SMTL ID : 7vvr.1 (1 other biounit)

Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 34 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, V.374, F.377, H.378, L.381, S.382, V.386, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 Ligands: TGL.7 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A: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: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, 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: CYN.6 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: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.438 Salt bridges: A:H.368, A:R.438, A:R.439 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: CYN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

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.13, H2O.14, 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:E.40 Water bridges: A:Q.43

1 x CYN: CYANIDE ION(Non-covalent)

CYN.6: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 24 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.24, F.27, F.28 Ligands: HEA.1 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:F.2, A:F.2, A:F.2, A:L.18, A:L.20, A:F.22, A:W.25, A:W.25, A:W.25, A:L.113, A:F.400, A:I.472, L:I.10, L:F.12, L:F.12, L:F.12, L:F.27, L:F.27, L:F.28, L:F.28 TGL.27: 17 residues within 4Å: Chain A: F.346, V.350, T.354, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 21 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:F.346, A:F.346, A:V.350, A:T.354, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:L.7, B:L.28, B:V.31, B:F.32, B:F.32, B:F.32, B:L.39 Water bridges: B:G.8 Salt bridges: B:H.24, I:R.43 TGL.52: 20 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, 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 17 PLIP interactions: 8 interactions with chain A, 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, A:V.419, D:W.75, 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 Water bridges: D:T.72

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

PGV.8: 12 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 Ligands: EDO.82 12 PLIP interactions: 4 interactions with chain D, 3 interactions with chain K, 5 interactions with chain A Hydrophobic interactions: D:T.77, D:A.81, D:F.84, D:F.84, K:F.4, K:F.4, A:T.408, A:W.409, A:W.409, A:W.409 Salt bridges: K:H.5 Hydrogen bonds: A:T.408 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151, L.152, V.155, I.158 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: PGV.39, PEK.63 16 PLIP interactions: 8 interactions with chain C, 8 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, A:F.148, A:L.152, A:V.155, A:I.158 Hydrogen bonds: C:W.55, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.39: 24 residues within 4Å: Chain C: N.48, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, 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.9 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: 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:T.211, C:F.212, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Water bridges: C:S.63, C:R.219, C:H.229, C:H.229, F:Q.12, F:E.17 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.40: 11 residues within 4Å: Chain A: F.237 Chain C: T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.16, N.18 Ligands: EDO.26, CHD.37 11 PLIP interactions: 6 interactions with chain H, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: H:N.16 Water bridges: H:N.16, H:N.18, H:N.18, H:N.18, H:N.18 Hydrophobic interactions: C:W.97, C:W.97, C:W.97, A:F.237 Salt bridges: C:H.101

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

EDO.10: 8 residues within 4Å: Chain A: V.56, T.59, A.60, L.112, S.115, S.116, G.121, A.122 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligands: CHD.30 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, S.84 Ligand excluded by PLIP EDO.13: 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.14: 5 residues within 4Å: Chain A: W.334, S.335, P.336, D.407, K.411 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: P.182, H.256, T.259, K.265, T.490, N.491 Ligands: EDO.59 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.20 Ligand excluded by PLIP EDO.17: 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.18: 5 residues within 4Å: Chain A: P.131, D.221, P.222 Ligands: EDO.19, EDO.33 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: D.221, P.222, A.223 Ligands: EDO.18, EDO.32, EDO.33, EDO.43 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, W.104 Ligands: EDO.16 Ligand excluded by PLIP EDO.21: 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.22: 6 residues within 4Å: Chain A: K.333, T.484, D.486 Chain M: I.1, T.2 Ligands: EDO.55 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, S.51, R.56, H.94 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: Y.502 Chain C: P.11 Chain L: Y.2 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: D.50, D.51 Chain B: S.202, N.203, F.206 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: Y.304 Ligands: CHD.37, PGV.40 Ligand excluded by PLIP EDO.31: 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.32: 5 residues within 4Å: Chain B: E.157, P.176 Ligands: EDO.19, EDO.33, EDO.43 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain A: L.136 Chain B: D.158, V.159 Ligands: EDO.18, EDO.19, EDO.32 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: H.102, E.157, D.158 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: 3 residues within 4Å: Chain B: T.66, I.67 Ligands: CHD.30 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.19, EDO.32, EDO.45 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain C: W.256, W.257 Ligands: EDO.50 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.43 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain C: W.144, S.148, H.156 Chain F: A.1 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain C: Y.53, R.57 Chain J: T.27, D.28, L.31 Ligands: CDL.41 Ligand excluded by PLIP EDO.48: 1 residues within 4Å: Chain C: V.245 Ligand excluded by PLIP EDO.49: 2 residues within 4Å: Chain C: F.249 Ligands: CDL.64 Ligand excluded by PLIP EDO.50: 2 residues within 4Å: Chain C: W.257 Ligands: EDO.44 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain D: K.118, L.121, D.122, W.135, N.140 Chain K: P.45 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain D: P.103, I.104 Chain K: G.32 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain A: T.484, V.485, D.486 Chain D: S.12, V.14 Ligands: EDO.22 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.57: 2 residues within 4Å: Chain E: R.49, R.53 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.15 Ligand excluded by PLIP EDO.60: 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.61: 6 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, S.84 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain C: N.228, H.229 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.65: 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.66: 2 residues within 4Å: Chain G: A.1, A.3 Ligand excluded by PLIP EDO.68: 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.72: 4 residues within 4Å: Chain J: A.6, Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain L: S.30, F.37 Ligands: DMU.79 Ligand excluded by PLIP EDO.77: 5 residues within 4Å: Chain A: M.1, F.2, R.5 Chain L: Y.2, E.3 Ligand excluded by PLIP EDO.81: 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.82: 5 residues within 4Å: Chain A: T.404, D.407 Chain M: I.1, A.3 Ligands: PGV.8 Ligand excluded by PLIP

