17, V.21 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:I.17, M:V.21, L:L.22, L:T.26 DMU.73: 10 residues within 4Å: Chain A: F.459 Chain D: W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 6 PLIP interactions: 3 interactions with chain M, 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: M:L.27, M:A.30, D:W.98, D:W.98, A:F.459 Hydrogen bonds: M:Y.35 DMU.74: 4 residues within 4Å: Chain K: F.9 Chain M: P.12, Q.15 Ligands: DMU.11 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain M Hydrophobic interactions: K:F.9, K:F.9, M:P.12, M:Q.15 DMU.76: 8 residues within 4Å: Chain G: N.34, H.38 Chain N: S.307, A.308, I.311 Chain O: L.81 Ligands: DMU.67, DMU.98 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:I.311 DMU.84: 2 residues within 4Å: Chain N: W.334 Ligands: DMU.130 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:W.334, N:W.334 DMU.85: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, R.480 Chain Q: T.80, A.84, F.87, F.88 Chain X: H.10 Chain Z: P.5, A.6 Ligands: DMU.147 9 PLIP interactions: 4 interactions with chain N, 3 interactions with chain Q, 1 interactions with chain Z, 1 interactions with chain X Hydrophobic interactions: N:W.409, N:I.412, Q:T.80, Q:F.87, Q:F.88 Hydrogen bonds: N:N.406, N:R.480, Z:A.6 Salt bridges: X:H.10 DMU.98: 11 residues within 4Å: Chain G: L.37, H.38 Chain N: S.307 Chain O: L.73, I.74, A.77, L.78, L.81, R.82 Ligands: DMU.67, DMU.76 6 PLIP interactions: 5 interactions with chain O, 1 interactions with chain G Hydrophobic interactions: O:L.73, O:I.74, O:A.77, O:L.78, O:L.81, G:L.37 DMU.101: 7 residues within 4Å: Chain O: H.26, M.29, I.30, L.33, I.34, I.72, L.75 6 PLIP interactions: 6 interactions with chain O Hydrophobic interactions: O:I.30, O:L.33, O:L.33, O:I.34, O:I.72, O:L.75 DMU.102: 4 residues within 4Å: Chain N: F.321 Chain O: L.37, I.64, W.65 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:F.321, O:L.37, O:I.64 DMU.103: 8 residues within 4Å: Chain N: A.325, H.328 Chain O: I.41, H.52, M.56, D.57 Chain R: D.40 Chain V: A.14 8 PLIP interactions: 4 interactions with chain O, 1 interactions with chain N, 2 interactions with chain R, 1 interactions with chain V Hydrophobic interactions: O:I.41, N:A.325 Hydrogen bonds: O:D.57, R:D.40, R:D.40 Water bridges: O:H.52, V:A.14 Salt bridges: O:H.52 DMU.111: 3 residues within 4Å: Chain P: W.34, M.40 Chain T: F.69 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:W.34, P:W.34 DMU.120: 8 residues within 4Å: Chain P: W.116, P.117, V.254, W.258, W.259, S.261 Ligands: LFA.42, LFA.105 5 PLIP interactions: 5 interactions with chain P Hydrophobic interactions: P:V.254, P:W.258 Hydrogen bonds: P:W.116, P:W.259 Water bridges: P:P.117 DMU.121: 5 residues within 4Å: Chain P: H.243, V.247 Ligands: LFA.117, LFA.118, DMU.122 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:H.243, P:V.247 DMU.122: 4 residues within 4Å: Chain P: V.247, F.251 Ligands: LFA.119, DMU.121 3 PLIP interactions: 3 interactions with chain P Hydrophobic interactions: