SMTL ID : 6nmp.1

SFX structure of oxidized cytochrome c oxidase at room temperature

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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: PER.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.29: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: PER.35 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: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.4, H2O.4 MG.30: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, 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.13, H2O.14

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

NA.3: 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:E.40 NA.31: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:E.40

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

HEA.4: 33 residues within 4Å: Chain A: L.20, A.24, G.27, 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, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:A.24, 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:F.377, A:L.381, A:V.386, A:V.386, A:F.393, A:T.424, A:F.425 Hydrogen bonds: A:R.38, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.425 Metal complexes: A:H.61, A:H.378 HEA.5: 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, I.72 Ligands: PER.9 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:F.348, A:T.349, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:P.69, B:I.72 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.32: 31 residues within 4Å: Chain N: G.27, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 31 PLIP interactions: 31 interactions with chain N, Hydrophobic interactions: N:I.37, 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:L.381, N:L.381, N:V.386, N:V.386, N:F.393, N:T.424, N:F.425, N:V.465 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: 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.33: 34 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, I.72, L.73 Ligands: PER.35 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:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:F.348, N:L.353, N:I.356, N:L.358, N:V.373, 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.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244, N:Y.244 Water bridges: N:D.369, 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

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: 12 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80 Chain K: H.10, S.20 Chain M: A.3, K.4, P.12, Q.15, A.16 8 PLIP interactions: 1 interactions with chain D, 2 interactions with chain M, 1 interactions with chain K, 4 interactions with chain A Hydrophobic interactions: D:T.80, M:P.12, A:T.408, A:W.409, A:W.409 Hydrogen bonds: M:K.4, A:T.408 Salt bridges: K:H.10 PGV.7: 11 residues within 4Å: Chain A: D.298 Chain C: W.99, Y.102, H.103, L.106 Chain H: N.22, N.24 Chain T: A.1 Ligands: CHD.15, PEK.20, CDL.51 8 PLIP interactions: 1 interactions with chain T, 2 interactions with chain H, 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: T:A.1, C:W.99, C:W.99, C:W.99 Hydrogen bonds: H:N.22, H:N.24 Water bridges: A:D.298, A:D.298 PGV.13: 21 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152, L.159 Chain C: H.9, V.11, T.28, N.50, M.54, W.57, W.58, E.64, H.71, L.79, G.82, F.86 Ligands: PGV.17, PEK.22 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:T.28, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, A:L.152, A:L.159 Hydrogen bonds: C:E.64, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.17: 21 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, M.83, F.86, E.90, H.207, I.210, T.213, F.214, R.221, H.226, F.227, H.231, H.232, F.233, G.234 Ligands: PGV.13, CDL.18 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:F.86, 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:R.221, C:F.233, C:G.234 Water bridges: C:H.231 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.34: 12 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.12, Q.15 9 PLIP interactions: 4 interactions with chain Q, 2 interactions with chain X, 1 interactions with chain Z, 2 interactions with chain N Hydrophobic interactions: Q:T.80, Q:A.84, Q:F.87, Q:F.87, X:F.9, N:T.408 Salt bridges: X:H.10 Hydrogen bonds: Z:A.3, N:T.408 PGV.40: 21 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, L.159 Chain P: H.9, V.11, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86 Ligands: PEK.42 12 PLIP interactions: 8 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: P:L.31, P:W.57, P:W.57, P:W.57, P:W.58, P:F.86, N:L.159 Hydrogen bonds: P:W.57, P:V.61, N:R.96, N:M.97 Salt bridges: N:R.96 PGV.43: 21 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, F.86, L.206, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.45 23 PLIP interactions: 22 interactions with chain P, 1 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:L.206, P:I.210, P:I.210, 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, S:E.17 Water bridges: P:R.221, P:H.231 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.44: 12 residues within 4Å: Chain G: A.1 Chain N: F.237, D.298 Chain P: W.99, Y.102, H.103, L.106, A.107 Chain U: N.22 Ligands: CDL.23, PEK.24, CHD.41 7 PLIP interactions: 1 interactions with chain U, 1 interactions with chain G, 3 interactions with chain P, 2 interactions with chain N Hydrogen bonds: U:N.22 Hydrophobic interactions: G:A.1, P:W.99, P:W.99, P:L.106, N:F.237, N:F.237