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

CUA.28: 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.29: 19 residues within 4Å: Chain A: F.321, L.324, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, E.60, V.61, I.64, W.65, P.69, I.72 Chain E: E.2, F.7 Chain I: R.10, A.14, L.17 12 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E, 6 interactions with chain B Hydrophobic interactions: A:F.321, A:F.321, A:L.324, A:H.328, B:I.41, B:M.56, B:I.64, B:W.65, B:P.69, B:I.72 Hydrogen bonds: E:E.2, E:D.4

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.30: 9 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Ligands: EDO.11, EDO.36 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.66, A:M.271, A:W.275, A:W.275, A:W.275 Hydrogen bonds: B:Q.59, B:E.62 CHD.37: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Ligands: EDO.26, PGV.40 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:D.298, A:D.300, A:T.301 Salt bridges: A:H.233, C:H.101 CHD.42: 5 residues within 4Å: Chain C: R.154, F.162, F.217, L.221 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: 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.71: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:Y.32, J:R.33, J:M.36, A:I.3 Hydrogen bonds: J:R.33, J:R.33 CHD.78: 5 residues within 4Å: Chain L: W.18, A.22 Chain M: E.14, I.17, V.21 6 PLIP interactions: 3 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:V.21, M:V.21, L:W.18, L:W.18, L:W.18 Hydrogen bonds: M:E.14

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.38: 11 residues within 4Å: Chain C: K.155, H.156, Q.159, T.166, Y.170 Chain F: A.1 Chain G: R.17, F.21, G.22, L.23 Ligands: CDL.64 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:Y.170, C:Y.170, G:F.21, G:L.23 Hydrogen bonds: C:K.155, C:K.155 Water bridges: C:Q.159 Salt bridges: G:R.17 PEK.63: 21 residues within 4Å: Chain A: H.151, 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.9, DMU.67 15 PLIP interactions: 9 interactions with chain G, 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: G:W.62, G:F.69, G:F.70, A:L.210, A:L.215, C:W.32, C:I.186, C:F.201 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.186 Water bridges: G:F.69, G:F.69

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.41: 24 residues within 4Å: Chain C: T.46, M.49, L.50, M.52, 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, R.219, K.222, H.224 Chain J: K.8, F.12, L.31 Ligands: EDO.47 23 PLIP interactions: 20 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:Y.53, C:W.56, C:W.56, C:V.169, C:T.172, C:I.214, C:I.214, C:F.218, J:L.31 Hydrogen bonds: C:Y.53 Water bridges: C:R.61, J:K.8, J:G.24 Salt bridges: C:R.61, C:K.222, C:K.222, C:H.224 CDL.64: 16 residues within 4Å: Chain C: N.123, L.125, L.129, L.136, V.140, Y.251, V.252 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.38, EDO.49 12 PLIP interactions: 5 interactions with chain G, 7 interactions with chain C Hydrophobic interactions: G:L.23, G:L.30, G:L.37, C:L.129, C:L.136, C:L.136, C:V.140, C:Y.251, C:V.252 Hydrogen bonds: G:N.34, G:H.38, C:N.123

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

DMU.51: 11 residues within 4Å: Chain C: M.31, N.36, S.37, T.39, I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.70 8 PLIP interactions: 3 interactions with chain J, 5 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45, C:I.43 Hydrogen bonds: C:N.36, C:S.37, C:S.37 Water bridges: C:M.38 DMU.67: 7 residues within 4Å: Chain C: L.29, W.32, M.38 Chain G: S.61, W.62, G.63 Ligands: PEK.63 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.29, C:W.32 Hydrogen bonds: G:S.61, G:G.63 DMU.70: 11 residues within 4Å: Chain A: L.110 Chain C: S.27, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.51 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: C:F.35, C:F.35, A:L.110, J:L.50 Hydrogen bonds: J:Y.45, J:Y.45 DMU.73: 6 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 Ligands: DMU.74 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: D:I.86, K:W.24, K:W.24, K:W.24 DMU.74: 5 residues within 4Å: Chain K: W.24, A.28, T.29 Ligands: DMU.73, DMU.75 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:W.24, K:A.28 DMU.75: 1 residues within 4Å: Ligands: DMU.74 No protein-ligand interaction detected (PLIP) DMU.79: 7 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: A.34, R.40, H.41, L.44 Ligands: EDO.76 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:R.40, L:R.40 Salt bridges: L:R.40, L:H.41 DMU.80: 13 residues within 4Å: Chain A: L.35, F.459, L.462 Chain D: W.95, Y.99 Chain L: F.36 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 12 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A, 1 interactions with chain L, 4 interactions with chain M Hydrophobic interactions: D:W.95, D:W.95, A:L.35, A:F.459, A:F.459, A:L.462, L:F.36, M:L.27, M:L.27, M:A.30 Water bridges: D:Y.99, M:H.36

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)

PO4.69: 4 residues within 4Å: Chain H: R.21, Q.25, L.28, R.32 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:Q.25, H:Q.25 Water bridges: H:R.21, H:R.21, H:R.21, H:R.21, H:R.21, H:R.21, H:R.32 Salt bridges: H:R.21, H:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J.Biol.Chem. (2023)

Release Date

2022-11-16

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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