SMTL ID : 6juw.1

BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION

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, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 32 PLIP interactions: 32 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:I.73, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:T.424, A:F.425 Hydrogen bonds: 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, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 33 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 40 PLIP interactions: 34 interactions with chain A, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:F.348, A:L.353, 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, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.290 Metal complexes: A:H.376, H2O.1 HEA.83: 37 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, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 32 PLIP interactions: 32 interactions with chain N, Hydrophobic interactions: N:A.24, 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:F.377, N:L.381, N:L.381, N:F.393, N:F.393, N:T.424, N:F.425 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:Y.371, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.425 Metal complexes: N:H.61, N:H.378 HEA.84: 32 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain O: I.34, P.69, I.72, L.73 39 PLIP interactions: 33 interactions with chain N, 5 interactions with chain O, 1 Ligand-Water 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:T.316, N:V.320, 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, 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 Water bridges: N:H.291, N:T.316, N:D.369, N:D.369, N:R.438, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 Metal complexes: N:H.376, H2O.54

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

CU.3: 3 residues within 4Å: Chain A: H.240, H.290, H.291 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.4 CU.85: 3 residues within 4Å: Chain N: H.240, H.290, H.291 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.59

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.13 MG.86: 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.64, H2O.65, H2O.67

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

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.441 NA.27: 3 residues within 4Å: Chain C: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.234 NA.87: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40 Water bridges: N:Q.43 NA.110: 3 residues within 4Å: Chain P: H.146, H.230, E.234 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:H.230, P:E.234