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 11 residues within 4Å: Chain A: W.334, K.411, A.415 Chain B: L.39, I.42, L.44, T.47 Chain D: E.77, W.78, V.81 Chain I: H.20 11 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:A.415, B:L.39, B:I.42, B:L.44, B:T.47, D:W.78, D:V.81 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 TGL.25: 14 residues within 4Å: Chain A: T.354, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: G.8, H.24, L.28, S.35, L.39 Chain I: F.31, R.43 12 PLIP interactions: 6 interactions with chain A, 2 interactions with chain I, 4 interactions with chain B Hydrophobic interactions: A:T.354, A:F.426, A:F.426, A:H.429, A:F.430, A:W.450, I:F.31, B:L.28 Salt bridges: I:R.43, B:H.24 Hydrogen bonds: B:G.8 Water bridges: B:F.9 TGL.27: 17 residues within 4Å: Chain A: F.2, T.17, L.20, W.25, W.81, L.113, F.400, S.401, I.472 Chain L: I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain L Hydrophobic interactions: A:T.17, A:L.20, A:W.25, A:W.25, A:W.81, A:L.113, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.29 TGL.39: 13 residues within 4Å: Chain N: W.334, F.414, A.415 Chain O: S.43, L.46, T.47, K.49 Chain Q: R.73, S.74, T.75, E.77, W.78, V.82 10 PLIP interactions: 5 interactions with chain N, 1 interactions with chain O, 4 interactions with chain Q Hydrophobic interactions: N:W.334, N:F.414, N:A.415, O:T.47, Q:E.77, Q:V.82 Water bridges: N:K.411 Salt bridges: N:K.411 Hydrogen bonds: Q:T.75, Q:W.78 TGL.52: 14 residues within 4Å: Chain N: Y.379, N.422, F.426, H.429, F.430 Chain O: L.7, G.8, L.28, F.32, L.39 Chain V: F.31, Y.35, K.42, R.43 10 PLIP interactions: 3 interactions with chain V, 4 interactions with chain N, 3 interactions with chain O Hydrophobic interactions: V:F.31, V:F.31, N:F.426, N:F.426, N:H.429, N:F.430, O:F.32, O:L.39 Salt bridges: V:R.43 Hydrogen bonds: O:G.8 TGL.54: 16 residues within 4Å: Chain N: F.2, W.6, T.17, L.21, W.25, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29 13 PLIP interactions: 9 interactions with chain Y, 4 interactions with chain N Hydrophobic interactions: Y:I.11, Y:F.13, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29, N:T.17, N:L.21, N:W.25, N:I.472

2 x PER: PEROXIDE ION(Non-covalent)

PER.9: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: CU.1, HEA.5 No protein-ligand interaction detected (PLIP) PER.35: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: CU.29, HEA.33 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.290

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

CUA.10: 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.36: 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.11: 16 residues within 4Å: Chain A: F.321, H.328 Chain B: L.37, I.41, M.45, M.56, D.57, V.61, W.65, L.68 Chain E: E.6, D.8, F.11 Chain I: R.10, L.17, I.21 13 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B, 1 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: A:F.321, A:F.321, B:L.37, B:I.41, B:M.56, B:V.61, B:W.65, B:W.65, B:L.68, I:L.17, I:I.21 Hydrogen bonds: B:D.57 Salt bridges: E:D.8 PSC.38: 15 residues within 4Å: Chain N: F.321, H.328 Chain O: L.37, I.41, H.52, M.56, D.57, E.60, V.61, W.65, L.68, P.69 Chain R: E.6, D.8, D.40 12 PLIP interactions: 9 interactions with chain O, 2 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: O:L.37, O:I.41, O:I.41, O:M.56, O:V.61, O:W.65, O:L.68, N:F.321, N:F.321 Hydrogen bonds: O:D.57 Salt bridges: O:H.52, R:D.8