P:V.247, P:F.251, P:F.251 DMU.123: 9 residues within 4Å: Chain P: N.38, S.39, T.41, I.45 Chain W: G.41, G.42, Y.45 Ligands: DMU.124, DMU.128 10 PLIP interactions: 3 interactions with chain W, 7 interactions with chain P Hydrophobic interactions: W:Y.45, W:Y.45, P:I.45 Hydrogen bonds: W:Y.45, P:N.38, P:N.38, P:S.39, P:S.39, P:S.39, P:T.41 DMU.124: 7 residues within 4Å: Chain P: W.34, N.38, S.39, M.40, T.41 Ligands: DMU.123, EDO.125 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:W.34, P:M.40, P:T.41 DMU.128: 13 residues within 4Å: Chain N: L.110, L.145 Chain P: T.32, M.33, F.37 Chain W: S.46, Y.48, C.49, L.50, W.52, A.53 Ligands: DMU.123, XE.129 8 PLIP interactions: 2 interactions with chain N, 4 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: N:L.110, N:L.145, P:T.32, P:M.33, P:F.37, P:F.37, W:L.50, W:A.53 DMU.130: 14 residues within 4Å: Chain N: I.332, W.334, M.339, K.411, A.415, F.418 Chain Q: R.73, S.74, T.75, N.76, E.77, W.78, V.81 Ligands: DMU.84 14 PLIP interactions: 6 interactions with chain N, 8 interactions with chain Q Hydrophobic interactions: N:A.415, N:F.418, Q:W.78, Q:V.81 Hydrogen bonds: N:W.334, N:K.411, Q:R.73, Q:T.75, Q:T.75, Q:T.75, Q:E.77, Q:W.78 Water bridges: N:I.332 Salt bridges: N:K.411 DMU.139: 11 residues within 4Å: Chain A: D.300, Y.304 Chain B: Y.85 Chain P: N.125, L.127, L.131 Chain T: C.31, N.34, H.38 Ligands: DMU.23, DMU.32 6 PLIP interactions: 4 interactions with chain P, 1 interactions with chain A, 1 interactions with chain T Hydrophobic interactions: P:L.127, P:L.131, A:Y.304 Hydrogen bonds: P:N.125, P:N.125 Salt bridges: T:H.38 DMU.141: 13 residues within 4Å: Chain N: D.298 Chain P: W.99, H.103, L.106, A.107 Chain U: F.20, P.21, N.22, N.24, R.27 Ligands: LFA.57, CHD.106, LFA.114 12 PLIP interactions: 4 interactions with chain P, 5 interactions with chain U, 3 interactions with chain N Hydrophobic interactions: P:W.99, P:W.99, P:W.99, P:L.106 Hydrogen bonds: U:N.22 Water bridges: U:N.22, U:N.24, U:N.24, U:N.24, N:T.301, N:T.301, N:T.301 DMU.143: 3 residues within 4Å: Chain W: G.41, Y.45, Y.48 2 PLIP interactions: 2 interactions with chain W Hydrophobic interactions: W:Y.45, W:Y.48 DMU.145: 8 residues within 4Å: Chain Y: W.19, L.22, A.23, T.26 Chain Z: K.13, E.14, I.17, V.21 7 PLIP interactions: 4 interactions with chain Y, 3 interactions with chain Z Hydrophobic interactions: Y:W.19, Y:L.22, Y:A.23, Y:T.26, Z:V.21 Hydrogen bonds: Z:K.13, Z:K.13 DMU.146: 11 residues within 4Å: Chain N: F.459, L.462 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, G.31, W.32, Y.35, H.36 8 PLIP interactions: 3 interactions with chain Z, 2 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: Z:L.27, N:F.459, N:L.462, Q:L.95, Q:W.98, Q:W.98 Hydrogen bonds: Z:Y.35 Water bridges: Z:H.36 DMU.147: 5 residues within 4Å: Chain N: W.409 Chain X: F.9 Chain Z: P.12, Q.15 Ligands: DMU.85 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain X, 1 interactions with chain Z Hydrophobic interactions: N:W.409, X:F.9, Z:Q.15