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

DMU.6: 5 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain K Hydrophobic interactions: D:I.86, K:V.21, K:W.24, K:W.24, K:W.24, K:V.25 DMU.21: 7 residues within 4Å: Chain B: H.26, I.30, L.33, I.34, L.37, I.72, L.75 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.30, B:L.33, B:I.34, B:L.37, B:I.72, B:L.75 Hydrogen bonds: B:H.26 DMU.28: 9 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: L.38, G.41, G.42, Y.45 Ligands: DMU.69 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:I.43, J:L.38, J:Y.45, J:Y.45 Hydrogen bonds: C:N.36, C:N.36, C:S.37, J:Y.45 DMU.29: 5 residues within 4Å: Chain C: W.32, M.38, L.41 Chain G: F.69 Ligands: PGV.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.32, C:L.41 Water bridges: G:F.69 DMU.30: 4 residues within 4Å: Chain C: Y.100, F.249, V.252 Ligands: CDL.65 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.249, C:F.249, C:F.249, C:V.252 DMU.44: 6 residues within 4Å: Chain D: L.91, I.94, W.95, H.98 Chain K: Y.26, I.31 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.95 Salt bridges: D:H.98 DMU.69: 12 residues within 4Å: Chain A: L.110, L.145 Chain C: S.27, T.30, M.31, F.35 Chain J: S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.28 6 PLIP interactions: 1 interactions with chain J, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: J:Y.45 Hydrophobic interactions: C:T.30, C:F.35, C:F.35, A:L.110, A:L.145 DMU.72: 4 residues within 4Å: Chain K: V.25, A.28, W.35 Ligands: DMU.75 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:V.25, K:A.28, K:W.35 DMU.73: 4 residues within 4Å: Chain K: A.28, I.33, W.35 Ligands: DMU.75 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:W.35, K:W.35, K:W.35 Hydrogen bonds: K:T.29, K:I.33 DMU.74: 6 residues within 4Å: Chain D: F.84 Chain K: A.14, S.15, T.18, F.19 Ligands: PGV.7 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:F.19, D:F.84 Hydrogen bonds: K:S.15, K:T.18 DMU.75: 3 residues within 4Å: Ligands: TGL.45, DMU.72, DMU.73 No protein-ligand interaction detected (PLIP) DMU.76: 10 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: S.30, A.34, F.37, R.40, H.41, L.44 Ligands: TGL.78, EDO.80 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:A.34 Hydrogen bonds: L:R.40, L:H.41 Water bridges: L:R.40, L:R.40 Salt bridges: L:R.40, L:R.40 DMU.81: 12 residues within 4Å: Chain A: F.459 Chain D: L.92, W.95, Y.99 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 7 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 3 interactions with chain M Hydrophobic interactions: D:L.92, D:W.95, D:W.95, A:F.459, M:L.27, M:A.30 Water bridges: M:Y.35 DMU.107: 7 residues within 4Å: Chain O: H.26, M.29, I.30, L.33, L.37, I.72, L.75 5 PLIP interactions: 5 interactions with chain O Hydrophobic interactions: O:L.33, O:L.37, O:I.72, O:L.75 Hydrogen bonds: O:H.26 DMU.111: 3 residues within 4Å: Chain P: W.32, M.38 Chain T: F.69 3 PLIP interactions: 1 interactions with chain T, 2 interactions with chain P Hydrophobic interactions: T:F.69, P:W.32, P:W.32 DMU.112: 11 residues within 4Å: Chain P: M.31, N.36, S.37, T.39, I.43 Chain W: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.147 7 PLIP interactions: 4 interactions with chain W, 3 interactions with chain P Hydrophobic interactions: W:L.38, W:Y.45, W:Y.45, W:Y.45 Hydrogen bonds: P:N.36, P:S.37, P:S.37 DMU.127: 8 residues within 4Å: Chain Q: L.91, I.94, W.95, H.98 Chain X: Y.26, Q.30, I.31, G.32 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain Q Hydrogen bonds: X:Y.26 Hydrophobic interactions: Q:L.91, Q:I.94 Salt bridges: Q:H.98 DMU.147: 13 residues within 4Å: Chain N: L.110, A.114, L.145 Chain P: S.27, M.31, F.35 Chain W: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.112 8 PLIP interactions: 3 interactions with chain N, 3 interactions with chain W, 2 interactions with chain P Hydrophobic interactions: N:L.110, N:A.114, N:L.145, W:L.50, P:M.31, P:F.35 Hydrogen bonds: W:Y.45, W:Y.45 DMU.149: 7 residues within 4Å: Chain N: M.423 Chain Q: I.86 Chain X: V.21, W.24, V.25 Ligands: DMU.151, DMU.153 6 PLIP interactions: 5 interactions with chain X, 1 interactions with chain Q Hydrophobic interactions: X:V.21, X:W.24, X:W.24, X:W.24, X:V.25, Q:I.86 DMU.150: 7 residues within 4Å: Chain O: M.5 Chain X: A.28, T.29, I.33, W.35 Ligands: DMU.151, DMU.153 1 PLIP interactions: 1 interactions with chain X Hydrophobic interactions: X:W.35 DMU.151: 6 residues within 4Å: Chain X: V.25, A.28, T.29 Ligands: DMU.149, DMU.150, DMU.153 3 PLIP interactions: 3 interactions with chain X Hydrophobic interactions: X:V.25, X:A.28, X:T.29 DMU.152: 2 residues within 4Å: Chain Q: L.91 Chain X: Y.26 4 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain X Hydrophobic interactions: Q:L.91, X:Y.26, X:Y.26, X:Y.26 DMU.153: 3 residues within 4Å: Ligands: DMU.149, DMU.150, DMU.151 No protein-ligand interaction detected (PLIP) DMU.154: 8 residues within 4Å: Chain N: M.117 Chain W: F.55 Chain Y: A.34, F.37, I.38, R.40, H.41, L.44 7 PLIP interactions: 7 interactions with chain Y Hydrophobic interactions: Y:A.34, Y:I.38 Hydrogen bonds: Y:H.41 Water bridges: Y:R.40, Y:R.40 Salt bridges: Y:R.40, Y:R.40 DMU.158: 13 residues within 4Å: Chain N: F.459, L.462 Chain Q: L.92, W.95, Y.99 Chain Z: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 10 PLIP interactions: 3 interactions with chain N, 3 interactions with chain Q, 4 interactions with chain Z Hydrophobic interactions: N:F.459, N:F.459, N:L.462, Q:L.92, Q:W.95, Z:A.30, Z:L.34 Water bridges: Q:Y.99, Z:H.36 Hydrogen bonds: Z:W.32

