SMTL ID : 7ev7.2 (1 other biounit)

Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a 50 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

PGV.1: 14 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 Ligands: EDO.19 18 PLIP interactions: 6 interactions with chain M, 4 interactions with chain D, 3 interactions with chain A, 5 interactions with chain K Hydrophobic interactions: M:P.12, M:Q.15, M:A.16, M:L.19, D:T.80, D:A.84, D:F.87, D:F.87, A:T.408, K:F.9, K:F.9, K:F.9 Water bridges: M:A.3, M:K.4, A:D.407, K:F.9 Hydrogen bonds: A:N.406 Salt bridges: K:H.10 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, V.155 Chain C: H.9, V.11, G.20, A.24, M.27, 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: PEK.41 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.93, A:F.148, A:L.152, A:V.155 Hydrogen bonds: C:W.57, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.43: 25 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, 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 Ligands: CDL.45 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:I.209, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.44: 11 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, L.106, A.107 Chain H: N.24 Ligands: EDO.23, EDO.26, CHD.38 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain C Water bridges: H:N.24 Hydrophobic interactions: C:W.99, C:W.99 Salt bridges: C:H.103

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

HEA.2: 35 residues within 4Å: Chain A: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, I.389, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: TGL.93 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:F.377, A:L.381, A:L.381, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.3: 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, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CMO.7 36 PLIP interactions: 31 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:L.353, A:I.356, A:I.356, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376

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

CU.4: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.7

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.11, H2O.12, H2O.15

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

NA.6: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43 Water bridges: A:Q.43 NA.39: 3 residues within 4Å: Chain C: H.148, H.232, E.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.236

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.7: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.3, CU.4 No protein-ligand interaction detected (PLIP)

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 18 residues within 4Å: Chain A: F.346, V.350, Y.379, F.418, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 20 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.7, B:V.31, B:F.32, B:F.32, A:F.346, A:F.346, A:V.350, A:Y.379, A:F.418, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:F.430 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.62: 19 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, V.419 Chain B: L.39, I.42, L.46, T.47, T.48, K.49 Chain D: R.73, T.75, E.77, W.78, V.81 Chain I: R.16 16 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: B:L.39, B:L.46, B:T.47, B:K.49, A:W.334, A:W.334, A:L.342, A:F.414, A:F.414, A:V.419, D:E.77, D:W.78, D:V.81 Salt bridges: A:K.411 Hydrogen bonds: D:E.77, D:W.78 TGL.93: 25 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.109, L.110, L.113, F.393, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, L.27, F.28, F.29, S.31 Ligands: HEA.2, EDO.16 22 PLIP interactions: 10 interactions with chain L, 12 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:F.13, L:L.27, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29, A:T.17, A:L.20, A:L.21, A:W.25, A:W.25, A:W.25, A:F.109, A:F.109, A:F.393, A:F.393, A:F.400, A:I.472