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

EDO.12: 5 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligands: CHD.30 Ligand excluded by PLIP EDO.14: 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.15: 3 residues within 4Å: Chain A: K.265, T.489 Chain F: P.83 Ligand excluded by PLIP EDO.29: 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.52: 2 residues within 4Å: Chain C: M.44, T.48 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.111 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain C: W.146, S.150, H.158 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain D: K.56 Chain E: L.93, N.94, G.97, I.98, S.99 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.61: 2 residues within 4Å: Chain E: R.53, R.57 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain C: N.230, H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.68: 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.86: 5 residues within 4Å: Chain N: H.256, T.259, K.265, T.490, N.491 Ligand excluded by PLIP EDO.87: 6 residues within 4Å: Chain N: G.269, M.271, G.272 Chain O: A.58, E.62 Ligands: CHD.66 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: 3 residues within 4Å: Chain N: K.265, T.489 Chain S: I.70 Ligand excluded by PLIP EDO.90: 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.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.125: 3 residues within 4Å: Chain P: M.44, T.48 Ligands: DMU.124 Ligand excluded by PLIP EDO.126: 5 residues within 4Å: Chain N: P.222, A.223 Chain O: G.177 Chain P: E.111 Chain U: W.68 Ligand excluded by PLIP EDO.127: 7 residues within 4Å: Chain P: W.146, S.150, D.155, H.158 Chain T: A.13, R.14, R.17 Ligand excluded by PLIP EDO.131: 7 residues within 4Å: Chain Q: K.56 Chain R: L.93, N.94, G.97, I.98, S.99, E.103 Ligand excluded by PLIP EDO.132: 3 residues within 4Å: Chain R: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.133: 2 residues within 4Å: Chain R: R.53, R.57 Ligand excluded by PLIP EDO.135: 6 residues within 4Å: Chain N: T.489, T.490 Chain S: S.67, T.68, V.69, W.71 Ligand excluded by PLIP EDO.136: 5 residues within 4Å: Chain P: P.73, N.230, H.231 Chain S: D.9, E.17 Ligand excluded by PLIP EDO.140: 6 residues within 4Å: Chain P: G.120 Chain T: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP

14 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.16: 4 residues within 4Å: Chain A: F.67, F.68, S.149, L.150 No protein-ligand interaction detected (PLIP) XE.17: 4 residues within 4Å: Chain A: L.150, L.202, A.203, I.206 No protein-ligand interaction detected (PLIP) XE.18: 2 residues within 4Å: Chain A: L.112, L.113 No protein-ligand interaction detected (PLIP) XE.19: 2 residues within 4Å: Chain A: L.33 Chain L: I.39 No protein-ligand interaction detected (PLIP) XE.20: 2 residues within 4Å: Chain A: V.394, I.471 No protein-ligand interaction detected (PLIP) XE.24: 5 residues within 4Å: Chain A: L.353, I.356 Chain B: T.27, V.31, I.76 No protein-ligand interaction detected (PLIP) XE.56: 2 residues within 4Å: Chain C: T.32 Ligands: DMU.55 No protein-ligand interaction detected (PLIP) XE.91: 4 residues within 4Å: Chain N: F.67, F.68, S.149, L.150 No protein-ligand interaction detected (PLIP) XE.92: 4 residues within 4Å: Chain N: L.150, L.202, A.203, I.206 No protein-ligand interaction detected (PLIP) XE.93: 2 residues within 4Å: Chain N: L.112, L.113 No protein-ligand interaction detected (PLIP) XE.94: 2 residues within 4Å: Chain N: L.33 Chain Y: I.39 No protein-ligand interaction detected (PLIP) XE.95: 2 residues within 4Å: Chain N: V.394, I.471 No protein-ligand interaction detected (PLIP) XE.99: 5 residues within 4Å: Chain N: L.353, I.356 Chain O: T.27, V.31, I.76 No protein-ligand interaction detected (PLIP) XE.129: 1 residues within 4Å: Ligands: DMU.128 No protein-ligand interaction detected (PLIP)

