SMTL ID : 2eik.1

Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.30: 3 residues within 4Å: Chain N: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.9, H2O.9, H2O.9 MG.31: 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.45, H2O.45, H2O.45

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

NA.3: 3 residues within 4Å: Chain A: E.40, G.45, S.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43, A:G.45 NA.32: 4 residues within 4Å: Chain N: E.40, G.45, T.46, S.441 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40 Water bridges: N:Q.43, N:G.45

6 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: H.503 Chain L: H.2 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: A:H.503, L:H.2, H2O.3, H2O.3 CD.15: 4 residues within 4Å: Chain C: H.148, M.152, H.232, E.236 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.148, C:H.232, C:E.236, H2O.15, H2O.17 CD.23: 2 residues within 4Å: Chain E: H.78, E.80 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.78, E:E.80, E:E.80, H2O.25 CD.33: 2 residues within 4Å: Chain N: H.503 Chain Y: H.2 4 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: Y:H.2, N:H.503, H2O.39, H2O.39 CD.43: 4 residues within 4Å: Chain P: H.148, M.152, H.232, E.236 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:H.148, P:H.232, P:E.236, H2O.49, H2O.51 CD.44: 2 residues within 4Å: Chain N: E.506 Chain P: H.3 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain N Metal complexes: P:H.3, N:E.506

4 x HEA: HEME-A(Covalent)(Non-covalent)

HEA.5: 34 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, V.374, F.377, H.378, L.381, S.382, V.386, F.393, M.417, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:I.37, 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:F.393, 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:Y.371, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.61, A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.6: 32 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 38 PLIP interactions: 33 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:Y.244, 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, 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 pi-Stacking: A:H.290 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.34: 33 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, F.393, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 35 PLIP interactions: 35 interactions with chain N, Hydrophobic interactions: N:T.31, 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:V.386, N:F.393, N:F.393, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:Y.54, N:W.126, N:Y.371, 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:H.61, N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.35: 32 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, 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 37 PLIP interactions: 32 interactions with chain N, 5 interactions with chain O, Hydrophobic interactions: N:W.236, 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: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, 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 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 15 residues within 4Å: Chain A: F.346, 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 17 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:F.346, A:N.422, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:L.28, B:V.31, B:F.32, B:F.32, B:L.39 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.8: 20 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain B: L.39, I.42, S.43, T.47 Chain D: R.73, S.74, E.77, W.78, V.81, M.86, I.89 Chain I: R.16 12 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, A:W.334, A:L.342, A:K.411, A:F.414, A:F.414, A:A.415, A:F.418, D:V.81, D:I.89 Salt bridges: A:K.411 TGL.28: 26 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, F.102, P.106, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.81, A:F.102, A:P.106, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:L.27, L:F.28, L:F.29, L:F.29 TGL.36: 17 residues within 4Å: Chain N: F.346, V.350, N.422, F.426, H.429, F.430, L.433, W.450 Chain O: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain V: R.43 18 PLIP interactions: 11 interactions with chain N, 6 interactions with chain O, 1 interactions with chain V Hydrophobic interactions: N:F.346, N:V.350, N:N.422, N:F.426, N:F.426, N:F.426, N:H.429, N:F.430, N:F.430, N:L.433, N:W.450, O:V.31, O:F.32, O:F.32 Water bridges: O:G.8, O:F.9 Salt bridges: O:H.24, V:R.43 TGL.52: 24 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain O: L.39, I.42, S.43, L.46, T.47, K.49 Chain Q: R.73, S.74, T.75, E.77, W.78, V.81, V.82, M.86, I.89 Chain V: R.16 16 PLIP interactions: 3 interactions with chain O, 5 interactions with chain Q, 8 interactions with chain N Hydrophobic interactions: O:L.39, O:I.42, O:L.46, Q:W.78, Q:V.81, Q:V.82, Q:I.89, N:W.334, N:L.342, N:K.411, N:F.414, N:F.414, N:A.415, N:F.418 Hydrogen bonds: Q:W.78 Salt bridges: N:K.411 TGL.57: 26 residues within 4Å: Chain N: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, P.106, L.110, L.113, F.393, F.397, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29 24 PLIP interactions: 14 interactions with chain N, 10 interactions with chain Y Hydrophobic interactions: N:T.17, N:L.18, N:L.20, N:L.21, N:F.22, N:W.25, N:W.25, N:W.25, N:W.81, N:L.113, N:F.393, N:F.397, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.13, Y:F.13, Y:L.27, Y:F.28, Y:F.28, Y:F.29, Y:F.29