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

EDO.10: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.71 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligands: EDO.68 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: Y.19, N.80, N.98, S.101, G.160, N.163, F.164 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, V.485, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 Ligands: EDO.64 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: M.423 Chain D: I.89 Chain K: W.29 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Ligands: TGL.93 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: H.503, E.506 Chain L: H.2 Ligands: EDO.57 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: H.503, T.504, F.505, E.506, E.507 Ligands: EDO.57, EDO.77 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: N.406, E.474, S.478, R.480 Chain M: P.9, T.10, Q.15 Ligands: PGV.1 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, W.104 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: P.131, D.221 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: I.229, H.233 Chain B: R.178 Ligands: CHD.38, PGV.44 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligands: EDO.75 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: I.286, W.288, Y.304 Ligands: CHD.38, PGV.44 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: C.498 Chain D: S.8, Y.11 Chain L: P.7 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50 Ligands: EDO.76 Ligand excluded by PLIP EDO.29: 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.10 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain A: P.444, D.445, A.446 Chain B: M.1, A.2, L.133, R.134, L.136 Ligand excluded by PLIP EDO.33: 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.34: 3 residues within 4Å: Chain B: T.125, L.135, F.206 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: S.14, P.15, I.16, L.168, T.183, L.184, M.185 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: D.227 Chain B: G.177, R.178 Chain H: N.24, T.26 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: T.55, M.56, D.57, A.58 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain C: W.146, S.150, H.158 Chain F: A.1 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.50: 2 residues within 4Å: Chain C: F.251, V.254 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligands: EDO.52 Ligand excluded by PLIP EDO.52: 8 residues within 4Å: Chain C: N.12, Q.68 Chain J: L.18, V.20, K.23 Ligands: EDO.51, EDO.53, EDO.92 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain C: Q.68, H.70 Chain J: Q.13 Ligands: EDO.52, EDO.56, EDO.92 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.111 Ligands: EDO.55 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain B: G.177 Chain C: E.111 Chain H: W.68, W.72 Ligands: EDO.54 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain C: H.3, H.70 Ligands: EDO.53 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain A: E.506 Chain C: H.3 Chain F: I.52 Ligands: EDO.17, EDO.18, EDO.77 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain C: M.152, E.153, G.154, S.229 Chain F: T.8 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain C: T.145, H.148, H.149 Chain G: W.16 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain D: K.121, D.125, W.138, N.143 Chain K: P.50 Ligand excluded by PLIP EDO.64: 9 residues within 4Å: Chain A: T.484, T.488, L.495 Chain D: Y.11, L.13, P.14, S.15 Ligands: EDO.14, EDO.78 Ligand excluded by PLIP EDO.65: 5 residues within 4Å: Chain E: Y.18, K.21, I.24, E.28 Ligands: EDO.69 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain E: R.14, W.15, Y.18 Ligand excluded by PLIP EDO.67: 7 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Chain F: P.83 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain D: Y.22 Chain E: T.35 Chain F: P.83 Ligands: EDO.11 Ligand excluded by PLIP EDO.69: 3 residues within 4Å: Chain E: E.28 Chain F: R.81 Ligands: EDO.65 Ligand excluded by PLIP EDO.71: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.10 Ligand excluded by PLIP EDO.72: 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.73: 4 residues within 4Å: Chain C: P.73, H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.74: 3 residues within 4Å: Chain F: G.3, G.4, G.5 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain A: E.266 Chain F: N.66, S.67, T.68 Ligands: EDO.25 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain A: Y.510 Chain F: N.32, P.36, P.50, R.56 Ligands: EDO.28, EDO.81 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain F: T.53 Ligands: EDO.18, EDO.57 Ligand excluded by PLIP EDO.78: 9 residues within 4Å: Chain A: L.495 Chain D: Y.11, A.12, L.13, P.14 Chain F: F.72, W.73 Ligands: EDO.64, EDO.79 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligands: EDO.78 Ligand excluded by PLIP EDO.80: 6 residues within 4Å: Chain A: Q.180, L.513, K.514 Chain F: I.61, E.64, D.65 Ligand excluded by PLIP EDO.81: 9 residues within 4Å: Chain A: P.174, T.509, Y.510, V.511 Chain F: N.32, L.34, P.36, R.56 Ligands: EDO.76 Ligand excluded by PLIP EDO.83: 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.84: 4 residues within 4Å: Chain G: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.85: 4 residues within 4Å: Chain G: I.48, P.49 Chain H: E.78, G.79 Ligand excluded by PLIP EDO.87: 5 residues within 4Å: Chain I: Y.54, D.55, K.58, D.59, E.62 Ligand excluded by PLIP EDO.90: 2 residues within 4Å: Chain J: K.10, Q.13 Ligand excluded by PLIP EDO.91: 1 residues within 4Å: Ligands: EDO.92 Ligand excluded by PLIP EDO.92: 7 residues within 4Å: Chain J: Q.13, E.14, D.15, K.23 Ligands: EDO.52, EDO.53, EDO.91 Ligand excluded by PLIP EDO.94: 2 residues within 4Å: Chain L: F.38 Ligands: CHD.96 Ligand excluded by PLIP EDO.95: 2 residues within 4Å: Chain L: H.2, Y.3 Ligand excluded by PLIP

1 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.31: 16 residues within 4Å: Chain A: F.321, L.324, A.325, H.328 Chain B: L.37, I.41, M.45, H.52, M.56, D.57, E.60, V.61, W.65 Chain E: D.8 Chain I: R.10, L.17 13 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B, 2 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: A:F.321, A:F.321, A:L.324, A:A.325, B:L.37, B:I.41, B:I.41, B:W.65, I:L.17 Hydrogen bonds: B:D.57, B:E.60 Salt bridges: E:D.8 pi-Cation interactions: E:F.11

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

CUA.32: 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

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.38: 11 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: EDO.23, EDO.26, PGV.44 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:D.300, A:T.301 Salt bridges: A:H.233, C:H.103 CHD.47: 5 residues within 4Å: Chain C: W.116, P.117, W.258, W.259, S.261 3 PLIP interactions: 3 interactions with chain C Water bridges: C:S.261, C:S.261, C:S.261 CHD.48: 7 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 9 PLIP interactions: 7 interactions with chain C, 2 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 Hydrogen bonds: J:F.1 CHD.89: 8 residues within 4Å: Chain A: I.3, L.7, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain J Hydrophobic interactions: A:I.3, J:R.33 Hydrogen bonds: J:Y.32, J:Y.32, J:R.33, J:R.33 CHD.96: 10 residues within 4Å: Chain A: L.113, M.117 Chain J: F.55 Chain L: A.35, F.38, I.39, R.41, H.42, L.45 Ligands: EDO.94 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L Hydrophobic interactions: J:F.55, L:L.45 Hydrogen bonds: L:R.41, L:R.41