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

PGV.7: 18 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.77, A.81, F.84 Chain K: F.4, H.5 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16, L.19, S.20 Ligands: DMU.74 19 PLIP interactions: 6 interactions with chain A, 4 interactions with chain M, 5 interactions with chain D, 4 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, M:P.12, M:Q.15, M:A.16, M:L.19, D:T.77, D:A.81, D:F.84, D:F.84, D:F.84, K:F.4, K:F.4, K:F.4 Hydrogen bonds: A:T.408 Water bridges: A:T.404, A:R.480 Salt bridges: K:H.5 PGV.8: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151 Chain C: H.7, V.9, G.18, A.22, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88, F.91 Ligands: DMU.29, PEK.35, PGV.36 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:F.148, C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.91 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55 Salt bridges: A:R.96 Water bridges: C:M.81 PGV.36: 25 residues within 4Å: Chain C: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, L.204, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.8, CDL.33 29 PLIP interactions: 2 interactions with chain F, 27 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.63, C:Q.74, C:R.219, C:H.229, C:H.229 Hydrophobic interactions: C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:F.84, C:L.204, C:I.208, C:I.208, C:I.208, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.88: 13 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.77, A.81, F.84 Chain X: F.4, H.5 Chain Z: P.12, Q.15, A.16, L.19, S.20 11 PLIP interactions: 4 interactions with chain Q, 2 interactions with chain X, 3 interactions with chain Z, 2 interactions with chain N Hydrophobic interactions: Q:T.77, Q:A.81, Q:F.84, Q:F.84, X:F.4, Z:P.12, Z:P.12, Z:L.19, N:T.408 Salt bridges: X:H.5 Hydrogen bonds: N:T.408 PGV.89: 28 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155 Chain P: H.7, V.9, G.18, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88, F.91 Ligands: PEK.117, PGV.118 14 PLIP interactions: 10 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: P:T.26, P:T.51, P:W.55, P:W.55, P:W.55, P:W.56, P:F.84, P:F.91, N:V.155 Hydrogen bonds: P:W.55, N:R.96, N:M.97 Water bridges: P:M.81 Salt bridges: N:R.96 PGV.118: 25 residues within 4Å: Chain P: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, E.88, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.89, CDL.115 27 PLIP interactions: 25 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:I.60, P:F.84, P:F.84, P:I.208, P:I.208, P:I.208, P:F.212, P:F.212 Hydrogen bonds: P:S.63, P:R.219, P:F.231, P:G.232 Water bridges: P:S.63, P:Q.74, P:R.219, P:H.229, P:H.229, S:Q.12, S:E.17 Salt bridges: P:R.219, P:R.219, P:H.229 PGV.119: 14 residues within 4Å: Chain G: A.1, S.2 Chain N: W.288 Chain P: V.89, L.90, T.93, W.97, H.101, L.104, A.105 Chain U: N.18 Ligands: CDL.65, CHD.113, PEK.116 13 PLIP interactions: 7 interactions with chain P, 3 interactions with chain N, 2 interactions with chain U, 1 interactions with chain G Hydrophobic interactions: P:V.89, P:L.90, P:T.93, P:W.97, P:W.97, P:W.97, P:W.97, N:W.288, G:A.1 Water bridges: N:D.298, N:D.298, U:N.18, U:N.18 PGV.141: 13 residues within 4Å: Chain A: D.298 Chain C: L.90, T.93, W.97, H.101, L.104, A.105 Chain H: N.16, N.18 Chain P: W.256 Chain T: A.1, S.2 Ligands: CHD.31 16 PLIP interactions: 7 interactions with chain H, 1 interactions with chain A, 6 interactions with chain C, 1 interactions with chain T, 1 interactions with chain P Hydrogen bonds: H:N.16, A:D.298 Water bridges: H:N.18, H:N.18, H:N.18, H:N.18, H:N.18, H:R.21 Hydrophobic interactions: C:L.90, C:T.93, C:W.97, C:W.97, C:W.97, C:W.97, T:A.1, P:W.256

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(Covalent)

PSC.9: 18 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: L.37, V.38, I.41, H.52, M.56, D.57, V.61, W.65 Chain E: D.4, F.7, L.37 Chain I: R.10, A.14, L.17 13 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B, 2 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: A:F.321, A:L.324, B:L.37, B:V.38, B:I.41, B:D.57, B:W.65, B:W.65, I:A.14, I:L.17 Salt bridges: B:H.52, E:D.4 pi-Cation interactions: E:F.7 PSC.146: 19 residues within 4Å: Chain N: F.268, F.321, A.325, H.328 Chain O: L.37, I.41, M.45, H.52, T.55, M.56, D.57, V.61, I.64, W.65, I.72 Chain R: D.4, F.7, L.37 Chain V: R.10 16 PLIP interactions: 10 interactions with chain O, 4 interactions with chain N, 2 interactions with chain R Hydrophobic interactions: O:L.37, O:I.41, O:I.41, O:M.56, O:V.61, O:I.64, O:W.65, O:I.72, N:F.268, N:F.321, N:F.321, N:A.325 Hydrogen bonds: O:D.57 Salt bridges: O:H.52, R:D.4 pi-Cation interactions: R:F.7

