SMTL ID : 7tii.1

Annealed 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 2.45 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: L.20, 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, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:T.31, 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:V.374, A:F.377, A:F.377, A:F.393, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:Q.428, A:R.439, A:Y.440 Water bridges: 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.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, 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.10 37 PLIP interactions: 33 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, 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:V.380, A:L.381, A:L.381, A:L.381, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Stacking: A:H.290 Metal complexes: A:H.376, OH.10 HEA.33: 35 residues within 4Å: Chain N: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, S.382, V.386, M.390, F.393, V.421, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 36 PLIP interactions: 36 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:I.73, N:V.374, N:F.377, N:V.386, N:V.386, N:F.393, N:V.421, N:T.424, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:W.126, N:Y.371, 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:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.34: 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, F.348, T.349, G.352, 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.40 35 PLIP interactions: 5 interactions with chain O, 29 interactions with chain N, 1 Ligand-Ligand interactions Hydrophobic interactions: O:I.34, O:I.34, O:P.69, O:I.72, O:L.73, 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:I.356, N:I.356, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:T.316, N:D.369, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240, N:H.290 Metal complexes: N:H.376, OH.40

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: OH.10 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.1, OH.10 CU.35: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: OH.40 5 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.21, OH.40

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 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, B:E.198, H2O.6, H2O.7, H2O.7 MG.36: 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.25, H2O.25, H2O.26

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

NA.5: 5 residues within 4Å: Chain A: E.40, G.45, T.46, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.442 NA.37: 5 residues within 4Å: Chain N: E.40, G.45, T.46, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40, 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.6: 24 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155 Chain C: H.9, V.11, G.20, T.28, N.50, T.53, W.57, W.58, V.61, E.64, H.71, V.75, L.79, F.86, S.89, E.90 Ligands: PEK.14, PGV.15 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, A:V.155 Hydrogen bonds: C:H.9, C:W.57, A:R.96, A:M.97 Water bridges: C:M.83 Salt bridges: A:R.96 PGV.7: 17 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87, F.88 Chain K: F.9, H.10 Chain M: K.4, P.5, P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D, 2 interactions with chain M, 3 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:W.409, D:T.80, D:A.84, D:F.87, D:F.87, D:F.88, M:P.12, M:L.19, K:F.9, K:F.9 Hydrogen bonds: A:T.408 Salt bridges: K:H.10 PGV.15: 23 residues within 4Å: Chain C: M.51, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.6, CDL.16 25 PLIP interactions: 24 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:F.86, C:I.210, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:H.71, C:R.221, C:F.233, C:G.234 Water bridges: C:R.221, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 10 residues within 4Å: Chain A: F.237, D.298 Chain C: W.99, Y.102, H.103, L.106 Chain H: N.22, N.24 Ligands: CHD.18, CDL.57 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: H:N.22 Hydrophobic interactions: C:W.99, C:W.99, A:F.237 Salt bridges: C:H.103 PGV.43: 25 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100 Chain P: H.9, G.20, S.23, A.24, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, E.90, F.93 Ligands: PGV.45, PEK.54 15 PLIP interactions: 11 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: P:A.24, P:L.31, P:W.57, P:W.57, P:W.57, P:W.58, P:F.86, P:F.93 Hydrogen bonds: P:H.9, P:W.57, P:E.64, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.44: 12 residues within 4Å: Chain C: W.258 Chain G: A.1 Chain N: F.237, D.298 Chain P: V.91, W.99, H.103, A.107 Chain U: N.22, N.24 Ligands: CDL.26, CHD.48 10 PLIP interactions: 4 interactions with chain P, 1 interactions with chain C, 4 interactions with chain U, 1 interactions with chain N Hydrophobic interactions: P:V.91, P:W.99, P:W.99, C:W.258, N:F.237 Salt bridges: P:H.103 Hydrogen bonds: U:N.22, U:N.24 Water bridges: U:N.22, U:N.24 PGV.45: 24 residues within 4Å: Chain P: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.43, CDL.46 26 PLIP interactions: 25 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, 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:R.221, P:F.233, P:G.234 Water bridges: P:R.221, P:H.231, P:H.231, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.63: 15 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, R.480 Chain Q: A.84 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.5, P.12, Q.15, A.16, S.20 12 PLIP interactions: 5 interactions with chain N, 2 interactions with chain X, 4 interactions with chain Z, 1 interactions with chain Q Hydrophobic interactions: N:W.409, N:W.409, N:I.412, X:F.9, Z:P.12, Z:P.12, Q:A.84 Hydrogen bonds: N:T.408 Water bridges: N:T.404, Z:A.3, Z:A.6 Salt bridges: X:H.10