3 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.40: 13 residues within 4Å: Chain A: V.193 Chain C: K.77, R.80, Y.81, I.84, L.85, V.91, T.95, F.98, W.240, F.244, V.247, F.251 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.81, C:I.84, C:L.85, C:V.91, C:F.98, C:F.98, C:W.240, C:W.240, C:F.244, C:V.247, A:V.193, A:V.193 Hydrogen bonds: C:K.77, C:Y.81, C:Y.81 Salt bridges: C:K.77 PEK.41: 28 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, F.35, Q.177, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205, I.209 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.9 21 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A, 8 interactions with chain G Hydrophobic interactions: C:W.34, C:F.35, C:Q.177, C:A.178, C:I.188, C:F.203, C:F.203, C:I.209, A:V.155, A:A.203, A:L.210, A:L.215, G:W.62, G:F.69 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.42: 13 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, P.26, T.32 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain G Hydrophobic interactions: C:I.165, C:I.165, C:I.165, C:T.168, C:Y.172, C:Y.172, G:F.21, G:F.21, G:L.25, G:P.26, G:T.32 Hydrogen bonds: C:K.157, C:K.157, G:R.17 Water bridges: G:R.14 Salt bridges: G:R.17

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.45: 21 residues within 4Å: Chain C: T.48, M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12 Ligands: PGV.43 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:R.59, C:V.171, C:T.213, C:I.216, C:V.217, C:F.220 Hydrogen bonds: C:Y.55, C:R.63 Water bridges: C:R.59, C:R.63 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 CDL.82: 13 residues within 4Å: Chain C: L.127, L.131, T.134, S.135, L.138, V.142 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:L.23, G:L.30, G:L.30, C:L.131, C:L.131, C:T.134, C:L.138, C:L.138 Hydrogen bonds: G:H.38 Water bridges: G:N.34, G:N.34, G:N.34 Salt bridges: G:H.38

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

DMU.46: 11 residues within 4Å: Chain A: L.110, A.114, L.145 Chain C: T.32, M.33, F.37 Chain J: S.46, Y.48, C.49, W.52 Ligands: DMU.60 10 PLIP interactions: 3 interactions with chain J, 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: J:Y.45, J:Y.45 Salt bridges: J:K.58 Hydrophobic interactions: C:T.32, C:M.33, C:F.37, C:F.37, A:L.110, A:A.114, A:L.145 DMU.60: 12 residues within 4Å: Chain C: M.33, N.38, S.39, T.41, I.45 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.46, DMU.61 10 PLIP interactions: 3 interactions with chain J, 7 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, C:I.45 Hydrogen bonds: J:Y.45, C:N.38, C:N.38, C:N.38, C:S.39, C:S.39, C:S.39 DMU.61: 9 residues within 4Å: Chain C: W.34, N.38, S.39, M.40 Chain G: S.61, W.62, G.63, F.69 Ligands: DMU.60 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:F.69, C:W.34, C:W.34 Hydrogen bonds: G:S.61, G:G.63, C:M.40 DMU.88: 10 residues within 4Å: Chain B: L.33, S.36, Y.40 Chain I: F.19, H.20, G.23, A.24, V.27, S.28, F.31 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: I:A.24, I:V.27, I:F.31, B:L.33, B:Y.40, B:Y.40 DMU.97: 13 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 12 PLIP interactions: 4 interactions with chain M, 4 interactions with chain D, 3 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: M:L.27, M:L.27, M:L.34, D:L.95, D:W.98, D:W.98, A:L.35, A:F.459, A:F.459, L:F.37 Water bridges: M:H.36, D:Y.102 DMU.98: 7 residues within 4Å: Chain L: W.19, A.23, T.26, L.27 Chain M: E.14, I.17, V.21 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:V.21, L:A.23, L:L.27 Hydrogen bonds: M:E.14

1 x ZN: ZINC ION(Non-covalent)

ZN.70: 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

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

PO4.86: 4 residues within 4Å: Chain H: R.27, Q.31, L.34, R.38 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:Q.31, H:Q.31 Water bridges: H:R.27, H:R.27 Salt bridges: H:R.27, H:R.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Structure of CO-bound fully reduced state of bovine heart cytochrome c oxidase. To Be Published

Release Date

2021-07-14

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1: D
Cytochrome c oxidase subunit 5A: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1: J
Cytochrome c oxidase subunit 7B: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
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

Cytochrome c oxidase subunit 5A

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1

Cytochrome c oxidase subunit 7B

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B

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