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.10: 16 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, H.24, L.28, F.32, S.35, S.36, L.39 Chain I: R.43 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain I, 5 interactions with chain B Hydrophobic interactions: A:F.346, A:F.426, A:F.426, A:F.426, A:F.430, B:L.7, B:F.32, B:F.32 Salt bridges: I:R.43, B:H.24 Water bridges: B:G.8 TGL.45: 21 residues within 4Å: Chain A: W.334, L.342, G.343, F.414, V.419 Chain B: L.39, I.42, S.43, T.47, T.48, K.49 Chain D: R.70, T.72, E.74, W.75, V.78, M.83, I.86 Chain I: R.16, H.20 Ligands: DMU.75 13 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:V.419, D:V.78, D:I.86, B:L.39, B:I.42, B:K.49 Salt bridges: A:K.411 Hydrogen bonds: D:E.74, D:W.75 TGL.78: 24 residues within 4Å: Chain A: T.17, L.18, L.20, L.21, F.22, W.25, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: N.9, I.10, P.11, F.12, S.13, R.19, M.23, F.27, F.28, S.30 Ligands: EDO.19, DMU.76 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:L.18, A:L.20, A:W.25, A:W.25, A:W.25, A:L.113, A:I.472, A:I.472, L:I.10, L:F.12, L:F.12, L:F.12, L:F.27, L:F.27, L:F.27, L:F.28 TGL.90: 15 residues within 4Å: Chain N: V.350, Y.379, F.418, N.422, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, L.28, F.32, S.35, L.39 Chain V: R.43 14 PLIP interactions: 8 interactions with chain N, 5 interactions with chain O, 1 interactions with chain V Hydrophobic interactions: N:V.350, N:Y.379, N:F.418, N:F.426, N:F.426, N:F.426, N:H.429, N:F.430, O:L.7, O:F.32, O:F.32 Water bridges: O:G.8 Salt bridges: O:H.24, V:R.43 TGL.128: 21 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, F.346, F.414, A.415, F.418, V.419 Chain O: L.39, I.42, L.46, T.47 Chain Q: R.70, T.72, E.74, W.75, V.78, M.83 Chain V: R.16, H.20 13 PLIP interactions: 4 interactions with chain Q, 7 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: Q:E.74, Q:V.78, N:W.334, N:W.334, N:W.334, N:F.346, N:A.415, N:F.418, O:L.39, O:I.42 Hydrogen bonds: Q:E.74, Q:W.75 Salt bridges: N:K.411 TGL.156: 23 residues within 4Å: Chain N: F.2, T.17, L.18, L.20, L.21, F.22, W.25, L.113, F.400, S.401, I.472 Chain Y: N.9, I.10, P.11, F.12, S.13, R.19, M.23, M.24, L.26, F.27, F.28, S.30 18 PLIP interactions: 9 interactions with chain N, 9 interactions with chain Y Hydrophobic interactions: N:L.20, N:L.21, N:L.21, N:F.22, N:W.25, N:W.25, N:L.113, N:F.400, N:I.472, Y:I.10, Y:F.12, Y:F.12, Y:L.26, Y:F.27, Y:F.27, Y:F.27, Y:F.28, Y:F.28