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

PGV.9: 14 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 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 17 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D, 5 interactions with chain M, 3 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, D:T.80, D:F.87, D:F.87, D:F.87, M:P.12, M:A.16, M:L.19, K:F.9, K:F.9 Hydrogen bonds: A:T.408 Water bridges: M:A.3, M:A.3 Salt bridges: K:H.10 PGV.10: 27 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, V.155 Chain C: H.9, V.11, G.20, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, S.89, E.90, F.93 Ligands: PEK.17, PGV.19 12 PLIP interactions: 7 interactions with chain C, 5 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.93, A:F.148, A:V.155 Hydrogen bonds: A:R.96, A:M.97 Salt bridges: A:R.96 PGV.19: 25 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, E.90, 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.10, PEK.17, CDL.21 28 PLIP interactions: 26 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.210, C:I.210, C:T.213, C:F.214, C:F.214, 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.20: 13 residues within 4Å: Chain A: F.237 Chain C: T.95, W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Chain P: W.258 Chain T: A.1 Ligands: CHD.16, CDL.55 9 PLIP interactions: 1 interactions with chain P, 3 interactions with chain C, 4 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: P:W.258, C:T.95, C:W.99, C:W.99, A:F.237 Hydrogen bonds: H:N.22 Water bridges: H:N.24, H:N.24, H:N.24 PGV.37: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: T.80, A.84, F.87 Chain X: H.10 Chain Z: P.12, Q.15, A.16, L.19, S.20 14 PLIP interactions: 6 interactions with chain Q, 3 interactions with chain Z, 4 interactions with chain N, 1 interactions with chain X Hydrophobic interactions: Q:T.80, Q:A.84, Q:F.87, Q:F.87, Q:F.87, Q:F.87, Z:P.12, Z:A.16, Z:L.19, N:T.408, N:W.409, N:I.412 Hydrogen bonds: N:T.408 Salt bridges: X:H.10 PGV.38: 25 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, V.155 Chain P: H.9, V.11, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, S.89, E.90, F.93 Ligands: PEK.46, PGV.48 12 PLIP interactions: 6 interactions with chain N, 6 interactions with chain P Hydrophobic interactions: N:F.148, N:V.155, P:T.28, P:W.57, P:W.57, P:W.57, P:W.58, P:F.93 Hydrogen bonds: N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.48: 25 residues within 4Å: Chain P: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, E.90, 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.38, PEK.46, CDL.50 28 PLIP interactions: 26 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: 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:T.213, P:F.214, P:F.214, 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:S.65, P:R.221, P:H.231, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.49: 11 residues within 4Å: Chain C: W.258 Chain N: F.237, D.298 Chain P: T.95, W.99, Y.102, H.103, A.107 Chain U: N.24 Ligands: CDL.25, CHD.45 8 PLIP interactions: 3 interactions with chain P, 1 interactions with chain N, 3 interactions with chain U, 1 interactions with chain C Hydrophobic interactions: P:T.95, P:W.99, P:W.99, N:F.237, C:W.258 Water bridges: U:N.24, U:N.24, U:N.24

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

CUA.11: 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.39: 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