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.12: 12 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, F.18, F.21, G.22 Ligands: PEK.50 9 PLIP interactions: 4 interactions with chain T, 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: T:F.18, T:F.18, A:M.271, A:W.275, A:W.275 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:Q.59, B:E.62 CHD.15: 9 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: PGV.7, CDL.51 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:T.301, A:Y.304, A:Y.304 CHD.19: 6 residues within 4Å: Chain C: R.156, K.157, Q.161, F.164, L.223 Chain J: F.1 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.157, C:F.164, C:F.164, C:L.223 Salt bridges: C:R.156 CHD.26: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:L.40, A:I.3 Hydrogen bonds: J:R.33, J:R.33 CHD.37: 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.16 7 PLIP interactions: 3 interactions with chain G, 2 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: G:F.18, N:M.271, N:W.275 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:E.62, O:T.63 CHD.41: 9 residues within 4Å: Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.23, PGV.44 8 PLIP interactions: 2 interactions with chain P, 6 interactions with chain N Hydrogen bonds: P:W.99, N:T.301 Salt bridges: P:H.103, N:H.233 Hydrophobic interactions: N:W.288, N:T.301, N:Y.304, N:Y.304 CHD.46: 6 residues within 4Å: Chain P: R.156, L.160, Q.161, F.164 Chain W: F.1 Ligands: PEK.50 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:L.160, P:F.164, P:F.164 Salt bridges: P:R.156 CHD.53: 5 residues within 4Å: Chain N: I.3, L.7 Chain W: R.33, T.37, L.40 2 PLIP interactions: 2 interactions with chain W Hydrophobic interactions: W:R.33, W:L.40

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

DMU.14: 7 residues within 4Å: Chain C: W.34, M.40, M.44 Chain G: S.61, W.62, G.63, F.69 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.61, G:G.63 DMU.28: 10 residues within 4Å: Chain A: F.459 Chain D: L.95, W.98, Y.102 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 11 PLIP interactions: 6 interactions with chain D, 3 interactions with chain M, 2 interactions with chain A Hydrophobic interactions: D:L.95, D:W.98, D:W.98, M:L.27, A:F.459, A:F.459 Hydrogen bonds: D:Y.102, D:Y.102, D:Y.102, M:W.32 Water bridges: M:Y.35 DMU.47: 10 residues within 4Å: Chain N: F.459 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, G.31, W.32, Y.35, H.36 8 PLIP interactions: 4 interactions with chain Q, 3 interactions with chain Z, 1 interactions with chain N Hydrophobic interactions: Q:L.95, Q:W.98, Q:W.98, Z:L.27, N:F.459 Hydrogen bonds: Q:Y.102, Z:L.28, Z:H.36 DMU.49: 4 residues within 4Å: Chain P: M.40 Chain T: W.62, F.69 Ligands: PEK.42 No protein-ligand interaction detected (PLIP)