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

EDO.11: 9 residues within 4Å: Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain L: N.9 Ligand excluded by PLIP EDO.12: 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.13: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.56 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, E.62 Ligands: CHD.138 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: P.444, D.445, A.446 Chain B: M.1, A.2, P.4, L.133 Chain D: Q.116, M.120 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligands: EDO.18 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: F.393, A.410, H.413, M.468, I.471, I.472 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: D.486, L.487 Chain D: Y.19 Ligands: EDO.16 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Ligands: TGL.78 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: S.94, L.95, Y.113, M.148, F.219 Chain H: Q.6 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: W.104, Y.121, N.203, F.206 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: T.125, R.134, L.135 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain C: N.10, Q.66, H.68 Chain J: L.18, V.20, K.23 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.40 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain C: W.144, S.148, D.153, H.156 Chain F: A.1 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.38 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain C: Q.66 Chain F: G.15 Chain J: Q.13 Ligands: EDO.42 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain C: H.1, H.68 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain C: T.143, H.146, A.237, H.241 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain A: T.488, L.495 Chain D: Y.8, A.9, L.10, S.12 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain D: K.53 Chain E: L.89, N.90, G.93, I.94, S.95 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: K.118, D.122, W.135, N.140 Chain K: P.45 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: E.111, W.112, K.115 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain D: V.14, D.15, K.62 Chain M: T.2 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain E: R.49, R.52, R.53 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain B: S.54 Chain E: T.31, Y.35 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain A: Q.180, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.13 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain A: E.266 Chain F: D.65, N.66, S.67, T.68 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.59: 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.60: 5 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligands: EDO.63 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain F: V.20, A.24, Q.28, D.29, I.33, L.34 Ligand excluded by PLIP EDO.62: 9 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, I.52, R.56, H.94, H.98 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain E: W.23 Chain F: E.78, A.79, Q.80, R.81 Ligands: EDO.60 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain C: G.118 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.68: 6 residues within 4Å: Chain A: D.227 Chain B: G.177, R.178 Chain C: T.107 Chain H: N.18, T.20 Ligand excluded by PLIP EDO.71: 7 residues within 4Å: Chain A: V.118, E.119 Chain J: A.53, S.54, F.55, P.56 Chain L: K.45 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain L: G.7, K.8, I.10, F.12, S.13 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain L: S.30, F.37 Ligands: DMU.76 Ligand excluded by PLIP EDO.82: 5 residues within 4Å: Chain A: T.46, L.47 Chain D: V.100 Chain M: D.38, K.41 Ligand excluded by PLIP EDO.91: 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.92: 7 residues within 4Å: Chain N: G.269, Y.270, M.271, G.272 Chain O: A.58, E.62 Ligands: CHD.64 Ligand excluded by PLIP EDO.93: 6 residues within 4Å: Chain N: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.133 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain N: N.496, T.504, F.505, E.507 Chain S: W.73 Ligand excluded by PLIP EDO.95: 5 residues within 4Å: Chain N: K.265, T.489 Chain S: I.70, P.83, S.84 Ligand excluded by PLIP EDO.96: 2 residues within 4Å: Chain N: P.131, D.221 Ligand excluded by PLIP EDO.97: 9 residues within 4Å: Chain N: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain Y: N.9 Ligand excluded by PLIP EDO.98: 8 residues within 4Å: Chain N: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain Q: Y.8 Ligand excluded by PLIP EDO.99: 9 residues within 4Å: Chain N: P.174, T.509, Y.510, V.511 Chain S: N.32, L.34, P.36, R.56 Ligands: EDO.100 Ligand excluded by PLIP EDO.100: 7 residues within 4Å: Chain N: G.88, P.90, P.174, P.508 Chain P: Y.6 Chain S: N.32 Ligands: EDO.99 Ligand excluded by PLIP EDO.101: 7 residues within 4Å: Chain N: T.10, N.11, D.91, Y.502, H.503 Chain P: V.9 Ligands: EDO.157 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain N: M.1, F.2, R.5 Chain Y: Y.2, E.3 Ligand excluded by PLIP EDO.103: 6 residues within 4Å: Chain N: E.507 Chain P: T.3 Chain S: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.104: 8 residues within 4Å: Chain N: Y.19, G.76, N.80, N.98, S.101, S.156, G.160, F.164 Ligand excluded by PLIP EDO.105: 3 residues within 4Å: Chain N: Q.52, A.137, H.138 Ligand excluded by PLIP EDO.108: 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.109: 2 residues within 4Å: Chain O: M.122, F.206 Ligand excluded by PLIP EDO.120: 5 residues within 4Å: Chain N: P.222, A.223 Chain O: G.177 Chain P: E.109 Ligands: EDO.123 Ligand excluded by PLIP EDO.121: 7 residues within 4Å: Chain P: W.144, S.148, H.156 Chain S: A.1 Chain T: A.13, R.14, R.17 Ligand excluded by PLIP EDO.122: 4 residues within 4Å: Chain P: Q.66, H.68 Chain W: Q.13 Ligands: EDO.136 Ligand excluded by PLIP EDO.123: 5 residues within 4Å: Chain O: G.177 Chain P: E.109 Chain U: W.62, W.66 Ligands: EDO.120 Ligand excluded by PLIP EDO.124: 4 residues within 4Å: Chain P: N.10, P.11 Chain W: G.17, P.19 Ligand excluded by PLIP EDO.125: 7 residues within 4Å: Chain P: Q.74, R.78, N.228, H.229, H.230, F.231, E.234 Ligand excluded by PLIP EDO.126: 4 residues within 4Å: Chain P: T.143, H.146, H.147 Chain T: T.11 Ligand excluded by PLIP EDO.129: 7 residues within 4Å: Chain Q: K.53 Chain R: R.86, L.89, N.90, G.93, I.94, S.95 Ligand excluded by PLIP EDO.130: 7 residues within 4Å: Chain N: L.495 Chain Q: Y.8, A.9, L.10, P.11 Chain S: F.72, W.73 Ligand excluded by PLIP EDO.131: 3 residues within 4Å: Chain Q: P.11, D.23 Chain R: R.26 Ligand excluded by PLIP EDO.133: 6 residues within 4Å: Chain N: T.490 Chain S: S.67, T.68, V.69, W.71 Ligands: EDO.93 Ligand excluded by PLIP EDO.134: 4 residues within 4Å: Chain S: A.24, Q.28, D.29, L.34 Ligand excluded by PLIP EDO.135: 4 residues within 4Å: Chain P: P.71, H.229 Chain S: D.9, E.17 Ligand excluded by PLIP EDO.136: 3 residues within 4Å: Chain S: G.15, E.19 Ligands: EDO.122 Ligand excluded by PLIP EDO.137: 6 residues within 4Å: Chain N: Y.510 Chain S: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.142: 5 residues within 4Å: Chain P: W.32, F.33 Chain T: K.58, P.59, S.61 Ligand excluded by PLIP EDO.143: 7 residues within 4Å: Chain P: G.118 Chain T: A.46, F.47, I.48, Y.50, L.53, R.54 Ligand excluded by PLIP EDO.145: 6 residues within 4Å: Chain N: D.227 Chain O: G.177, R.178 Chain P: T.107 Chain U: N.18, T.20 Ligand excluded by PLIP EDO.148: 7 residues within 4Å: Chain N: V.118, E.119 Chain W: A.53, S.54, F.55, P.56 Chain Y: K.45 Ligand excluded by PLIP EDO.157: 4 residues within 4Å: Chain P: P.11 Chain Y: H.1, Y.2 Ligands: EDO.101 Ligand excluded by PLIP