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.12: 16 residues within 4Å: Chain A: F.321, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, W.65 Chain E: H.5, D.8, F.11, L.41 Chain I: R.10, A.14, L.17 14 PLIP interactions: 4 interactions with chain I, 5 interactions with chain B, 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: I:A.14, I:L.17, I:L.17, B:I.41, B:M.56, B:V.61, B:W.65, A:F.321, A:F.321, A:H.328 Water bridges: I:G.11 Salt bridges: B:H.52, E:D.8 pi-Cation interactions: E:F.11 PSC.41: 20 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, M.45, H.52, M.56, D.57, E.60, V.61, W.65, L.68 Chain R: H.5, E.6, D.8, F.11, D.40, L.41 Chain V: R.10, A.14 14 PLIP interactions: 5 interactions with chain O, 4 interactions with chain N, 3 interactions with chain R, 2 interactions with chain V Hydrophobic interactions: O:I.41, O:M.56, O:V.61, O:W.65, N:F.321, N:F.321, N:A.325, N:H.328, V:A.14 Salt bridges: O:H.52, R:H.5, R:D.8 pi-Cation interactions: R:F.11 Water bridges: V:G.11

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.13: 12 residues within 4Å: Chain A: M.271, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.47 11 PLIP interactions: 4 interactions with chain A, 5 interactions with chain T, 2 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, T:F.18, T:F.18 Hydrogen bonds: T:R.17, B:E.62, B:T.63 Water bridges: T:R.17 Salt bridges: T:R.14 CHD.16: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: PGV.20, CDL.55 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:W.99, A:D.300, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:W.288, A:Y.304 Water bridges: A:T.301 CHD.22: 8 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164, F.219, L.223 Chain J: F.1 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.160, C:L.160, C:F.164, C:F.164, C:F.219, C:L.223 Hydrogen bonds: C:Q.161, J:F.1 Salt bridges: C:R.156 CHD.27: 7 residues within 4Å: Chain A: L.7, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:M.36, J:L.40 Hydrogen bonds: J:R.33, J:R.33 CHD.40: 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: Q.59, E.62, T.63, T.66 Ligands: PEK.18 13 PLIP interactions: 2 interactions with chain O, 4 interactions with chain N, 7 interactions with chain G Hydrogen bonds: O:E.62, O:T.63 Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, G:F.18, G:F.18 Water bridges: G:R.14, G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.45: 9 residues within 4Å: Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.25, PGV.49 7 PLIP interactions: 5 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:W.288, N:Y.304 Hydrogen bonds: N:T.301, P:W.99 Water bridges: N:T.301 Salt bridges: N:H.233, P:H.103 CHD.51: 8 residues within 4Å: Chain P: R.156, K.157, L.160, Q.161, F.164, F.219, L.223 Chain W: F.1 10 PLIP interactions: 9 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:K.157, P:L.160, P:L.160, P:F.164, P:F.164, P:F.219, P:L.223 Hydrogen bonds: P:Q.161, W:F.1 Salt bridges: P:R.156 CHD.56: 8 residues within 4Å: Chain N: I.3, L.7, F.8 Chain W: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 5 interactions with chain W Hydrophobic interactions: W:Y.32, W:R.33, W:M.36, W:L.40 Hydrogen bonds: W:R.33

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

DMU.14: 7 residues within 4Å: Chain C: W.34, M.40 Chain G: S.61, W.62, G.63, F.69 Ligands: PEK.17 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.61, G:G.63 DMU.29: 12 residues within 4Å: Chain A: L.462 Chain D: L.95, W.98 Chain L: F.37 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 6 PLIP interactions: 1 interactions with chain L, 2 interactions with chain M, 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: L:F.37, M:A.30, M:L.34, D:L.95, D:W.98, A:L.462 DMU.42: 6 residues within 4Å: Chain P: W.34, M.40 Chain T: S.61, W.62, G.63 Ligands: PEK.46 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:S.61, T:G.63 DMU.58: 13 residues within 4Å: Chain N: F.459 Chain Q: L.95, W.98, Y.102 Chain Y: F.37 Chain Z: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 10 PLIP interactions: 1 interactions with chain N, 4 interactions with chain Z, 4 interactions with chain Q, 1 interactions with chain Y Hydrophobic interactions: N:F.459, Z:L.27, Z:A.30, Z:L.34, Q:L.95, Q:W.98, Q:W.98, Y:F.37 Water bridges: Z:H.36 Hydrogen bonds: Q:Y.102

