SMTL ID : 8gcq.1

SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: OH.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.2 CU.30: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: OH.37 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.14

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: 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.2, H2O.5, H2O.5 MG.31: 3 residues within 4Å: Chain N: H.368, D.369 Chain O: E.198 5 PLIP interactions: 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, H2O.14, H2O.16, H2O.17

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

NA.3: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:D.442, A:D.442 NA.32: 6 residues within 4Å: Chain N: E.40, L.41, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:D.442

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

PGV.4: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80 Chain K: F.9, H.10 Chain M: I.2, T.3, A.4, P.13, Q.16 9 PLIP interactions: 2 interactions with chain K, 3 interactions with chain M, 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: K:F.9, K:F.9, M:P.13, A:T.408, A:W.409, A:W.409, D:T.80 Hydrogen bonds: M:A.4, M:A.4 PGV.11: 18 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100 Chain C: H.9, N.50, M.54, W.57, W.58, V.61, E.64, H.71, G.82, F.86, S.89 Ligands: PEK.13, PGV.15 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.57, C:W.57, C:F.86 Hydrogen bonds: C:E.64, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.15: 23 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, F.86, I.210, T.213, F.214, R.221, H.226, F.227, H.231, H.232, F.233, G.234 Ligands: PGV.11, CDL.16, DMU.24 25 PLIP interactions: 23 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:T.213, C:F.214, C:F.214, C:F.214, C:F.233 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, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.25: 9 residues within 4Å: Chain C: T.95, W.99, Y.102, L.106, A.107 Chain H: N.22 Chain T: A.1 Ligands: CHD.12, PEK.21 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain C, 1 interactions with chain T Hydrogen bonds: H:N.22 Hydrophobic interactions: C:T.95, C:Y.102, C:L.106, T:A.1 PGV.34: 23 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155, I.158, A.203 Chain P: H.9, G.20, A.24, M.27, N.50, W.57, W.58, V.61, E.64, H.71, G.82, M.83, F.86 Ligands: PEK.46, PGV.47 17 PLIP interactions: 8 interactions with chain N, 9 interactions with chain P Hydrophobic interactions: N:V.155, N:I.158, N:A.203, P:A.24, P:M.27, P:W.57, P:W.57, P:F.86, P:F.86, P:F.86 Hydrogen bonds: N:R.96, N:R.96, N:M.97, P:H.9, P:V.61 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.39: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, R.480 Chain Q: T.80, A.84, F.87 Chain X: H.10 Chain Z: A.7, T.11, P.13, Q.16 10 PLIP interactions: 3 interactions with chain N, 3 interactions with chain Q, 4 interactions with chain Z Hydrophobic interactions: N:T.408, N:W.409, N:I.412, Q:A.84, Q:F.87, Q:F.87, Z:P.13, Z:P.13, Z:Q.16 Hydrogen bonds: Z:A.7 PGV.47: 23 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, M.83, F.86, I.209, I.210, T.213, F.214, R.221, H.226, F.227, H.231, H.232, F.233, G.234 Ligands: PGV.34, PEK.46, CDL.49 22 PLIP interactions: 22 interactions with chain P Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:I.209, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.233 Hydrogen bonds: P:S.65, P:T.66, P:R.221, P:F.233, P:G.234 Water bridges: P:H.231 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.48: 13 residues within 4Å: Chain G: A.1, S.2 Chain N: F.237, W.288, D.298 Chain P: T.95, W.99, Y.102, H.103, L.106, A.107 Ligands: PEK.43, CHD.45 8 PLIP interactions: 3 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:W.99, P:W.99, P:L.106, N:F.237, N:F.237, N:W.288 Hydrogen bonds: N:D.298, N:D.298

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

HEA.5: 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, 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: HEA.6, OH.7 38 PLIP interactions: 33 interactions with chain A, 4 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:F.348, 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:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:H.291, A:T.316, A:D.369, A:R.438, A:R.438, A:R.438, A:R.438 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240, A:H.240 Metal complexes: A:H.376, OH.7 HEA.6: 32 residues within 4Å: Chain A: A.24, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, V.70, I.73, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, S.458, V.465, M.468 Ligands: HEA.5 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:I.37, A:V.58, A:A.62, A:M.65, A:I.66, A:I.66, A:V.70, A:I.73, A:F.377, A:F.377, A:L.381, 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: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.35: 33 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, H.290, H.291, T.309, I.312, A.313, T.316, G.317, F.321, 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, R.439 Chain O: I.34, P.69, I.72, L.73 Ligands: OH.37 33 PLIP interactions: 27 interactions with chain N, 5 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:W.236, N:V.243, N:T.309, N:A.313, N:T.316, N:F.321, N:T.349, N:L.353, N:I.356, N:L.358, N:L.358, N:F.377, N:F.377, N:V.380, N:V.380, N:L.381, O:I.34, O:I.34, O:P.69, O:I.72, O:L.73 Hydrogen bonds: N:Y.244, N:Y.244, N:D.364 Water bridges: N:R.438, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Stacking: N:H.376 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, OH.37 HEA.36: 29 residues within 4Å: Chain N: A.24, 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, F.377, H.378, L.381, S.382, M.390, F.393, T.424, F.425, R.438, R.439, Y.440, V.465 29 PLIP interactions: 29 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:F.377, N:L.381, N:F.393, N:T.424, N:F.425 Hydrogen bonds: N:R.38, N:Y.54, N:Y.54, N:W.126, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:Y.371 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378

