SMTL ID : 6nkn.1

Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 5 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: O.10, OH.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, OH.11 CU.30: 5 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: O.39, OH.40 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 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.7, H2O.8, H2O.8 MG.31: 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.23, H2O.23

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

NA.3: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.441 NA.32: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40, N:E.40

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

HEA.4: 32 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, 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, M.468 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:T.424 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.5: 35 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, L.73 Ligands: O.10, OH.11 36 PLIP interactions: 31 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, 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, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:H.291, A:D.369, A:D.369, A:R.438, A:R.438, A:R.438 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376, O.10 HEA.33: 31 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, 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 33 PLIP interactions: 33 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:V.386, N:V.386, N:F.393, N:T.424, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:R.38, N:W.126, N:Y.371, N:S.382, 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:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.34: 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, 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: O.39, OH.40 34 PLIP interactions: 29 interactions with chain N, 4 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:T.309, N:A.313, N:T.316, N:F.348, N:L.353, N:I.356, N:L.358, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, O:I.34, O:I.34, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:Y.244, N:T.316, N:D.369, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, O.39

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, R.480 Chain D: T.80, F.87 Chain K: F.9, H.10, S.20 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16 16 PLIP interactions: 7 interactions with chain A, 5 interactions with chain M, 2 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: A:T.408, A:W.409, A:W.409, M:P.12, M:P.12, M:A.16, K:F.9, D:T.80, D:F.87 Hydrogen bonds: A:T.408, M:K.4 Water bridges: A:T.404, A:D.407, A:R.480, M:A.6 Salt bridges: K:H.10 PGV.7: 19 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155 Chain C: H.9, V.11, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82 Ligands: PEK.22 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:T.28, C:W.57, C:W.57, A:V.155 Hydrogen bonds: C:H.9, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.8: 10 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, L.106 Chain H: N.22, N.24 Ligands: CHD.16, PEK.51 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain C Hydrogen bonds: H:N.22, H:N.24 Hydrophobic interactions: C:T.95, C:W.99, C:W.99 PGV.18: 22 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, 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 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.210, C:I.210, C:F.214, C:F.214 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, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.36: 19 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, L.159 Chain P: H.9, M.27, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82 Ligands: PEK.44, PGV.46 9 PLIP interactions: 5 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: P:W.57, P:W.57, N:L.159 Hydrogen bonds: P:H.9, P:W.57, P:E.64, N:R.96, N:M.97 Salt bridges: N:R.96 PGV.38: 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: 3 interactions with chain Z, 3 interactions with chain Q, 2 interactions with chain X, 1 interactions with chain N Hydrophobic interactions: Z:P.12, Z:P.12, Q:A.84, Q:F.87, Q:F.87, X:F.9, N:W.409 Hydrogen bonds: Z:K.4 Salt bridges: X:H.10 PGV.46: 22 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, L.79, F.86, 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.36, CDL.47 19 PLIP interactions: 19 interactions with chain P Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:L.206, P:I.210, 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 PGV.53: 9 residues within 4Å: Chain G: A.1 Chain N: F.237, D.298 Chain P: W.99, Y.102, H.103, A.107 Chain U: N.24 Ligands: CHD.43 5 PLIP interactions: 1 interactions with chain P, 2 interactions with chain U, 1 interactions with chain G, 1 interactions with chain N Hydrophobic interactions: P:W.99, G:A.1, N:F.237 Hydrogen bonds: U:N.24, U:N.24

