SMTL ID : 5wau.1

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 37 residues within 4Å: Chain A: L.20, 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, T.424, F.425, Q.428, R.438, R.439, Y.440, S.461, V.465, M.468 34 PLIP interactions: 34 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:L.381, A:L.381, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:W.126, 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:F.377, A:F.425 pi-Cation interactions: A:H.378 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, 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, L.73 Ligands: CMO.10 37 PLIP interactions: 33 interactions with chain A, 4 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:V.320, 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:L.381, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244, A:H.290 Water bridges: A:H.368, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376 HEA.29: 38 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, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, S.461, V.465, M.468 39 PLIP interactions: 39 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, N:R.38, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:F.377, N:L.381, N:L.381, N:V.386, N:F.393, N:F.393, N:T.424, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:W.126, N:Y.371, 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 pi-Cation interactions: N:H.378 Metal complexes: N:H.61, N:H.378 HEA.30: 33 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, 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, L.73 Ligands: CMO.36 35 PLIP interactions: 32 interactions with chain N, 3 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:T.316, N:V.320, N:F.348, 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:P.69, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:H.291, N:T.316, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 Metal complexes: N:H.376

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.10 CU.31: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CMO.36 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, CMO.36

2 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: 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.11, H2O.11, H2O.14 MG.32: 3 residues within 4Å: Chain N: H.368, D.369 Chain O: E.198 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.53, H2O.54

2 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.43 Water bridges: A:Q.43, A:T.46 NA.33: 4 residues within 4Å: Chain N: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40, N:S.441, 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: 15 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: A.84, F.87, F.91 Chain K: D.8, F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 12 PLIP interactions: 4 interactions with chain D, 1 interactions with chain K, 4 interactions with chain A, 3 interactions with chain M Hydrophobic interactions: D:A.84, D:F.87, D:F.87, D:F.91, K:F.9, A:T.408, A:W.409, A:W.409, A:I.412, M:Q.15, M:A.16, M:L.19 PGV.7: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.104, L.152, I.158, L.159 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, E.90 Ligands: PEK.14 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:L.104, A:L.152, A:I.158, A:L.159, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:H.9 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.15: 22 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, 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 Ligands: PEK.14, CDL.17 28 PLIP interactions: 2 interactions with chain F, 26 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.65, C:R.221, C:H.231, C:H.231 Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:I.210, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:T.66, C:H.71, C:R.221, C:F.233, C:G.234 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.16: 12 residues within 4Å: Chain A: D.298 Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Chain P: W.258, W.259 Chain T: A.1 Ligands: CHD.13 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain C Hydrogen bonds: H:N.22, H:N.24 Water bridges: H:N.22 Hydrophobic interactions: C:W.99, C:W.99, C:L.106, C:L.106 PGV.34: 16 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.80, A.84, F.91 Chain X: F.9, H.10, S.20 Chain Z: P.9, T.10, S.11, P.12, Q.15, L.19, S.20 7 PLIP interactions: 4 interactions with chain Z, 2 interactions with chain Q, 1 interactions with chain N Hydrophobic interactions: Z:P.12, Z:L.19, Q:A.84, Q:F.91, N:W.409 Hydrogen bonds: Z:T.10 Water bridges: Z:A.6 PGV.35: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151 Chain P: H.9, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, E.90 Ligands: PEK.43, PGV.45 13 PLIP interactions: 8 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:A.24, P:T.28, P:W.57, P:W.57, P:W.57, P:W.58, N:F.148 Hydrogen bonds: P:H.9, P:E.64, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.41: 11 residues within 4Å: Chain C: W.258, W.259 Chain G: A.1 Chain N: D.298 Chain P: T.95, W.99, H.103, L.106, A.107 Chain U: N.24 Ligands: CHD.42 6 PLIP interactions: 1 interactions with chain N, 4 interactions with chain P, 1 interactions with chain U Hydrogen bonds: N:D.298, P:H.103 Hydrophobic interactions: P:W.99, P:W.99, P:L.106 Water bridges: U:N.24 PGV.45: 25 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, M.83, F.86, E.90, L.206, 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.35, CDL.46 29 PLIP interactions: 27 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:F.86, P:F.86, P:L.206, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:T.228, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 15 residues within 4Å: Chain A: V.350, N.422, F.426, H.429, F.430, L.433 Chain B: M.5, L.7, G.8, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 12 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.7, B:V.31, B:F.32, B:L.39, A:V.350, A:N.422, A:F.426, A:H.429, A:F.430, A:F.430, A:L.433 Salt bridges: I:R.43 TGL.9: 22 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.103, P.106, L.113, F.393, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:F.2, A:L.18, A:F.22, A:W.25, A:W.25, A:W.103, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29 TGL.21: 20 residues within 4Å: Chain A: W.334, M.339, L.342, K.411, F.414, A.415 Chain B: L.39, I.42, L.46, T.47, T.48, K.49 Chain D: R.73, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 13 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: D:V.81, D:I.89, B:L.39, B:I.42, B:K.49, A:W.334, A:W.334, A:L.342, A:F.414, A:A.415 Water bridges: D:T.75, D:E.77 Salt bridges: A:K.411 TGL.38: 13 residues within 4Å: Chain N: N.422, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35 Chain V: R.43 8 PLIP interactions: 4 interactions with chain O, 1 interactions with chain V, 3 interactions with chain N Hydrophobic interactions: O:L.28, O:V.31, O:F.32, N:H.429, N:F.430, N:L.433 Water bridges: O:F.9 Salt bridges: V:R.43 TGL.49: 18 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, F.414, A.415 Chain O: L.39, I.42, S.43, T.47 Chain Q: R.73, S.74, T.75, E.77, W.78, V.81, M.86 Chain V: R.16 11 PLIP interactions: 5 interactions with chain Q, 4 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: Q:E.77, Q:W.78, Q:V.81, N:W.334, N:L.342, N:F.414, N:A.415, O:L.39, O:I.42 Hydrogen bonds: Q:E.77, Q:W.78 TGL.53: 22 residues within 4Å: Chain N: F.2, L.7, T.17, L.18, L.20, L.21, F.22, W.25, L.113, F.393, F.400, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, L.27, F.28, F.29, A.35 22 PLIP interactions: 12 interactions with chain N, 10 interactions with chain Y Hydrophobic interactions: N:F.2, N:T.17, N:L.18, N:L.20, N:W.25, N:W.25, N:W.25, N:W.25, N:L.113, N:F.393, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:L.27, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29, Y:A.35