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

EDO.8: 6 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.260, A:Y.261, A:H.395 EDO.9: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: C:T.5, F:N.32, A:E.507 EDO.21: 8 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain F: A.1 Chain G: A.13, R.14, R.17 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:A.1, C:S.150 EDO.29: 5 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, R.54 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:A.46, G:I.48, G:R.54, G:R.54, C:G.120 EDO.39: 7 residues within 4Å: Chain N: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain Z: I.1 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:Y.260, N:V.394, N:H.395 EDO.51: 7 residues within 4Å: Chain N: E.507 Chain P: T.5 Chain S: P.30, N.32, P.50, R.56, L.96 3 PLIP interactions: 2 interactions with chain S, 1 interactions with chain N Hydrogen bonds: S:P.30, S:N.32, N:E.507 EDO.52: 7 residues within 4Å: Chain P: W.146, S.150, H.158 Chain S: A.1 Chain T: A.13, R.14, R.17 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain S Hydrogen bonds: P:W.146, S:A.1 EDO.58: 8 residues within 4Å: Chain P: G.120 Chain T: P.45, A.46, F.47, I.48, L.53, R.54, Y.82 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain P Hydrogen bonds: T:I.48, T:R.54, T:R.54, P:G.120

2 x OH: HYDROXIDE ION(Non-covalent)

OH.10: 5 residues within 4Å: Chain A: H.240, V.243, H.290 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) OH.40: 4 residues within 4Å: Chain N: H.240, H.290 Ligands: HEA.34, CU.35 No protein-ligand interaction detected (PLIP)

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.11: 15 residues within 4Å: Chain A: F.346, Y.379, N.422, F.426, F.430, L.433, W.450 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35 Chain I: R.43 10 PLIP interactions: 6 interactions with chain A, 1 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: A:F.346, A:F.426, A:F.426, A:F.430, A:L.433, A:W.450, B:V.31 Salt bridges: I:R.43 Hydrogen bonds: B:G.8 Water bridges: B:F.9 TGL.22: 18 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415 Chain B: I.42, S.43, T.47, K.49 Chain D: R.73, T.75, E.77, W.78, V.81 Chain I: R.16, H.20 10 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, D:W.78, D:V.81, B:I.42 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 TGL.32: 20 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.81, F.393, F.397, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29 17 PLIP interactions: 9 interactions with chain L, 8 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:F.13, L:M.24, L:F.28, L:F.28, L:F.29, L:F.29, A:F.2, A:L.18, A:F.22, A:W.25, A:W.81, A:F.393, A:F.397, A:F.400 TGL.38: 17 residues within 4Å: Chain N: F.346, Y.379, N.422, 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, L.39 Chain V: R.43 12 PLIP interactions: 5 interactions with chain O, 1 interactions with chain V, 6 interactions with chain N Hydrophobic interactions: O:L.28, O:V.31, O:F.32, O:L.39, N:F.346, N:F.426, N:H.429, N:F.430, N:L.433, N:W.450 Water bridges: O:F.9 Salt bridges: V:R.43 TGL.49: 15 residues within 4Å: Chain N: W.334, F.414, A.415 Chain O: L.39, I.42, S.43, T.47, K.49 Chain Q: R.73, T.75, E.77, W.78, V.81 Chain V: R.16, H.20 13 PLIP interactions: 5 interactions with chain Q, 4 interactions with chain N, 4 interactions with chain O Hydrophobic interactions: Q:E.77, Q:W.78, Q:V.81, N:W.334, N:W.334, N:F.414, N:A.415, O:L.39, O:I.42, O:T.47, O:K.49 Hydrogen bonds: Q:E.77, Q:W.78 TGL.62: 19 residues within 4Å: Chain N: F.2, T.17, L.21, W.25, W.81, P.106, L.113, F.393, F.400, I.472 Chain Y: I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29, S.31 16 PLIP interactions: 8 interactions with chain N, 8 interactions with chain Y Hydrophobic interactions: N:T.17, N:W.25, N:W.81, N:P.106, N:L.113, N:F.393, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.28, Y:F.28, Y:F.29

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

CUA.12: 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.41: 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