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 13 residues within 4Å: Chain A: W.334, M.339, F.346, K.411, F.414, A.415 Chain B: L.39, I.42, S.43, L.46 Chain D: R.73, E.77, W.78 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:F.346, A:F.414, B:L.39, B:I.42 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 TGL.14: 17 residues within 4Å: Chain A: F.346, V.350, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, H.24, L.28, F.32, S.35, S.36, L.39 Chain I: R.43 14 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:L.7, B:L.7, B:F.32, B:L.39, A:F.346, A:V.350, A:F.426, A:F.426, A:H.429, A:F.430, A:W.450 Water bridges: B:F.9 Salt bridges: B:H.24, I:R.43 TGL.27: 21 residues within 4Å: Chain A: T.17, L.18, L.21, F.22, W.25, L.113, F.393, F.397, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:W.25, A:W.25, A:L.113, A:F.393, A:F.397, 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.29 TGL.35: 15 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, F.32, S.35, S.36, L.39 Chain V: F.31, R.43 9 PLIP interactions: 5 interactions with chain N, 2 interactions with chain V, 2 interactions with chain O Hydrophobic interactions: N:F.426, N:F.426, N:F.426, N:H.429, N:F.430, V:F.31, O:L.39 Salt bridges: V:R.43, O:H.24 TGL.37: 15 residues within 4Å: Chain N: W.334, M.339, K.411, F.414, A.415 Chain O: L.39, I.42, L.46, T.47, T.48, K.49 Chain Q: E.77, W.78, V.81 Chain V: R.16 11 PLIP interactions: 3 interactions with chain Q, 5 interactions with chain N, 3 interactions with chain O Hydrophobic interactions: Q:V.81, N:W.334, N:W.334, N:F.414, N:A.415, O:L.39, O:I.42, O:L.46 Hydrogen bonds: Q:E.77, Q:W.78 Salt bridges: N:K.411 TGL.56: 15 residues within 4Å: Chain N: F.2, W.6, T.17, L.21, W.25, F.400, I.472 Chain Y: I.11, P.12, F.13, R.20, M.24, M.25, 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:W.25, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.29, Y:F.29

2 x O: OXYGEN ATOM(Non-covalent)

O.10: 6 residues within 4Å: Chain A: H.240, V.243, H.376 Ligands: CU.1, HEA.5, OH.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.240 O.39: 6 residues within 4Å: Chain N: H.240, V.243, H.376 Ligands: CU.30, HEA.34, OH.40 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.240

2 x OH: HYDROXIDE ION(Non-covalent)

OH.11: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: CU.1, HEA.5, O.10 No protein-ligand interaction detected (PLIP) OH.40: 7 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: CU.30, HEA.34, O.39 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:H.291, N:H.291

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

CUA.12: 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

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: 16 residues within 4Å: Chain A: F.321 Chain B: L.37, I.41, M.45, H.52, M.56, D.57, V.61, W.65, L.68, P.69 Chain E: D.8, L.41 Chain I: R.10, G.11, L.17 14 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B, 2 interactions with chain E, 1 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:L.68, B:P.69, I:L.17 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, E:D.8 pi-Cation interactions: E:F.11 PSC.42: 17 residues within 4Å: Chain N: F.321 Chain O: L.37, I.41, H.52, M.56, E.60, V.61, W.65, L.68 Chain R: E.6, T.7, D.8, F.11 Chain V: R.10, A.14, R.18, I.21 10 PLIP interactions: 1 interactions with chain R, 2 interactions with chain V, 6 interactions with chain O, 1 interactions with chain N Salt bridges: R:D.8, O:H.52 Hydrophobic interactions: V:R.18, V:I.21, O:L.37, O:I.41, O:V.61, O:W.65, O:L.68, N:F.321

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.15: 13 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, R.17, F.18, F.21, G.22 Ligands: PEK.45 10 PLIP interactions: 4 interactions with chain T, 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: T:F.18, A:M.271, A:W.275, A:W.275 Water bridges: T:R.17 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:Q.59, B:E.62, B:T.63 CHD.16: 8 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.8, CDL.52 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.304 Hydrogen bonds: A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.24: 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.17 9 PLIP interactions: 2 interactions with chain O, 3 interactions with chain N, 4 interactions with chain G Hydrogen bonds: O:E.62, O:T.63 Hydrophobic interactions: N:M.271, N:W.275, N:W.275, G:F.18, G:F.18 Salt bridges: G:R.14, G:R.17 CHD.25: 4 residues within 4Å: Chain C: R.156, Q.161, F.164 Chain J: F.1 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:F.164, C:F.164, C:F.164 Water bridges: C:R.156 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.26: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:R.33, J:L.40 Hydrogen bonds: J:R.33, J:R.33 CHD.43: 10 residues within 4Å: Chain C: L.127 Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.29, PGV.53 8 PLIP interactions: 2 interactions with chain P, 6 interactions with chain N Hydrogen bonds: P:W.99, N:T.301, N:T.301 Salt bridges: P:H.103, N:H.233 Hydrophobic interactions: N:W.288, N:Y.304, N:Y.304 CHD.54: 5 residues within 4Å: Chain P: R.156, K.157, L.160, F.164 Chain W: F.1 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.55: 5 residues within 4Å: Chain W: Y.32, R.33, M.36, T.37, L.40 2 PLIP interactions: 2 interactions with chain W Hydrophobic interactions: W:R.33, W:L.40