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

CUA.20: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204 CUA.106: 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

9 x CHD: CHOLIC ACID(Non-covalent)

CHD.31: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Chain P: L.125 Ligands: CDL.139, PGV.141 8 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A, 1 interactions with chain P Hydrogen bonds: C:W.97, A:T.301 Salt bridges: C:H.101, A:H.233 Hydrophobic interactions: A:W.288, A:Y.304, P:L.125 Water bridges: A:T.301 CHD.32: 6 residues within 4Å: Chain C: R.154, L.158, F.162, F.217, L.221 Chain J: F.1 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.158, C:F.162, C:F.162, C:F.162, C:F.217, C:L.221 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.64: 13 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: E.62, T.63, T.66 Ligands: PEK.55, EDO.92 13 PLIP interactions: 6 interactions with chain G, 3 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: G:F.18, G:F.21, 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:T.63 CHD.70: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:T.37 Hydrogen bonds: J:R.33 CHD.77: 5 residues within 4Å: Chain L: W.18, A.22 Chain M: E.14, I.17, V.21 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:I.17, M:V.21 Water bridges: M:E.14 CHD.113: 11 residues within 4Å: Chain C: L.125 Chain N: H.233, W.288, D.300, T.301, Y.304, F.305 Chain P: W.97, H.101 Ligands: CDL.65, PGV.119 9 PLIP interactions: 2 interactions with chain P, 1 interactions with chain C, 6 interactions with chain N Hydrogen bonds: P:W.97, N:T.301 Salt bridges: P:H.101, N:H.233 Hydrophobic interactions: C:L.125, N:W.288, N:Y.304, N:F.305 Water bridges: N:T.301 CHD.114: 7 residues within 4Å: Chain P: R.154, L.158, Q.159, F.162, F.217, L.221 Chain W: F.1 10 PLIP interactions: 8 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:L.158, P:F.162, P:F.162, P:F.162, P:F.162, P:F.217, P:L.221, W:F.1 Salt bridges: P:R.154 Hydrogen bonds: W:F.1 CHD.138: 13 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: EDO.14, PEK.140 13 PLIP interactions: 4 interactions with chain A, 6 interactions with chain T, 3 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, T:F.18, T:F.21 Water bridges: T:R.17, T:R.17, B:T.63 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:E.62, B:T.63 CHD.155: 5 residues within 4Å: Chain Y: W.18, A.22 Chain Z: E.14, I.17, V.21 3 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain Y Hydrophobic interactions: Z:I.17, Y:W.18 Hydrogen bonds: Z:E.14