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

DMU.13: 13 residues within 4Å: Chain A: L.110, A.114 Chain C: S.29, T.32, M.33, F.37, S.39 Chain J: S.46, Y.48, C.49, L.50, W.52, A.53 11 PLIP interactions: 5 interactions with chain C, 4 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: C:T.32, C:M.33, C:F.37, J:L.50, J:A.53, A:L.110, A:A.114 Hydrogen bonds: C:F.37, C:F.37, J:Y.48, J:Y.48 DMU.23: 12 residues within 4Å: Chain A: F.459, L.462 Chain D: W.98, Y.102 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 M, 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: M:L.27, M:L.27, M:A.30, M:L.34, D:W.98, A:F.459, A:F.459, A:L.462 Hydrogen bonds: M:Y.35 Water bridges: M:H.36, D:Y.102 DMU.60: 11 residues within 4Å: Chain N: A.114 Chain P: S.29, M.33, F.37 Chain W: Y.45, S.46, Y.48, C.49, L.50, W.52, A.53 8 PLIP interactions: 3 interactions with chain P, 4 interactions with chain W, 1 interactions with chain N Hydrophobic interactions: P:M.33, P:F.37, W:L.50, W:A.53, N:A.114 Hydrogen bonds: P:F.37, W:Y.45, W:Y.45 DMU.64: 13 residues within 4Å: Chain N: F.459, L.462 Chain Q: L.95, W.98, Y.102 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 Z, 3 interactions with chain N, 4 interactions with chain Q Hydrophobic interactions: Z:L.27, Z:A.30, Z:L.34, N:F.459, N:F.459, N:L.462, Q:L.95, Q:W.98, Q:W.98, Q:W.98

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.14: 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.6 13 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: C:W.34, C:Y.181, C:F.203, C:F.203, A:V.155, A:A.203, A:L.210, G:F.69 Hydrogen bonds: C:Y.181, C:I.188, G:T.68, G:F.70, G:N.76 PEK.19: 12 residues within 4Å: Chain C: K.157, H.158, L.169, Y.172 Chain F: A.1 Chain G: R.17, F.21, P.26 Chain N: W.275 Chain O: Q.59 Ligands: CDL.26, CHD.28 11 PLIP interactions: 1 interactions with chain F, 1 interactions with chain N, 3 interactions with chain C, 1 interactions with chain O, 5 interactions with chain G Hydrogen bonds: F:A.1, C:K.157, C:H.158, O:Q.59 Hydrophobic interactions: N:W.275, C:L.169, G:F.21, G:P.26 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.17 PEK.27: 16 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8, L.23 Chain P: R.80, Y.81, I.84, L.85, V.91, T.95, F.98, W.240, V.247, F.251 11 PLIP interactions: 7 interactions with chain P, 4 interactions with chain G Hydrophobic interactions: P:L.85, P:V.91, P:F.98, P:W.240, P:V.247, P:F.251, G:A.3, G:K.5, G:K.5, G:L.23 Hydrogen bonds: P:Y.81 PEK.54: 22 residues within 4Å: Chain N: H.151, V.155, A.203, L.215 Chain P: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, I.209 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.43 16 PLIP interactions: 6 interactions with chain P, 6 interactions with chain T, 4 interactions with chain N Hydrophobic interactions: P:W.34, P:Y.181, P:F.203, P:I.209, T:W.62, T:F.69, N:V.155, N:A.203, N:L.215, N:L.215 Hydrogen bonds: P:Y.181, P:I.188, T:T.68, T:F.69, T:F.70, T:N.76 PEK.55: 12 residues within 4Å: Chain C: R.80, Y.81, V.91, T.95, F.98, W.240, V.247, F.251 Chain T: S.2, A.3, K.5, G.6 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain T Hydrophobic interactions: C:V.91, C:V.91, C:F.98, C:W.240, C:W.240, C:F.251, C:F.251, T:A.3, T:K.5, T:K.5 Water bridges: C:R.80 PEK.56: 11 residues within 4Å: Chain A: W.275 Chain B: Q.59 Chain P: K.157, H.158, Q.161, T.168 Chain S: A.1 Chain T: R.17, F.21 Ligands: CHD.53, CDL.57 8 PLIP interactions: 4 interactions with chain T, 3 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: T:F.21, P:T.168, A:W.275 Hydrogen bonds: T:R.17, P:K.157, P:K.157 Water bridges: T:R.17 Salt bridges: T:R.17