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

CMO.10: 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) CMO.36: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.30, CU.31 No protein-ligand interaction detected (PLIP)

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, G.272, W.275 Chain B: E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.44 12 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 4 interactions with chain T Hydrogen bonds: B:E.62, B:E.62, B:T.63 Water bridges: B:T.63, T:R.17, T:R.17 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 Salt bridges: T:R.14, T:R.17 CHD.13: 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.16, CDL.51 9 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A, 1 interactions with chain P Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:W.288, A:Y.304, P:L.127 Water bridges: A:D.300, A:T.301 CHD.18: 5 residues within 4Å: Chain C: R.156, F.164, F.219, L.223 Chain J: F.1 7 PLIP interactions: 1 interactions with chain J, 6 interactions with chain C Hydrophobic interactions: J:F.1, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 CHD.26: 12 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: E.62, T.63, T.66 Ligands: PEK.24 10 PLIP interactions: 4 interactions with chain N, 4 interactions with chain G, 2 interactions with chain O Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275 Water bridges: G:R.17, G:R.17, O:T.63 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:E.62 CHD.27: 5 residues within 4Å: 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:T.37, J:L.40 Hydrogen bonds: J:R.33, J:R.33 CHD.42: 9 residues within 4Å: Chain C: L.127 Chain N: H.233, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.25, PGV.41 8 PLIP interactions: 5 interactions with chain N, 1 interactions with chain C, 2 interactions with chain P Hydrophobic interactions: N:T.301, N:Y.304, C:L.127 Hydrogen bonds: N:T.301, P:W.99 Water bridges: N:D.300 Salt bridges: N:H.233, P:H.103 CHD.47: 5 residues within 4Å: Chain P: R.156, F.164, F.219, L.223 Chain W: F.1 9 PLIP interactions: 8 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:F.164, P:F.164, P:F.164, P:F.219, P:L.223, W:F.1 Water bridges: P:R.156, P:Q.161 Salt bridges: P:R.156 CHD.52: 4 residues within 4Å: Chain W: Y.32, R.33, T.37, L.40 4 PLIP interactions: 4 interactions with chain W Hydrophobic interactions: W:Y.32, W:R.33 Hydrogen bonds: W:Y.32, W:R.33