2 x OH: HYDROXIDE ION(Non-covalent)

OH.7: 4 residues within 4Å: Chain A: H.240, V.243 Ligands: CU.1, HEA.5 No protein-ligand interaction detected (PLIP) OH.37: 4 residues within 4Å: Chain N: H.240, V.243 Ligands: CU.30, HEA.35 No protein-ligand interaction detected (PLIP)

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

CUA.8: 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

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 12 residues within 4Å: Chain A: F.426, F.430, L.433, W.450 Chain B: Y.3, L.7, G.8, L.28, F.32, L.39 Chain D: K.137 Chain I: R.43 9 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:F.426, A:F.426, A:F.430, A:F.430, A:W.450, B:L.7, B:F.32 Water bridges: I:R.43 Salt bridges: I:R.43 TGL.22: 11 residues within 4Å: Chain A: W.334, M.339, F.414 Chain B: L.46, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:F.414, D:W.78, D:V.81 Hydrogen bonds: D:T.75 TGL.28: 17 residues within 4Å: Chain A: F.2, I.3, T.17, L.20, L.21, W.25, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29 26 PLIP interactions: 16 interactions with chain A, 10 interactions with chain L Hydrophobic interactions: A:F.2, A:F.2, A:F.2, A:F.2, A:I.3, A:I.3, A:T.17, A:L.20, A:L.20, A:L.21, A:L.21, A:W.25, A:W.25, A:W.25, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:M.24, L:F.28, L:F.28, L:F.29, L:F.29 Hydrogen bonds: L:S.14 Salt bridges: L:R.20 TGL.33: 19 residues within 4Å: Chain N: F.2, L.7, T.17, L.21, W.25, W.81, F.109, L.113, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29 14 PLIP interactions: 8 interactions with chain N, 6 interactions with chain Y Hydrophobic interactions: N:T.17, N:W.81, N:F.109, N:F.109, N:L.113, N:L.113, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.13, Y:F.28, Y:F.29 TGL.38: 14 residues within 4Å: Chain N: W.334, M.339, K.411 Chain O: I.42, S.43, L.46, T.47, K.49 Chain Q: R.73, E.77, W.78, V.81 Chain V: R.16, H.20 8 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: Q:E.77, Q:W.78, Q:V.81, O:I.42, O:L.46, O:T.47, N:W.334 Salt bridges: N:K.411 TGL.40: 11 residues within 4Å: Chain N: F.346, F.426, F.430, L.433, W.450 Chain O: M.5, L.7, G.8, L.28, L.39 Chain V: R.43 8 PLIP interactions: 5 interactions with chain N, 2 interactions with chain O, 1 interactions with chain V Hydrophobic interactions: N:F.346, N:F.426, N:F.430, N:L.433, N:W.450, O:L.28, O:L.39 Salt bridges: V:R.43

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.10: 12 residues within 4Å: Chain A: A.325, H.328 Chain B: M.45, H.52, D.57, V.61, I.64 Chain E: D.8, D.40 Chain I: A.14, L.17, I.21 9 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 2 interactions with chain E, 3 interactions with chain I Hydrophobic interactions: B:D.57, B:V.61, A:A.325, I:A.14, I:L.17, I:I.21 Salt bridges: B:H.52, E:D.8 Hydrogen bonds: E:D.40 PSC.57: 16 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, H.52, D.57, V.61, W.65, L.68, P.69 Chain R: D.8, F.11, D.40, L.41 Chain V: R.10, A.14 10 PLIP interactions: 2 interactions with chain N, 6 interactions with chain O, 2 interactions with chain R Hydrophobic interactions: N:F.321, N:A.325, O:I.41, O:I.41, O:D.57, O:V.61, O:L.68 Salt bridges: O:H.52, R:D.8 pi-Cation interactions: R:F.11

10 x CHD: CHOLIC ACID(Non-covalent)