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.17: 24 residues within 4Å: Chain A: H.151, V.155, 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, G.205 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.10, DMU.14, PGV.19 13 PLIP interactions: 7 interactions with chain G, 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: G:W.62, G:F.69, C:W.34, C:F.203, A:V.155, A:L.210 Hydrogen bonds: G:T.68, G:F.70, G:N.76, C:Y.181, C:I.188 Water bridges: G:F.69, G:F.69 PEK.18: 19 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain F: A.1 Chain G: K.5, R.17, F.21, G.22, L.25 Chain N: W.275, S.279, I.314 Chain O: Q.59, T.66 Ligands: CDL.25, CHD.40 15 PLIP interactions: 2 interactions with chain O, 2 interactions with chain N, 5 interactions with chain G, 5 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: O:T.66, N:W.275, N:I.314, G:F.21, G:F.21, G:L.25, C:I.165, C:Y.172, C:Y.172, C:Y.172 Hydrogen bonds: O:Q.59, G:R.17, C:K.157, F:A.1 Salt bridges: G:R.17 PEK.26: 16 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8, L.19 Chain P: K.77, R.80, Y.81, I.84, L.85, F.98, W.240, F.244, V.247, V.248 14 PLIP interactions: 9 interactions with chain P, 5 interactions with chain G Hydrophobic interactions: P:Y.81, P:L.85, P:F.98, P:W.240, P:W.240, P:F.244, P:V.247, P:V.248, G:A.3, G:K.5, G:K.5, G:K.5, G:L.19 Salt bridges: P:K.77 PEK.46: 24 residues within 4Å: Chain N: H.151, T.207, L.210, L.215 Chain P: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.38, DMU.42, PGV.48 13 PLIP interactions: 2 interactions with chain N, 4 interactions with chain P, 7 interactions with chain T Hydrophobic interactions: N:L.210, N:L.215, P:W.34, P:Y.181, P:F.203, T:F.69 Hydrogen bonds: P:I.188, T:T.68, T:F.70, T:N.76, T:N.76 Water bridges: T:F.69, T:F.69 PEK.47: 19 residues within 4Å: Chain A: W.275, S.279, L.283, I.314 Chain B: Q.59 Chain P: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain S: A.1 Chain T: K.5, R.17, F.21, G.22, L.25 Ligands: CHD.13, CDL.55 16 PLIP interactions: 3 interactions with chain A, 5 interactions with chain T, 1 interactions with chain B, 6 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: A:W.275, A:L.283, A:I.314, T:F.21, T:L.25, P:I.165, P:Y.172, P:Y.172, P:Y.172 Hydrogen bonds: T:R.17, B:Q.59, P:K.157, P:K.157, S:A.1 Salt bridges: T:R.17, T:R.17 PEK.54: 17 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, L.85, V.91, T.95, F.98, W.240, F.244, V.247, V.248 Chain T: S.2, A.3, K.5, G.6, H.8 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain T Hydrophobic interactions: C:Y.81, C:I.84, C:L.85, C:V.91, C:F.98, C:W.240, C:W.240, C:F.244, C:V.247, C:V.248, T:A.3, T:K.5, T:K.5, T:K.5 Water bridges: C:K.77, C:K.77 Salt bridges: C:K.77, C:R.80

