SMTL ID : 6nmf.1

SFX structure of reduced cytochrome c oxidase at room temperature

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

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

HEA.1: 32 residues within 4Å: Chain A: 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, F.377, H.378, L.381, S.382, V.386, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:T.31, 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:F.377, A:L.381, A:L.381, A:V.386, A:T.424, A:F.425, A:F.425 Hydrogen bonds: A:S.34, A:S.34, A:R.38, 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:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 30 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, I.72 34 PLIP interactions: 31 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:F.348, A:L.353, A:I.356, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:V.380, A:L.381, B:I.34, B:I.34, B:I.72 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:R.438, A:R.438, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.29: 32 residues within 4Å: Chain N: 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, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 36 PLIP interactions: 36 interactions with chain N, Hydrophobic interactions: 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:Y.371, N:V.374, N:F.377, N:F.377, N:L.381, N:V.386, N:V.386, N:F.393, N:T.424, 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:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.30: 30 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, F.348, T.349, G.352, 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 31 PLIP interactions: 28 interactions with chain N, 3 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:F.348, N:I.356, N:L.358, N:F.377, N:F.377, N:V.380, N:V.380, N:L.381, N:L.381, O:I.34, O:I.34, O:P.69 Hydrogen bonds: N:W.126, N:Y.244, N:Y.244 Water bridges: N:H.291, N:D.369, N:D.369, N:R.438 Salt bridges: N:H.368, N:R.438 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

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

CU.3: 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.31: 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.4: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, H2O.5, H2O.6, H2O.7 MG.32: 5 residues within 4Å: Chain N: H.368, D.369 Chain O: D.173, S.197, E.198 5 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 2 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.21, H2O.22

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

NA.5: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:G.45 NA.33: 3 residues within 4Å: Chain N: E.40, G.45, S.441 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.6: 20 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, L.152 Chain C: H.9, V.11, G.20, M.27, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86 Ligands: PEK.15 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.57, C:W.57, C:W.58, C:F.86, A:L.152 Hydrogen bonds: C:H.9, C:E.64, C:H.71, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.7: 12 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, F.87 Chain K: F.9, H.10 Chain M: A.3, K.4, P.12, Q.15, A.16 8 PLIP interactions: 1 interactions with chain A, 3 interactions with chain M, 2 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: A:W.409, M:P.12, M:A.16, K:F.9, D:T.80, D:F.87 Hydrogen bonds: M:A.3 Salt bridges: K:H.10 PGV.16: 22 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234, Y.241 Ligands: CDL.17 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:F.86, 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:R.221, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 8 residues within 4Å: Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: N.24 Ligands: CDL.9, CHD.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:W.99, C:W.99 Hydrogen bonds: H:N.24 PGV.34: 10 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: A.84, F.87 Chain X: F.9, H.10 Chain Z: P.12, Q.15 10 PLIP interactions: 2 interactions with chain X, 3 interactions with chain Q, 1 interactions with chain Z, 4 interactions with chain N Hydrophobic interactions: X:F.9, Q:A.84, Q:F.87, Q:F.87, Z:P.12, N:T.408, N:W.409, N:I.412 Salt bridges: X:H.10 Hydrogen bonds: N:T.408 PGV.38: 22 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155 Chain P: H.9, V.11, G.20, A.24, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, F.93 Ligands: PEK.45 9 PLIP interactions: 5 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: P:A.24, P:W.57, P:W.57, P:F.86, P:F.93, N:V.155 Hydrogen bonds: N:R.96, N:M.97 Salt bridges: N:R.96 PGV.39: 10 residues within 4Å: Chain G: A.1 Chain N: D.298 Chain P: W.99, Y.102, H.103, L.106, A.107 Chain U: N.22 Ligands: CDL.24, CHD.44 5 PLIP interactions: 2 interactions with chain U, 2 interactions with chain P, 1 interactions with chain G Hydrogen bonds: U:N.22 Water bridges: U:Q.23 Hydrophobic interactions: P:W.99, P:W.99, G:A.1 PGV.41: 19 residues within 4Å: Chain P: M.51, W.58, V.61, S.65, T.66, H.71, L.79, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.42 18 PLIP interactions: 18 interactions with chain P Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:I.210, P:T.213, 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:R.221, P:H.231 Salt bridges: P:R.221, P:R.221, P:H.231