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.14: 22 residues within 4Å: Chain A: H.151, V.155, L.215 Chain C: W.34, T.174, 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.7, PGV.15 16 PLIP interactions: 6 interactions with chain G, 2 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: G:W.62, A:V.155, A:L.215, C:W.34, C:T.174, C:Y.181, C:I.188, C:F.203, C:F.203, C:F.203 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.188 Water bridges: G:F.69 PEK.19: 14 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, F.251 Chain T: K.5, T.11 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain T Hydrophobic interactions: C:I.84, C:L.85, C:V.91, C:T.95, C:F.98, C:F.98, C:W.240, C:W.240, C:V.247, C:F.251, C:F.251 Hydrogen bonds: C:K.77 Water bridges: C:R.80 Salt bridges: C:K.77, T:H.8 PEK.24: 16 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain G: R.17, F.21, G.22, L.23 Chain N: W.275, S.279, L.283 Chain O: Q.59 Ligands: CDL.25, CHD.26 12 PLIP interactions: 2 interactions with chain N, 3 interactions with chain G, 7 interactions with chain C Hydrophobic interactions: N:W.275, N:L.283, G:F.21, G:L.23, C:Q.161, C:I.165, C:I.165, C:Y.172, C:Y.172 Salt bridges: G:R.17 Hydrogen bonds: C:K.157, C:Q.161 PEK.40: 15 residues within 4Å: Chain G: A.3, K.5, T.11, W.16 Chain P: I.84, L.85, V.91, T.95, F.98, W.240, H.243, F.244, V.247, F.251 Ligands: CDL.25 10 PLIP interactions: 8 interactions with chain P, 2 interactions with chain G Hydrophobic interactions: P:L.85, P:V.91, P:F.98, P:F.98, P:H.243, P:F.244, P:F.244, P:V.247, G:K.5, G:W.16 PEK.43: 20 residues within 4Å: Chain N: H.151, V.155 Chain P: F.35, T.174, 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.35 13 PLIP interactions: 6 interactions with chain P, 6 interactions with chain T, 1 interactions with chain N Hydrophobic interactions: P:F.35, P:T.174, P:Y.181, P:F.203, P:F.203, T:W.62, N:V.155 Hydrogen bonds: P:I.188, T:T.68, T:F.70, T:N.76, T:N.76 Water bridges: T:F.69 PEK.44: 12 residues within 4Å: Chain A: W.275 Chain B: Q.59, T.66 Chain P: K.157, H.158, Q.161, T.168, Y.172 Chain S: A.1 Chain T: R.17, F.21 Ligands: CHD.12 13 PLIP interactions: 6 interactions with chain P, 2 interactions with chain B, 3 interactions with chain T, 1 interactions with chain S, 1 interactions with chain A Hydrophobic interactions: P:T.168, P:Y.172, P:Y.172, B:T.66, T:F.21, A:W.275 Hydrogen bonds: P:K.157, P:K.157, P:Q.161, B:Q.59, T:R.17, S:A.1 Salt bridges: T:R.17