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 22 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27, L.31 Ligands: PGV.19 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:M.51, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:R.59, C:I.62, C:T.213, C:I.216, C:F.220, C:F.220 Hydrogen bonds: C:Y.55, C:R.59, J:D.28 Water bridges: C:R.59, C:R.59, C:R.63, J:K.8 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.25: 32 residues within 4Å: Chain C: L.127, L.131, T.134, S.135, L.138, V.142, L.250, Y.253, V.254 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, I.311 Chain O: A.70, I.74, A.77, L.78, L.81, Y.85 Ligands: PEK.18, CHD.45, PGV.49 28 PLIP interactions: 6 interactions with chain C, 9 interactions with chain G, 7 interactions with chain O, 6 interactions with chain N Hydrophobic interactions: C:L.131, C:L.138, C:V.142, C:L.250, C:Y.253, C:V.254, G:L.23, G:L.30, G:L.30, G:L.30, G:L.37, O:A.70, O:I.74, O:I.74, O:A.77, O:L.78, O:L.81, O:L.81, N:F.282, N:F.282, N:I.286, N:Y.304, N:I.311, N:I.311 Hydrogen bonds: G:N.34, G:R.42 Salt bridges: G:H.38, G:H.38 CDL.50: 21 residues within 4Å: Chain P: M.51, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, F.12, T.27, L.31 Ligands: PGV.48 22 PLIP interactions: 18 interactions with chain P, 4 interactions with chain W Hydrophobic interactions: P:Y.55, P:Y.55, P:Y.55, P:Y.55, P:W.58, P:R.59, P:I.62, P:T.213, P:I.216, P:F.220, W:L.31 Hydrogen bonds: P:Y.55, P:R.59, W:D.28 Water bridges: P:R.59, P:R.59 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, W:K.8, W:K.8 CDL.55: 33 residues within 4Å: Chain A: F.282, I.286, D.300, Y.304, S.307, I.311 Chain B: A.70, I.74, A.77, L.78, L.81, Y.85 Chain P: L.127, L.131, T.134, S.135, L.138, V.142, L.250, Y.253, V.254 Chain T: L.23, S.27, L.30, C.31, L.33, N.34, L.37, H.38, R.42 Ligands: CHD.16, PGV.20, PEK.47 26 PLIP interactions: 5 interactions with chain B, 8 interactions with chain T, 6 interactions with chain A, 7 interactions with chain P Hydrophobic interactions: B:A.70, B:I.74, B:I.74, B:A.77, B:L.81, T:L.30, T:L.30, T:L.30, T:L.33, T:L.37, A:F.282, A:F.282, A:I.286, A:Y.304, A:I.311, A:I.311, P:L.131, P:L.138, P:V.142, P:L.250, P:Y.253, P:V.254 Hydrogen bonds: T:N.34, T:R.42, P:N.125 Salt bridges: T:H.38

2 x ZN: ZINC ION(Non-covalent)

ZN.24: 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.53: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muramoto, K. et al., A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-05-29

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: DQ
Cytochrome c oxidase polypeptide Va: ER
Cytochrome c oxidase polypeptide Vb: FS
Cytochrome c oxidase polypeptide VIa-heart: GT
Cytochrome c oxidase subunit VIb isoform 1: HU
Cytochrome c oxidase polypeptide VIc: IV
Cytochrome c oxidase polypeptide VIIa-heart: JW
Cytochrome c oxidase polypeptide VIIb: KX
Cytochrome c oxidase polypeptide VIIc: LY
Cytochrome c oxidase polypeptide VIII-heart: 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

Cytochrome c oxidase polypeptide Va

Cytochrome c oxidase polypeptide Vb

Cytochrome c oxidase polypeptide VIa-heart

Cytochrome c oxidase subunit VIb isoform 1

Cytochrome c oxidase polypeptide VIc

Cytochrome c oxidase polypeptide VIIa-heart

Cytochrome c oxidase polypeptide VIIb

Cytochrome c oxidase polypeptide VIIc

Cytochrome c oxidase polypeptide VIII-heart

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