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 19 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, R.20, M.24, F.28, F.29 15 PLIP interactions: 9 interactions with chain A, 6 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:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29 TGL.10: 10 residues within 4Å: Chain A: N.422, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, S.35 Chain I: Y.35, R.43 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:N.422, A:F.430, B:L.7 Water bridges: I:R.43 Salt bridges: I:R.43 TGL.21: 14 residues within 4Å: Chain A: W.334, M.339, L.342, K.411, A.415 Chain B: I.42, S.43, L.46, T.47 Chain D: R.73, T.75, E.77, W.78 Chain I: H.20 8 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:A.415, B:I.42, D:W.78 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 TGL.35: 13 residues within 4Å: Chain N: I.332, W.334, F.414 Chain O: S.43, L.46, T.47, T.48 Chain Q: R.73, E.77, W.78, V.81, M.86 Chain V: R.16 6 PLIP interactions: 4 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: N:W.334, N:W.334, N:F.414, Q:V.81 Salt bridges: N:K.411 Hydrogen bonds: Q:W.78 TGL.50: 12 residues within 4Å: Chain N: N.422, F.426, H.429, F.430, L.433, W.450 Chain O: L.7, G.8, L.28, F.32, L.39 Chain V: R.43 9 PLIP interactions: 3 interactions with chain O, 1 interactions with chain V, 5 interactions with chain N Hydrophobic interactions: O:F.32, O:L.39, N:F.426, N:H.429, N:F.430, N:L.433, N:W.450 Salt bridges: O:H.24, V:R.43 TGL.52: 16 residues within 4Å: Chain N: F.2, T.17, L.18, L.21, W.81, F.393, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, R.20, M.24, F.28, F.29 10 PLIP interactions: 5 interactions with chain N, 5 interactions with chain Y Hydrophobic interactions: N:T.17, N:L.21, N:F.393, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.29

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 25 residues within 4Å: Chain A: F.282, D.300, Y.304, S.307, I.311 Chain B: A.70, I.74, A.77, L.78, Y.85 Chain P: L.127, L.131, S.135, L.250, F.251, V.254 Chain T: S.27, C.31, N.34, L.37, H.38 Ligands: CHD.19, PGV.20, PEK.46, PEK.49 14 PLIP interactions: 6 interactions with chain P, 2 interactions with chain T, 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: P:L.131, P:L.250, P:F.251, P:V.254, T:L.37, B:A.70, B:I.74, B:A.77, B:L.78, A:F.282, A:I.311 Water bridges: P:N.125, P:N.125 Salt bridges: T:H.38 CDL.17: 17 residues within 4Å: Chain C: M.51, L.52, Y.55, R.59, I.62, R.63, F.67, T.213, I.216, F.220, R.221, K.224, H.226 Chain J: K.8, D.28, L.31 Ligands: PGV.16 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:L.52, C:Y.55, C:Y.55, C:R.59, C:I.62, C:I.216, C:I.216, C:F.220 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 Hydrogen bonds: J:D.28 Water bridges: J:T.27 CDL.24: 26 residues within 4Å: Chain C: L.127, L.131, L.138, V.142 Chain G: S.27, L.30, C.31, N.34, L.37, H.38 Chain N: F.282, I.286, D.300, A.303, Y.304, S.307, I.311 Chain O: A.70, A.77, L.78, L.81, Y.85 Ligands: PEK.23, PEK.25, PGV.39, CHD.44 16 PLIP interactions: 5 interactions with chain G, 4 interactions with chain O, 5 interactions with chain N, 2 interactions with chain C Hydrophobic interactions: G:L.30, G:L.30, G:L.37, O:A.70, O:A.77, O:L.78, O:L.81, N:F.282, N:F.282, N:I.286, N:A.303, N:Y.304, C:L.138, C:V.142 Hydrogen bonds: G:N.34 Salt bridges: G:H.38 CDL.42: 17 residues within 4Å: Chain P: M.51, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, T.213, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, T.27 Ligands: PGV.41 18 PLIP interactions: 17 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:M.54, P:Y.55, P:Y.55, P:Y.55, P:W.58, P:W.58, P:T.213, P:V.217, P:V.217, P:F.220 Hydrogen bonds: P:Y.55, P:R.63 Salt bridges: P:R.63, P:K.224, P:K.224, P:K.224, P:H.226, W:K.8

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.37: 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

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.12: 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.46 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 3 interactions with chain T Hydrophobic interactions: B:T.66, A:M.271, A:W.275, A:W.275, T:F.18 Hydrogen bonds: B:Q.59, B:E.62 Salt bridges: T:R.14, T:R.17 CHD.18: 5 residues within 4Å: Chain C: R.156, Q.161, F.164, L.223 Chain J: F.1 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:L.223 Hydrogen bonds: C:Q.161 Salt bridges: C:R.156 CHD.19: 8 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: CDL.9, PGV.20 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.301, A:Y.304 Hydrogen bonds: A:T.301, A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.26: 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.23 11 PLIP interactions: 4 interactions with chain N, 4 interactions with chain O, 3 interactions with chain G Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, G:F.18 Hydrogen bonds: O:Q.59, O:Q.59, O:E.62, O:T.63 Salt bridges: G:R.14, G:R.17 CHD.27: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:I.3, J:R.33, J:L.40 Hydrogen bonds: J:R.33, J:R.33 CHD.43: 4 residues within 4Å: Chain P: R.156, Q.161, F.164 Chain W: F.1 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164 Salt bridges: P:R.156 Hydrogen bonds: W:F.1 CHD.44: 9 residues within 4Å: Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.24, PGV.39 7 PLIP interactions: 5 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:W.288, N:Y.304, N:Y.304 Hydrogen bonds: N:T.301, P:W.99 Salt bridges: N:H.233, P:H.103 CHD.51: 6 residues within 4Å: Chain N: I.3, L.7 Chain W: Y.32, R.33, M.36, T.37 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:R.33, W:M.36, W:T.37