CHD.12: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Chain P: L.127 Ligands: PGV.25, CDL.51 11 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C, 1 interactions with chain P Hydrophobic interactions: A:W.288, A:T.301, A:Y.304, A:Y.304, P:L.127 Hydrogen bonds: A:D.300, A:T.301, A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.17: 6 residues within 4Å: Chain C: R.156, L.160, Q.161, F.164, L.223 Chain J: F.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:L.160, C:Q.161, C:F.164, C:L.223, J:F.1 Hydrogen bonds: C:Q.161, J:F.1 Salt bridges: C:R.156 CHD.27: 4 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:R.33, J:M.36 Hydrogen bonds: J:Y.32, J:R.33, J:R.33 CHD.42: 12 residues within 4Å: Chain G: R.14, R.17, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: Q.59, E.62, T.63, T.66 Ligands: PEK.14 10 PLIP interactions: 3 interactions with chain N, 3 interactions with chain G, 4 interactions with chain O Hydrophobic interactions: N:M.271, N:W.275, N:W.275, G:F.21 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:Q.59, O:E.62, O:E.62, O:T.63 CHD.45: 8 residues within 4Å: Chain N: H.233, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.18, PGV.48 6 PLIP interactions: 4 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:T.301, N:Y.304 Hydrogen bonds: N:T.301, P:W.99 Salt bridges: N:H.233, P:H.103 CHD.50: 5 residues within 4Å: Chain P: R.156, Q.161, F.164, L.223 Chain W: F.1 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164, P:L.223 Salt bridges: P:R.156 Hydrogen bonds: W:F.1 CHD.54: 11 residues within 4Å: Chain A: M.271, W.275 Chain B: Q.59, E.62, T.63 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.55 5 PLIP interactions: 2 interactions with chain T, 2 interactions with chain A, 1 interactions with chain B Salt bridges: T:R.14, T:R.17 Hydrophobic interactions: A:M.271, A:W.275 Hydrogen bonds: B:E.62 CHD.56: 6 residues within 4Å: Chain T: D.7, H.8, G.10, T.11, T.15, W.16 5 PLIP interactions: 5 interactions with chain T Hydrophobic interactions: T:T.15, T:W.16 Hydrogen bonds: T:H.8, T:G.10, T:T.15 CHD.59: 5 residues within 4Å: Chain W: Y.32, R.33, M.36, T.37, L.40 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:R.33, W:L.40 Hydrogen bonds: W:R.33 CHD.60: 5 residues within 4Å: Chain N: M.117 Chain W: F.55 Chain Y: I.39, R.41, H.42 1 PLIP interactions: 1 interactions with chain Y Hydrophobic interactions: Y:H.42

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.13: 19 residues within 4Å: Chain A: A.203, L.215 Chain C: A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, V.199, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.11 14 PLIP interactions: 5 interactions with chain C, 7 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: C:A.178, C:V.199, C:F.203, G:W.62, G:F.69, A:A.203, A:L.215 Hydrogen bonds: C:A.184, C:I.188, G:T.68, G:F.69, G:F.70, G:N.76, G:N.76 PEK.14: 9 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168 Chain G: R.17, F.21, V.28 Chain O: Q.59 Ligands: CHD.42 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:F.21, G:V.28, C:T.168 Salt bridges: G:R.17, C:K.157, C:K.157, C:H.158 PEK.21: 17 residues within 4Å: Chain A: V.193, L.197 Chain C: I.84, I.88, F.98, Y.102, W.240, H.243, F.244, V.247, F.251, V.254, S.255 Chain T: A.3, D.7 Ligands: DMU.19, PGV.25 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.88, C:F.98, C:Y.102, C:F.244, C:V.247, C:V.247, C:F.251, C:F.251, C:V.254, A:V.193, A:L.197, A:L.197 Salt bridges: C:H.243 PEK.43: 8 residues within 4Å: Chain G: A.1 Chain P: I.84, V.91, T.95, F.98, W.240, H.243 Ligands: PGV.48 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: P:I.84, P:V.91, P:F.98, P:W.240, P:H.243, G:A.1 PEK.46: 24 residues within 4Å: Chain N: H.151, V.155, T.207, L.210, L.215 Chain P: Q.177, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, V.199, G.202, F.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.34, PGV.47 15 PLIP interactions: 7 interactions with chain P, 5 interactions with chain T, 3 interactions with chain N Hydrophobic interactions: P:Q.177, P:F.203, P:F.203, P:F.203, T:W.62, T:F.69, N:V.155, N:L.210, N:L.215 Hydrogen bonds: P:Y.181, P:A.184, P:I.188, T:F.69, T:F.70, T:N.76 PEK.55: 10 residues within 4Å: Chain B: Q.59 Chain P: K.157, H.158, I.165, T.168 Chain T: R.17, F.21, L.25 Ligands: CDL.51, CHD.54 8 PLIP interactions: 4 interactions with chain T, 4 interactions with chain P Hydrophobic interactions: T:L.25, P:I.165, P:T.168 Salt bridges: T:R.17, T:R.17, T:R.17, P:K.157, P:H.158

