SMTL ID : 5b3s.1 (1 other biounit)

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

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

Ligands

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

HEA.1: 38 residues within 4Å: Chain A: L.20, 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, 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 Ligands: EDO.22 35 PLIP interactions: 35 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:V.374, 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: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.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CMO.6 39 PLIP interactions: 34 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:F.348, 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.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

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.6

1 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.12, H2O.13, H2O.15

1 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43

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

CMO.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)

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

PGV.7: 14 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.77, A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16, L.19 Ligands: DMU.81, EDO.89 17 PLIP interactions: 3 interactions with chain M, 5 interactions with chain D, 4 interactions with chain A, 5 interactions with chain K Hydrophobic interactions: M:P.12, M:Q.15, M:L.19, D:T.77, D:A.81, D:F.84, D:F.84, D:F.84, A:T.408, A:W.409, K:F.4, K:F.4, K:F.4 Hydrogen bonds: A:T.408 Water bridges: A:N.406, K:F.4 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, I.158, P.200 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 Ligands: PEK.34, PGV.36 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.84, C:F.84, A:F.148, A:I.158, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:R.96, A:M.97 Water bridges: C:M.81 Salt bridges: A:R.96 PGV.36: 23 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, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.8, CDL.38 28 PLIP interactions: 2 interactions with chain F, 26 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.63, 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:I.208, C:I.208, C:I.208, C:F.212, 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.37: 13 residues within 4Å: Chain A: F.237, D.298 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: F.14, N.18, R.21 Ligands: EDO.14, CHD.33 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: C:W.97, C:W.97, A:F.237 Salt bridges: C:H.101 Water bridges: H:N.18, H:R.21 PGV.67: 2 residues within 4Å: Chain C: W.256 Chain G: A.1 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.256

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

EDO.9: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.8 Ligand excluded by PLIP 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: 5 residues within 4Å: Chain A: G.269, M.271, G.272 Chain B: A.58, E.62 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Ligands: TGL.82 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: Y.304 Ligands: CHD.33, PGV.37 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, S.51 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: Y.19, M.71, P.72, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.59 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: P.131, D.221, P.222 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83 Ligands: EDO.63 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: M.390, H.413, M.417, A.464, V.465, M.468 Ligands: HEA.1 Ligand excluded by PLIP EDO.27: 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.28: 3 residues within 4Å: Chain B: H.102, E.157, D.158 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.41 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: Y.40 Chain I: A.24, V.27 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: T.125, R.134, F.206 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: W.104, Y.121, N.203, F.206 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.29, EDO.44 Ligand excluded by PLIP EDO.42: 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.43: 2 residues within 4Å: Chain A: W.103 Chain J: L.40 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.41 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: H.1, Q.2, H.68 Chain F: L.16 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain C: Q.66 Chain F: G.15 Chain J: Q.13 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain C: T.143, H.146, H.147 Chain G: W.16 Ligand excluded by PLIP EDO.48: 1 residues within 4Å: Chain C: F.249 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain C: G.139, T.143, H.241 Chain G: W.16 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain D: P.22, V.24, A.25, K.60 Chain E: R.26 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain A: I.332, W.334 Ligands: TGL.26 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain D: Y.19, D.23 Chain E: W.23, R.26, K.27, N.30 Chain F: P.83 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain A: T.488, L.495 Chain D: Y.8, A.9, L.10, S.12 Chain F: W.73 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain D: W.45, S.46, L.48, I.50, K.53 Ligands: EDO.57 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain E: R.49, R.52, R.53 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain D: K.53 Chain E: L.89, N.90, G.93, I.94, S.95 Ligands: EDO.54 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.18 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain C: H.229 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.61: 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.62: 5 residues within 4Å: Chain D: P.11 Chain F: F.72, Q.80, R.81, P.83 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain D: R.16, Y.19 Chain E: T.31 Chain F: P.83 Ligands: EDO.21 Ligand excluded by PLIP EDO.68: 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.69: 5 residues within 4Å: Chain G: G.10, G.12, A.13, R.14, T.15 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain I: Q.70, S.71, K.73 Ligand excluded by PLIP EDO.74: 5 residues within 4Å: Chain C: N.10, P.11 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.75: 2 residues within 4Å: Chain J: K.10, Q.13 Ligand excluded by PLIP EDO.84: 5 residues within 4Å: Chain L: G.7, K.8, I.10, F.12, S.13 Ligand excluded by PLIP EDO.86: 2 residues within 4Å: Chain M: H.36 Ligands: DMU.85 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain L: R.40 Chain M: W.32, H.36, Y.40 Ligand excluded by PLIP EDO.88: 6 residues within 4Å: Chain A: T.46, L.47 Chain D: V.100 Chain M: L.37, D.38, K.41 Ligand excluded by PLIP EDO.89: 5 residues within 4Å: Chain A: T.404, D.407 Chain M: I.1, A.3 Ligands: PGV.7 Ligand excluded by PLIP