4 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.33: 22 residues within 4Å: Chain C: T.46, M.49, L.50, Y.53, W.56, R.57, I.60, R.61, F.65, V.169, T.172, S.210, T.211, I.214, V.215, F.218, K.222, H.224 Chain J: K.8, F.12, D.28 Ligands: PGV.36 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.46, C:M.49, C:L.50, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:V.169, C:T.172, C:T.211, C:I.214, C:V.215, C:F.218 Hydrogen bonds: C:Y.53, C:R.61, C:R.61, J:D.28 Water bridges: C:R.57, C:R.57 Salt bridges: C:R.61, C:K.222, C:K.222, C:H.224, J:K.8, J:K.8 CDL.65: 35 residues within 4Å: Chain C: N.123, L.125, L.129, T.132, L.136, V.140, L.248, V.252, W.256 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Chain N: F.282, L.283, I.286, D.300, Y.304, S.307, A.308, I.311 Chain O: L.73, I.74, A.77, L.78, L.81, R.82, Y.85 Ligands: DMU.30, PEK.55, CHD.113, PGV.119 27 PLIP interactions: 6 interactions with chain O, 8 interactions with chain C, 6 interactions with chain N, 7 interactions with chain G Hydrophobic interactions: O:L.73, O:I.74, O:L.81, O:L.81, O:R.82, C:L.129, C:T.132, C:L.136, C:L.248, C:V.252, C:W.256, N:F.282, N:L.283, N:I.286, N:Y.304, N:A.308, N:I.311, G:L.23, G:L.23, G:L.30, G:L.30 Hydrogen bonds: O:Y.85, C:N.123, C:N.123, G:N.34 Salt bridges: G:H.38, G:H.38 CDL.115: 22 residues within 4Å: Chain P: M.49, L.50, Y.53, W.56, R.57, I.60, R.61, F.65, T.172, S.210, T.211, I.214, V.215, F.218, R.219, K.222, H.224 Chain W: K.8, F.12, T.27, L.31 Ligands: PGV.118 21 PLIP interactions: 3 interactions with chain W, 18 interactions with chain P Hydrophobic interactions: W:L.31, P:L.50, P:Y.53, P:Y.53, P:Y.53, P:W.56, P:R.57, P:T.172, P:T.211, P:I.214, P:V.215, P:F.218 Salt bridges: W:K.8, W:K.8, P:K.222, P:K.222, P:H.224 Hydrogen bonds: P:Y.53, P:R.61, P:R.61 Water bridges: P:R.57 CDL.139: 36 residues within 4Å: Chain A: F.282, L.283, D.300, A.303, Y.304, S.307, I.311, I.314 Chain B: A.70, L.73, I.74, A.77, L.78, L.81, Y.85 Chain P: N.123, L.125, E.126, L.129, T.132, S.133, L.136, V.140, L.248, Y.251 Chain T: L.23, A.24, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.31, PEK.34, PEK.140 29 PLIP interactions: 7 interactions with chain A, 7 interactions with chain T, 9 interactions with chain P, 6 interactions with chain B Hydrophobic interactions: A:F.282, A:L.283, A:A.303, A:Y.304, A:I.311, A:I.314, T:L.23, T:L.30, T:N.34, T:L.37, T:L.37, P:L.129, P:L.129, P:T.132, P:L.136, P:V.140, P:L.248, P:Y.251, B:A.70, B:L.73, B:I.74, B:I.74, B:L.81, B:Y.85 Hydrogen bonds: A:D.300, P:N.123, P:E.126 Water bridges: T:N.34 Salt bridges: T:H.38

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)(Covalent)