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 19 residues within 4Å: Chain C: T.48, M.51, L.52, Y.55, 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, T.27, L.31 Ligands: PGV.15 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:I.62, C:T.213, C:I.216, C:V.217, C:F.220, J:L.31 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:H.226 CDL.18: 24 residues within 4Å: Chain C: N.125, L.127, L.131, L.138, A.139, V.142, Y.253, W.258 Chain G: L.23, S.27, L.30, N.34, L.37, H.38 Chain N: F.282, I.286, D.300, Y.304, S.307, I.311 Chain O: L.78, L.81, Y.85 Ligands: CHD.45 19 PLIP interactions: 8 interactions with chain C, 3 interactions with chain N, 5 interactions with chain G, 3 interactions with chain O Hydrophobic interactions: C:L.127, C:L.127, C:L.131, C:L.138, C:V.142, C:W.258, C:W.258, N:F.282, N:I.311, G:L.23, G:L.30, G:L.37, O:L.78, O:L.81, O:Y.85 Hydrogen bonds: C:N.125, N:D.300, G:N.34 Salt bridges: G:H.38 CDL.49: 18 residues within 4Å: Chain P: M.44, T.48, M.51, Y.55, W.58, R.59, I.62, R.63, F.67, T.213, F.220, R.221, K.224, H.226 Chain W: K.8, F.12, T.27 Ligands: PGV.47 16 PLIP interactions: 15 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:Y.55, P:Y.55, P:W.58, P:W.58, P:I.62, P:T.213, P:F.220, P:F.220, P:F.220 Hydrogen bonds: P:Y.55 Water bridges: P:R.63 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, W:K.8 CDL.51: 28 residues within 4Å: Chain A: F.282, D.300, Y.304, S.307, I.311 Chain B: A.70, I.74, L.78, L.81, Y.85 Chain P: N.125, P.126, L.127, L.131, T.134, Y.253, V.254, W.258 Chain T: G.22, L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.12, PEK.55 20 PLIP interactions: 7 interactions with chain P, 4 interactions with chain A, 4 interactions with chain B, 5 interactions with chain T Hydrophobic interactions: P:P.126, P:L.127, P:L.127, P:T.134, P:V.254, P:W.258, A:F.282, A:I.311, A:I.311, B:A.70, B:I.74, B:L.78, B:L.81, T:L.23, T:N.34, T:L.37 Hydrogen bonds: P:N.125, A:D.300 Salt bridges: T:H.38, T:H.38

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

DMU.19: 12 residues within 4Å: Chain C: G.141, V.142, T.145, H.149, D.246 Chain G: H.8, G.9, G.10, T.11, T.15, W.16 Ligands: PEK.21 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Salt bridges: C:H.149, C:H.149 Hydrogen bonds: G:H.8, G:G.10 DMU.20: 8 residues within 4Å: Chain C: N.38, S.39, T.41, I.45 Chain J: L.38, G.41, G.42, Y.45 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain C Hydrophobic interactions: J:L.38, C:I.45 Hydrogen bonds: J:Y.45, C:S.39, C:T.41 DMU.24: 6 residues within 4Å: Chain C: W.34, M.40 Chain G: W.62, G.63, F.69 Ligands: PGV.15 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.63 DMU.29: 12 residues within 4Å: Chain A: F.459 Chain D: L.95, W.98, Y.102 Chain M: L.28, L.29, A.31, G.32, W.33, L.35, Y.36, H.37 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain M, 2 interactions with chain A Hydrophobic interactions: D:W.98, D:W.98, D:W.98, M:A.31, M:L.35, A:F.459, A:F.459 DMU.44: 4 residues within 4Å: Chain P: N.38, S.39, T.41 Chain W: Y.45 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:Y.45 Hydrogen bonds: W:Y.45, W:Y.45 DMU.52: 10 residues within 4Å: Chain N: F.459, L.462 Chain Q: W.98, Y.102 Chain Z: L.28, L.29, G.32, W.33, Y.36, H.37 6 PLIP interactions: 2 interactions with chain N, 1 interactions with chain Z, 3 interactions with chain Q Hydrophobic interactions: N:F.459, N:L.462, Q:W.98, Q:W.98, Q:W.98 Hydrogen bonds: Z:Y.36

2 x ZN: ZINC ION(Non-covalent)

ZN.23: 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: 5 residues within 4Å: Chain S: C.60, C.62, C.82, S.84, 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.26: 1 residues within 4Å: Chain I: T.2 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:T.2, I:T.2 SAC.58: 1 residues within 4Å: Chain V: T.2 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:T.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishigami, I. et al., Structural insights into functional properties of the oxidized form of cytochrome c oxidase. Nat Commun (2023)

Release Date

2023-09-27

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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