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 21 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, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, L.31 Ligands: PGV.15 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:L.52, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:I.216, C:I.216, C:V.217, C:F.220, J:L.31 Hydrogen bonds: C:Y.55, C:R.63 Water bridges: C:R.59, C:K.224, J:D.28 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 CDL.26: 26 residues within 4Å: Chain C: L.127, L.131, V.142 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Chain N: F.282, I.286, D.300, Y.304, S.307, A.308, I.311 Chain O: A.70, A.77, L.78, L.81, Y.85 Ligands: PEK.19, PGV.44, CHD.48 19 PLIP interactions: 5 interactions with chain N, 3 interactions with chain O, 9 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: N:F.282, N:I.286, N:A.308, N:I.311, N:I.311, O:A.70, O:A.77, O:L.81, G:L.23, G:L.30, G:L.30, G:N.34, G:L.37, C:V.142 Hydrogen bonds: G:H.38, G:R.42, C:N.125 Salt bridges: G:H.38, G:H.38 CDL.46: 20 residues within 4Å: Chain P: M.51, L.52, M.54, 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 Ligands: PGV.45 18 PLIP interactions: 17 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:M.51, P:Y.55, P:Y.55, P:W.58, P:R.59, P:T.213, P:I.216, P:V.217, P:F.220 Hydrogen bonds: P:Y.55, P:R.63 Water bridges: P:Y.55, P:R.59 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, W:K.8 CDL.57: 28 residues within 4Å: Chain A: F.282, I.286, D.300, Y.304, S.307, A.308 Chain B: A.70, I.74, A.77, L.78, L.81, R.82, Y.85 Chain P: L.127, L.131, S.135, L.138, L.250, V.254 Chain T: S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.18, PGV.20, PEK.56 20 PLIP interactions: 7 interactions with chain T, 4 interactions with chain B, 5 interactions with chain A, 4 interactions with chain P Hydrophobic interactions: T:L.30, T:L.30, T:L.37, B:I.74, B:I.74, B:A.77, B:L.81, A:F.282, A:F.282, A:I.286, P:L.138, P:L.138, P:L.250, P:V.254 Hydrogen bonds: T:N.34 Salt bridges: T:H.38, T:H.38, T:H.38 Water bridges: A:D.300, A:D.300

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.17: 7 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223, J:F.1 Salt bridges: C:R.156 CHD.18: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.20, CDL.57 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, C:W.99 Water bridges: A:D.300 Salt bridges: A:H.233, C:H.103 CHD.28: 12 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: E.62, T.63, T.66 Ligands: PEK.19 14 PLIP interactions: 4 interactions with chain N, 7 interactions with chain G, 3 interactions with chain O Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, G:F.21, O:T.66 Water bridges: G:R.17, G:R.17, G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:E.62, O:T.63 CHD.31: 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:T.37, J:L.40 Hydrogen bonds: J:Y.32, J:R.33, J:R.33 CHD.47: 5 residues within 4Å: Chain P: R.156, F.164, F.219, L.223 Chain W: F.1 7 PLIP interactions: 5 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164, P:F.219, P:L.223, W:F.1 Salt bridges: P:R.156 Hydrogen bonds: W:F.1 CHD.48: 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.26, PGV.44 11 PLIP interactions: 3 interactions with chain P, 7 interactions with chain N, 1 interactions with chain C Hydrophobic interactions: P:W.99, N:W.288, N:T.301, N:Y.304, C:L.127 Hydrogen bonds: P:W.99, N:T.301, N:T.301 Salt bridges: P:H.103, N:H.233 Water bridges: N:T.301 CHD.53: 11 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.21, G.22 Ligands: PEK.56 10 PLIP interactions: 4 interactions with chain T, 3 interactions with chain B, 3 interactions with chain A Water bridges: T:R.17, T:R.17 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:E.62, B:E.62, B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275 CHD.61: 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:Y.32, W:R.33

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.24: 14 residues within 4Å: Chain A: F.321, H.328 Chain B: L.37, I.41, H.52, M.56, D.57, E.60, W.65 Chain E: H.5, E.6, D.8, D.40 Chain I: A.14 10 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 1 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: B:L.37, B:I.41, B:M.56, B:W.65, A:F.321, A:F.321, I:A.14 Salt bridges: B:H.52, E:D.8 Hydrogen bonds: E:D.40 PSC.42: 20 residues within 4Å: Chain N: F.268, F.321, A.325, H.328 Chain O: L.37, I.41, M.45, H.52, M.56, D.57, V.61, W.65 Chain R: E.6, T.7, D.8, F.11, D.40 Chain V: R.10, A.14, L.17 16 PLIP interactions: 8 interactions with chain O, 1 interactions with chain V, 5 interactions with chain N, 2 interactions with chain R Hydrophobic interactions: O:L.37, O:I.41, O:M.56, O:V.61, O:W.65, V:L.17, N:F.268, N:F.321, N:F.321, N:F.321, N:A.325 Hydrogen bonds: O:D.57, R:D.40 Salt bridges: O:H.52, O:H.52, R:D.8

2 x ZN: ZINC ION(Non-covalent)

ZN.25: 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.50: 4 residues within 4Å: Chain S: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

2 x SAC: N-ACETYL-SERINE(Non-covalent)

SAC.30: 1 residues within 4Å: Chain I: T.2 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.2 SAC.59: 1 residues within 4Å: Chain V: T.2 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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