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.23: 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, G.8, L.28, F.32, S.35, S.36, L.39 Chain I: R.43 13 PLIP interactions: 5 interactions with chain B, 1 interactions with chain I, 7 interactions with chain A Hydrophobic interactions: B:F.32, B:F.32, B:L.39, A:F.346, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430 Water bridges: B:F.9 Salt bridges: B:H.24, I:R.43 TGL.26: 24 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418, V.419 Chain B: L.39, I.42, T.47, K.49 Chain D: R.70, S.71, T.72, E.74, W.75, V.78, M.83, I.86 Chain I: R.16 Ligands: EDO.51, DMU.79 14 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, A:F.418, A:V.419, D:V.78, D:I.86, B:L.39, B:I.42 Salt bridges: A:K.411 Hydrogen bonds: D:W.75 Water bridges: D:T.72 TGL.82: 26 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, P.106, 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.13, DMU.83 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:F.22, A:F.22, A:W.25, A:W.25, A:P.106, A:F.393, A:I.472, L:I.10, L:F.12, L:F.12, L:F.27, L:F.27, L:F.28, L:F.28

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

CUA.24: 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

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.25: 22 residues within 4Å: Chain A: F.321, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69, I.72 Chain E: T.3, D.4, F.7, D.36, L.37 Chain I: R.10, A.14, L.17 17 PLIP interactions: 10 interactions with chain B, 2 interactions with chain E, 3 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:V.61, B:I.64, B:L.68, B:P.69, B:I.72, I:A.14, I:L.17, A:F.321, A:F.321 Hydrogen bonds: B:E.60 Salt bridges: B:H.52, E:D.4 pi-Cation interactions: E:F.7 Water bridges: I:A.14

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.33: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.97, H.101 Ligands: EDO.14, PGV.37 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.101 CHD.66: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.35 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.21 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.72: 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:L.158, C:F.162, C:F.162, C:F.217, C:L.221 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.73: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:R.33, J:T.37, A:I.3

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.34: 22 residues within 4Å: Chain A: H.151, T.207, L.210, L.215 Chain C: W.32, 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, DMU.65 16 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A, 9 interactions with chain G Hydrophobic interactions: C:W.32, C:I.186, C:F.201, C:F.201, A:L.210, A:L.215, G:W.62, G:F.69, G:F.69 Hydrogen bonds: C:I.186, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.35: 15 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 Ligands: CDL.64, CHD.66 16 PLIP interactions: 10 interactions with chain C, 4 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: C:I.163, C:T.166, C:L.167, C:Y.170, C:Y.170, C:Y.170, G:F.21, G:L.25, G:P.26 Hydrogen bonds: C:K.155, C:H.156, F:A.1 Water bridges: C:Q.159, F:G.3 Salt bridges: C:H.156, G:R.17