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.13: 15 residues within 4Å: Chain A: F.321, A.325 Chain B: I.41, M.45, M.56, D.57, E.60, I.64, W.65, L.68 Chain E: E.6, D.8, F.11 Chain I: R.10, L.17 11 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 1 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: B:I.41, B:M.56, B:W.65, B:L.68, A:F.321, A:F.321, I:L.17 Hydrogen bonds: B:D.57, B:E.60 Water bridges: B:H.52 Salt bridges: E:D.8 PSC.36: 15 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: L.37, I.41, H.52, M.56, D.57, V.61, W.65 Chain R: E.6, T.7, D.8, F.11 Chain V: R.10 12 PLIP interactions: 9 interactions with chain O, 1 interactions with chain R, 2 interactions with chain N Hydrophobic interactions: O:L.37, O:I.41, O:I.41, O:M.56, O:V.61, O:W.65, O:W.65, N:F.321, N:F.321 Hydrogen bonds: O:D.57 Salt bridges: O:H.52, R:D.8

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

DMU.14: 9 residues within 4Å: Chain C: S.29, M.33, F.37, S.39 Chain J: S.46, Y.48, C.49, L.50, W.52 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:M.33, C:F.37, J:L.50 Hydrogen bonds: C:F.37, C:S.39, C:S.39, J:Y.45, J:Y.48, J:Y.48 DMU.28: 12 residues within 4Å: Chain A: F.459, L.462 Chain D: L.95, W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 7 PLIP interactions: 2 interactions with chain M, 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: M:L.27, M:A.30, D:L.95, D:W.98, D:W.98, A:F.459, A:L.462 DMU.40: 8 residues within 4Å: Chain P: S.29, M.33, F.37 Chain W: S.46, C.49, L.50, W.52, A.53 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:M.33, P:F.37, W:L.50, W:A.53 DMU.47: 12 residues within 4Å: Chain N: F.459, L.462 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, A.30, W.32, L.34, Y.35, H.36 13 PLIP interactions: 5 interactions with chain Z, 3 interactions with chain N, 5 interactions with chain Q Hydrophobic interactions: Z:L.27, Z:L.27, Z:A.30, Z:L.34, N:F.459, N:F.459, N:L.462, Q:L.95, Q:W.98, Q:W.98, Q:W.98 Hydrogen bonds: Z:W.32, 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.15: 21 residues within 4Å: Chain A: H.151, V.155, T.207, L.210 Chain C: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.6 12 PLIP interactions: 6 interactions with chain G, 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: 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, G:N.76, C:A.184, C:I.188 Water bridges: G:F.69 PEK.23: 10 residues within 4Å: Chain C: K.157, H.158, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21 Chain O: Q.59 Ligands: CDL.24, CHD.26 7 PLIP interactions: 2 interactions with chain G, 1 interactions with chain O, 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:F.21, C:T.168 Salt bridges: G:R.17 Hydrogen bonds: O:Q.59, C:K.157, C:K.157, F:A.1 PEK.25: 15 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Chain P: R.80, I.84, L.85, V.91, F.98, W.240, F.244, V.247, F.251 Ligands: CDL.24 12 PLIP interactions: 9 interactions with chain P, 3 interactions with chain G Hydrophobic interactions: P:L.85, P:V.91, P:V.91, P:F.98, P:F.98, P:W.240, P:V.247, P:F.251, P:F.251, G:A.3, G:K.5 Hydrogen bonds: G:H.8 PEK.45: 21 residues within 4Å: Chain N: H.151, V.155, T.207, L.215 Chain P: A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.38 11 PLIP interactions: 5 interactions with chain P, 1 interactions with chain N, 5 interactions with chain T Hydrophobic interactions: P:F.203, P:F.203, N:V.155, T:W.62, T:F.69 Hydrogen bonds: P:Y.181, P:A.184, P:I.188, T:F.69, T:F.70, T:N.76 PEK.46: 12 residues within 4Å: Chain A: W.275, S.279 Chain P: Q.161, I.165, T.168, Y.172 Chain S: A.1 Chain T: R.17, F.21, L.23 Ligands: CDL.9, CHD.12 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain P, 3 interactions with chain T Hydrophobic interactions: A:W.275, P:I.165, P:T.168, P:Y.172, T:F.21, T:L.23 Salt bridges: T:R.17 PEK.49: 16 residues within 4Å: Chain C: R.80, Y.81, I.84, V.91, T.95, W.240, V.247, F.251 Chain T: S.2, A.3, K.5, G.6, D.7, H.8, T.11 Ligands: CDL.9 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain T Hydrophobic interactions: C:Y.81, C:I.84, C:I.84, C:V.91, C:W.240, C:F.251, C:F.251, T:A.3, T:K.5 Hydrogen bonds: C:Y.81 Water bridges: C:R.80

2 x ZN: ZINC ION(Non-covalent)

ZN.22: 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.48: 5 residues within 4Å: Chain S: C.60, C.62, C.82, C.85, T.87 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

Ishigami, I. et al., Snapshot of an oxygen intermediate in the catalytic reaction of cytochromecoxidase. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-03-13

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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