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.16: 11 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168 Chain G: R.17, F.21, L.30 Chain N: S.279 Chain O: Q.59 Ligands: CDL.23, CHD.37 7 PLIP interactions: 4 interactions with chain G, 1 interactions with chain O, 2 interactions with chain C Hydrophobic interactions: G:F.21, G:L.30 Salt bridges: G:R.17, G:R.17 Hydrogen bonds: O:Q.59, C:K.157, C:H.158 PEK.20: 18 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, L.85, T.95, F.98, W.240, V.247, F.251 Chain T: S.2, A.3, K.5, G.6, D.7, H.8 Ligands: PGV.7, CDL.51 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain T Hydrophobic interactions: C:Y.81, C:Y.81, C:I.84, C:I.84, C:I.84, C:L.85, C:F.98, C:W.240, C:V.247, C:F.251, T:A.3, T:H.8 Hydrogen bonds: C:Y.81 Salt bridges: C:K.77, C:R.80 PEK.22: 16 residues within 4Å: Chain A: H.151 Chain C: Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.13 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:F.69 Hydrogen bonds: G:T.68, G:F.69, G:F.70, G:N.76, C:A.184, C:A.184, C:I.188 PEK.24: 13 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Chain P: R.80, I.84, T.95, F.98, W.240, F.244, F.251 Ligands: PGV.44 7 PLIP interactions: 4 interactions with chain P, 3 interactions with chain G Hydrophobic interactions: P:F.98, P:W.240, P:F.251, P:F.251, G:A.3, G:K.5 Hydrogen bonds: G:H.8 PEK.42: 23 residues within 4Å: Chain N: H.151, T.207, L.215 Chain P: F.35, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, F.203, L.206, I.209 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.40, DMU.49 13 PLIP interactions: 6 interactions with chain P, 1 interactions with chain N, 6 interactions with chain T Hydrophobic interactions: P:F.35, P:F.203, P:L.206, P:I.209, N:L.215, T:W.62, T:F.69 Hydrogen bonds: P:A.184, P:I.188, T:F.69, T:F.70, T:N.76, T:N.76 PEK.50: 9 residues within 4Å: Chain A: W.275, S.279 Chain B: T.66 Chain P: Q.161 Chain T: R.17, F.21 Ligands: CHD.12, CHD.46, CDL.51 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain T, 1 interactions with chain B Hydrophobic interactions: A:W.275, T:F.21, B:T.66 Salt bridges: T:R.17

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 18 residues within 4Å: Chain C: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, T.27, D.28 Ligands: PGV.17 15 PLIP interactions: 2 interactions with chain J, 13 interactions with chain C Salt bridges: J:K.8, J:K.8, C:R.63, C:K.224, C:K.224, C:H.226 Hydrophobic interactions: C:M.51, C:Y.55, C:Y.55, C:W.58, C:R.59, C:I.62, C:I.216, C:V.217, C:F.220 CDL.23: 25 residues within 4Å: Chain C: L.127, L.131, L.138, V.142, V.254 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Chain N: F.282, D.300, Y.304, S.307, I.311 Chain O: A.70, A.77, L.78, Y.85 Ligands: PEK.16, CHD.41, PGV.44 15 PLIP interactions: 4 interactions with chain C, 7 interactions with chain G, 2 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: C:L.131, C:L.138, C:V.142, C:V.254, G:L.23, G:L.30, G:L.30, G:L.37, O:A.70, O:A.77, N:F.282, N:F.282 Hydrogen bonds: G:N.34, G:R.42 Salt bridges: G:H.38 CDL.45: 16 residues within 4Å: Chain P: T.48, M.51, Y.55, W.58, R.59, I.62, R.63, F.67, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, D.28 Ligands: PGV.43 15 PLIP interactions: 13 interactions with chain P, 2 interactions with chain W Hydrophobic interactions: P:T.48, P:Y.55, P:W.58, P:I.62, P:V.217, P:F.220, P:F.220 Hydrogen bonds: P:Y.55, W:D.28 Salt bridges: P:R.63, P:K.224, P:K.224, P:K.224, P:H.226, W:K.8 CDL.51: 27 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, L.81, Y.85 Chain P: L.127, L.131, V.142, V.254 Chain T: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Ligands: PGV.7, CHD.15, PEK.20, PEK.50 18 PLIP interactions: 3 interactions with chain A, 6 interactions with chain T, 5 interactions with chain P, 4 interactions with chain B Hydrophobic interactions: A:F.282, A:F.282, A:Y.304, T:L.23, T:L.30, T:L.37, P:L.131, P:L.131, P:V.142, P:V.254, B:A.70, B:I.74, B:A.77, B:L.78 Hydrogen bonds: T:N.34, T:R.42 Salt bridges: T:H.38 Water bridges: P:L.127

2 x ZN: ZINC ION(Non-covalent)

ZN.21: 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: 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., 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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