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.38: 20 residues within 4Å: Chain C: T.46, M.49, L.50, Y.53, W.56, R.57, I.60, F.65, V.169, T.211, I.214, V.215, F.218, R.219, K.222, H.224 Chain J: K.8, T.27, L.31 Ligands: PGV.36 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:W.56, C:W.56, C:R.57, C:V.169, C:V.169, C:I.214, C:I.214, C:V.215, C:F.218, J:L.31 Hydrogen bonds: C:Y.53 Salt bridges: C:K.222, C:K.222, C:H.224, J:K.8 CDL.64: 20 residues within 4Å: Chain C: N.123, L.125, L.129, T.132, S.133, L.136, V.140, L.248, Y.251, V.252, W.256 Chain G: L.23, S.27, L.30, C.31, L.33, N.34, L.37, H.38 Ligands: PEK.35 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain G Hydrophobic interactions: C:L.129, C:T.132, C:L.136, C:V.140, C:L.248, C:Y.251, C:V.252, C:W.256, G:L.23, G:L.30, G:L.30, G:L.33, G:L.37 Hydrogen bonds: C:N.123, G:N.34 Salt bridges: G:H.38, G:H.38

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

DMU.39: 11 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.40, DMU.65 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45 Hydrogen bonds: J:Y.45, C:S.37, C:T.39 DMU.40: 13 residues within 4Å: Chain A: L.110, L.145 Chain C: S.27, T.30, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.39 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: A:L.110, A:L.145, C:T.30, C:M.31, C:F.35, C:F.35, J:L.50 Hydrogen bonds: J:Y.45, J:Y.45 DMU.65: 8 residues within 4Å: Chain C: W.32, M.38 Chain G: S.61, W.62, G.63, F.69 Ligands: PEK.34, DMU.39 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:F.69, C:W.32 Hydrogen bonds: G:S.61, G:G.63 DMU.76: 6 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: DMU.77 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:V.21, K:W.24, K:W.24, D:I.86 DMU.77: 6 residues within 4Å: Chain K: W.24, A.28, T.29 Ligands: DMU.76, DMU.78, DMU.79 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:W.24, K:W.24, K:T.29 DMU.78: 8 residues within 4Å: Chain A: M.449, I.453 Chain K: A.28, T.29, Q.30, W.35 Ligands: DMU.77, DMU.79 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:W.35, K:W.35, A:I.453 Hydrogen bonds: K:Q.30 DMU.79: 3 residues within 4Å: Ligands: TGL.26, DMU.77, DMU.78 No protein-ligand interaction detected (PLIP) DMU.80: 6 residues within 4Å: Chain D: L.91, I.94 Chain K: T.18, A.22, Y.26 Ligands: DMU.81 6 PLIP interactions: 4 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: K:Y.26, D:L.91, D:I.94 Water bridges: K:T.18, K:A.22, K:Y.26 DMU.81: 7 residues within 4Å: Chain D: L.91 Chain K: A.14, S.15, T.18, F.19 Ligands: PGV.7, DMU.80 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:L.91 Hydrogen bonds: K:T.18, K:T.18 DMU.83: 8 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: S.30, F.37, R.40, H.41, L.44 Ligands: TGL.82 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain M Hydrogen bonds: L:R.40, L:R.40, L:H.41 Water bridges: L:H.41, L:L.44, M:S.43 Salt bridges: L:R.40, L:H.41 DMU.85: 13 residues within 4Å: Chain A: L.35, F.459 Chain D: W.95, Y.99 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 Ligands: EDO.86 10 PLIP interactions: 4 interactions with chain M, 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: M:L.27, M:A.30, M:L.34, D:W.95, D:W.95, A:L.35, A:F.459, A:F.459 Hydrogen bonds: M:W.32 Water bridges: D:Y.99 DMU.90: 8 residues within 4Å: Chain L: W.18, L.21, A.22, T.25, L.26 Chain M: K.13, E.14, I.17 7 PLIP interactions: 4 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: L:L.21, L:A.22, L:T.25, L:L.26 Hydrogen bonds: M:K.13, M:E.14 Salt bridges: M:K.13

1 x ZN: ZINC ION(Non-covalent)

ZN.58: 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)

PO4.70: 4 residues within 4Å: Chain H: R.21, Q.25, L.28, R.32 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K). To Be Published

Release Date

2017-03-22

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

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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