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 19 residues within 4Å: Chain C: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12 Ligands: PGV.15 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:V.171, C:T.213 Hydrogen bonds: C:Y.55, C:R.63, C:R.63, C:R.221 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 Water bridges: J:D.28, J:D.28 CDL.25: 31 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, L.138, V.142, L.250, F.251, V.254 Chain G: L.23, A.24, 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.77, L.78, L.81, Y.85 Ligands: PEK.24, PEK.40, CHD.42 25 PLIP interactions: 7 interactions with chain C, 7 interactions with chain G, 9 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: C:T.134, C:L.138, C:L.138, C:L.250, C:F.251, C:V.254, G:L.23, G:L.23, G:L.30, G:L.37, N:F.282, N:F.282, N:I.286, N:A.303, N:Y.304, N:I.311, N:I.311, O:A.77, O:L.78 Hydrogen bonds: C:N.125, G:N.34, G:N.34, N:D.300, N:Y.304 Salt bridges: G:H.38 CDL.46: 20 residues within 4Å: Chain P: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, I.209, T.213, I.216, V.217, F.220, K.224, H.226 Chain W: K.8, F.12, T.27 Ligands: PGV.45 19 PLIP interactions: 17 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:M.51, P:Y.55, P:W.58, P:R.59, P:I.62, P:V.171, P:I.209, P:T.213, P:I.216, P:V.217, P:F.220 Hydrogen bonds: P:Y.55, P:R.63, W:T.27 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, W:K.8 CDL.51: 24 residues within 4Å: Chain A: F.282, L.283, D.300, Y.304, S.307, I.311 Chain B: A.77, L.78, L.81, Y.85 Chain P: N.125, L.127, L.131, T.134, L.138, V.142 Chain T: W.16, L.23, S.27, C.31, N.34, L.37, H.38 Ligands: CHD.13 20 PLIP interactions: 5 interactions with chain A, 6 interactions with chain T, 6 interactions with chain P, 3 interactions with chain B Hydrophobic interactions: A:F.282, A:L.283, A:Y.304, A:I.311, T:W.16, T:N.34, T:L.37, T:L.37, P:L.131, P:L.131, P:T.134, P:L.138, B:A.77, B:Y.85 Hydrogen bonds: A:D.300, P:N.125, P:N.125 Salt bridges: T:H.38, T:H.38 Water bridges: B:R.82

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

DMU.20: 6 residues within 4Å: Chain C: W.34, N.38, S.39, M.40 Chain G: W.62, G.63 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.34, C:W.34 Hydrogen bonds: C:M.40, G:G.63 Water bridges: C:S.39 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, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A, 4 interactions with chain M Hydrophobic interactions: D:L.95, D:W.98, D:W.98, A:F.459, A:L.462, M:L.27, M:L.34 Hydrogen bonds: M:Y.35 Water bridges: M:H.36 DMU.48: 8 residues within 4Å: Chain P: W.34, N.38, S.39, M.40, T.41 Chain T: W.62, G.63, F.69 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain T Hydrophobic interactions: P:W.34, P:W.34, T:W.62, T:F.69 Hydrogen bonds: P:T.41 DMU.54: 12 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, G.31, W.32, L.34, Y.35, H.36 8 PLIP interactions: 3 interactions with chain Z, 1 interactions with chain Y, 1 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: Z:L.27, Z:L.34, Y:F.37, N:F.459, Q:L.95, Q:W.98, Q:W.98 Hydrogen bonds: Z:W.32

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.22: 15 residues within 4Å: Chain A: F.321, H.328 Chain B: I.41, H.52, M.56, D.57, E.60, V.61, W.65, I.72 Chain E: D.8, F.11, L.41 Chain I: R.10, L.17 8 PLIP interactions: 5 interactions with chain B, 1 interactions with chain I, 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: B:W.65, B:I.72, I:L.17, A:F.321 Hydrogen bonds: B:D.57 Water bridges: B:E.60 Salt bridges: B:H.52 pi-Cation interactions: E:F.11 PSC.39: 19 residues within 4Å: Chain N: F.321, L.324, H.328 Chain O: L.37, I.41, H.52, M.56, D.57, V.61, I.64, W.65, P.69 Chain R: E.6, D.8, F.11, L.41 Chain V: R.10, A.14, L.17 15 PLIP interactions: 2 interactions with chain V, 2 interactions with chain R, 3 interactions with chain N, 8 interactions with chain O Hydrophobic interactions: V:A.14, V:L.17, N:F.321, N:F.321, N:L.324, O:L.37, O:I.41, O:I.41, O:M.56, O:D.57, O:I.64, O:W.65, O:P.69 Salt bridges: R:D.8 pi-Cation interactions: R:F.11

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.50: 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

Ishigami, I. et al., Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-09

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
a

B
B

O
b

C
C

P
c

D
D

Q
d

E
E

R
e

F
F

S
f

G
G

T
g

H
H

U
h

I
I

V
i

J
J

W
j

K
K

X
k

L
L

Y
l

M
M

Z
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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