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

PGV.21: 27 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152, V.155, I.158, P.200 Chain C: H.9, V.11, G.20, A.24, T.28, L.31, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86 Ligands: PEK.65 19 PLIP interactions: 12 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:L.31, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, A:L.152, A:V.155, A:I.158, A:P.200 Hydrogen bonds: C:H.9, C:E.64, A:R.96, A:M.97 Water bridges: C:M.83 Salt bridges: A:R.96 PGV.35: 22 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, H.207, I.209, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 31 PLIP interactions: 29 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:W.58, C:I.62, C:F.86, C:F.86, C:I.209, C:I.210, C:I.210, C:I.210, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:T.66, C:H.71, 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.96: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, V.155, I.158 Chain P: 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, F.93 Ligands: PGV.108, PEK.137 19 PLIP interactions: 12 interactions with chain P, 7 interactions with chain N Hydrophobic interactions: P:A.24, P:T.28, P:T.53, P:W.57, P:W.57, P:W.57, P:W.58, P:F.86, P:F.86, P:F.93, N:V.155, N:I.158 Hydrogen bonds: P:H.9, P:E.64, N:R.96, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.108: 21 residues within 4Å: Chain P: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, H.207, I.210, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.96 25 PLIP interactions: 23 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:I.62, P:F.86, P:F.86, P:I.210, P:F.214, P:F.214 Hydrogen bonds: P:S.65, 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

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

CUA.25: 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 CHD: CHOLIC ACID(Non-covalent)

CHD.30: 15 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: EDO.13, LFA.31, LFA.138 13 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B, 5 interactions with chain T Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, B:T.66, T:F.21 Hydrogen bonds: B:Q.59, B:E.62, B:E.62 Water bridges: T:R.17, T:R.17 Salt bridges: T:R.14, T:R.17 CHD.33: 12 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: DMU.22, LFA.41, LFA.105, LFA.112 9 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A, 1 interactions with chain P Hydrogen bonds: C:W.99, A:T.301, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:W.288, A:Y.304, P:L.127 Water bridges: A:T.301 CHD.37: 6 residues within 4Å: Chain C: R.156, L.160, F.164, F.219, L.223 Chain J: F.1 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.160, C:L.160, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 CHD.66: 14 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: LFA.75, EDO.87, LFA.97 14 PLIP interactions: 5 interactions with chain G, 5 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: G:F.21, O:T.66, N:M.271, N:W.275, N:W.275, N:W.275 Water bridges: G:R.17, G:R.17, O:T.63 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:E.62, O:E.62, O:T.63 CHD.106: 12 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: LFA.39, LFA.57, LFA.114, DMU.141 9 PLIP interactions: 6 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:T.301, P:W.99 Water bridges: N:T.301, N:T.301 Salt bridges: N:H.233, P:H.103 CHD.110: 6 residues within 4Å: Chain P: R.156, L.160, F.164, F.219, L.223 Chain W: F.1 7 PLIP interactions: 7 interactions with chain P Hydrophobic interactions: P:L.160, P:F.164, P:F.164, P:F.164, P:F.219, P:L.223 Salt bridges: P:R.156

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.34: 3 residues within 4Å: Chain C: H.148, H.232, E.236 No protein-ligand interaction detected (PLIP) UNX.107: 3 residues within 4Å: Chain P: H.148, H.232, E.236 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.62: 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.134: 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 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.65: 23 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 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.21 12 PLIP interactions: 3 interactions with chain C, 7 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: C:W.34, C:F.203, G:F.69, A:V.155, A:L.210 Hydrogen bonds: C:I.188, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.137: 25 residues within 4Å: Chain N: H.151, V.155, A.203, T.207, L.210 Chain P: W.34, T.174, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.96 15 PLIP interactions: 8 interactions with chain T, 3 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: T:W.62, T:F.69, P:W.34, P:F.203, N:V.155, N:A.203, N:T.207, N:L.210 Hydrogen bonds: T:T.68, T:F.70, T:N.76, T:N.76, P:I.188 Water bridges: T:F.69, T:F.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muramoto, K. et al., The binding sites of carbon dioxide, nitrous oxide, and xenon reveal a putative exhaust channel for bovine cytochrome c oxidase. J.Biol.Chem. (2025)

Release Date

2025-07-02

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: 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: 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

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

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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