PEK.34: 16 residues within 4Å: Chain A: V.193 Chain C: I.82, L.83, V.89, T.93, F.96, W.238, F.242, V.245, F.249 Chain T: A.4, K.5, G.6, H.8, L.23 Ligands: CDL.139 14 PLIP interactions: 11 interactions with chain C, 2 interactions with chain T, 1 interactions with chain A Hydrophobic interactions: C:I.82, C:I.82, C:L.83, C:V.89, C:F.96, C:W.238, C:W.238, C:W.238, C:V.245, C:F.249, C:F.249, T:K.5, T:L.23, A:V.193 PEK.35: 25 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.215 Chain C: W.32, T.172, Q.175, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8 20 PLIP interactions: 9 interactions with chain C, 7 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: C:W.32, C:Q.175, C:Y.179, C:I.186, C:F.201, C:F.201, C:F.201, G:W.62, G:F.69, A:V.155, A:A.203, A:T.207, A:L.215 Hydrogen bonds: C:Y.179, C:I.186, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.55: 19 residues within 4Å: Chain C: K.155, H.156, Q.159, I.163, T.166, L.167, Y.170 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, P.26 Chain N: W.275, S.279 Chain O: Q.59, T.66 Ligands: CHD.64, CDL.65 13 PLIP interactions: 7 interactions with chain C, 2 interactions with chain O, 3 interactions with chain G, 1 interactions with chain N Hydrophobic interactions: C:I.163, C:T.166, C:L.167, C:Y.170, O:T.66, G:L.25, N:W.275 Hydrogen bonds: C:K.155, C:K.155, O:Q.59, G:R.17 Water bridges: C:Q.159 Salt bridges: G:R.17 PEK.116: 16 residues within 4Å: Chain G: H.8 Chain N: V.193, L.197 Chain P: R.78, Y.79, I.82, V.89, L.90, T.93, F.96, W.238, F.242, V.245, V.246, F.249 Ligands: PGV.119 14 PLIP interactions: 2 interactions with chain N, 12 interactions with chain P Hydrophobic interactions: N:V.193, N:L.197, P:V.89, P:V.89, P:L.90, P:F.96, P:F.96, P:W.238, P:W.238, P:V.245, P:V.246, P:F.249 Hydrogen bonds: P:Y.79 Salt bridges: P:R.78 PEK.117: 26 residues within 4Å: Chain N: H.151, V.155, A.203, T.207, L.210, L.215 Chain P: W.32, F.33, Q.175, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.89 18 PLIP interactions: 4 interactions with chain N, 6 interactions with chain P, 8 interactions with chain T Hydrophobic interactions: N:V.155, N:A.203, N:L.210, N:L.215, P:W.32, P:F.33, P:Q.175, P:I.186, P:F.201, T:W.62, T:F.69 Hydrogen bonds: P:I.186, T:T.68, T:F.70, T:N.76, T:N.76 Water bridges: T:F.69, T:F.69 PEK.140: 19 residues within 4Å: Chain A: W.275, S.279, I.311 Chain B: Q.59, T.66 Chain P: K.155, H.156, Q.159, I.163, T.166, L.167, Y.170 Chain S: A.1 Chain T: R.17, F.21, G.22, L.23 Ligands: CHD.138, CDL.139 17 PLIP interactions: 2 interactions with chain A, 4 interactions with chain T, 2 interactions with chain B, 9 interactions with chain P Hydrophobic interactions: A:W.275, A:I.311, T:F.21, T:L.23, B:T.66, P:I.163, P:T.166, P:L.167, P:Y.170, P:Y.170, P:Y.170 Hydrogen bonds: T:R.17, B:Q.59, P:K.155, P:K.155 Salt bridges: T:R.17 Water bridges: P:Q.159

2 x ZN: ZINC ION(Non-covalent)

ZN.54: 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.132: 4 residues within 4Å: Chain S: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

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

PO4.67: 4 residues within 4Å: Chain H: R.21, Q.25, L.28, R.32 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:Q.25, H:Q.25, H:Q.25 Water bridges: H:R.21, H:R.21, H:R.21 Salt bridges: H:R.21, H:R.32 PO4.144: 4 residues within 4Å: Chain U: R.21, Q.25, L.28, R.32 8 PLIP interactions: 8 interactions with chain U Hydrogen bonds: U:Q.25, U:Q.25 Water bridges: U:R.21, U:R.21, U:R.32, U:R.32 Salt bridges: U:R.21, U:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., X-ray structures of catalytic intermediates of cytochromecoxidase provide insights into its O2activation and unidirectional proton-pump mechanisms. J.Biol.Chem. (2020)

Release Date

2020-03-25

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: 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.
Show / Hide

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

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

Related Entries With Identical Sequence