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: 10 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168 Chain G: R.17, F.21 Chain N: S.279 Chain O: Q.59 Ligands: CHD.24, CDL.29 8 PLIP interactions: 3 interactions with chain C, 1 interactions with chain O, 4 interactions with chain G Hydrophobic interactions: C:T.168, G:F.21 Hydrogen bonds: C:K.157, C:H.158, O:Q.59 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.17 PEK.22: 17 residues within 4Å: Chain A: H.151, V.155, L.210 Chain C: Y.181, Y.182, A.184, F.186, T.187, I.188, F.198 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 11 PLIP interactions: 7 interactions with chain G, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: G:W.62, G:F.69, A:V.155, A:L.210 Hydrogen bonds: G:T.68, G:F.69, G:F.70, G:N.76, G:N.76, C:A.184, C:I.188 PEK.23: 15 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, D.7, H.8 Chain P: R.80, I.84, L.85, W.240, H.243, F.244, V.247, F.251 Ligands: CDL.29 10 PLIP interactions: 6 interactions with chain P, 4 interactions with chain G Hydrophobic interactions: P:L.85, P:W.240, P:H.243, P:V.247, P:F.251, P:F.251, G:A.3, G:K.5, G:K.5, G:H.8 PEK.44: 25 residues within 4Å: Chain N: H.151, V.155, A.203, T.207, L.215 Chain P: L.31, W.34, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, I.209 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.36 14 PLIP interactions: 3 interactions with chain T, 8 interactions with chain P, 3 interactions with chain N Hydrophobic interactions: T:W.62, P:L.31, P:W.34, P:A.178, P:F.203, P:I.209, N:V.155, N:A.203, N:L.215 Hydrogen bonds: T:F.70, T:N.76, P:Y.181, P:A.184, P:I.188 PEK.45: 11 residues within 4Å: Chain A: W.275 Chain B: Q.59, T.66 Chain P: K.157, H.158, Q.161, T.168 Chain T: R.17, F.21 Ligands: CHD.15, CDL.52 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain P, 2 interactions with chain T, 1 interactions with chain B Hydrophobic interactions: A:W.275, P:T.168, T:F.21, B:T.66 Hydrogen bonds: P:K.157, P:H.158 Salt bridges: T:R.17 PEK.51: 17 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, 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.8, CDL.52 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain T Hydrophobic interactions: C:Y.81, C:I.84, C:F.98, C:V.247, C:F.251, T:A.3, T:K.5 Salt bridges: C:R.80

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 14 residues within 4Å: Chain C: M.51, L.52, Y.55, R.59, R.63, F.67, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:R.59, C:V.217, C:F.220 Hydrogen bonds: C:Y.55, C:R.63 Water bridges: C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.29: 27 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, L.138 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Chain N: F.282, L.283, I.286, D.300, S.307, I.311, I.314 Chain O: L.73, I.74, A.77, L.78, Y.85 Ligands: PEK.17, PEK.23, CHD.43 18 PLIP interactions: 5 interactions with chain G, 5 interactions with chain N, 4 interactions with chain C, 4 interactions with chain O Hydrophobic interactions: G:L.23, G:L.30, G:L.30, N:F.282, N:F.282, N:L.283, N:I.311, N:I.314, C:L.131, C:T.134, C:L.138, O:L.73, O:I.74, O:A.77, O:Y.85 Hydrogen bonds: G:N.34, C:N.125 Salt bridges: G:H.38 CDL.47: 18 residues within 4Å: Chain P: M.51, L.52, M.54, Y.55, R.59, I.62, R.63, F.67, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, T.27, L.31, V.34 Ligands: PGV.46 16 PLIP interactions: 13 interactions with chain P, 3 interactions with chain W Hydrophobic interactions: P:L.52, P:M.54, P:Y.55, P:I.62, P:V.217, P:F.220, P:F.220, W:L.31, W:V.34 Hydrogen bonds: P:R.63 Salt bridges: P:R.63, P:K.224, P:K.224, P:K.224, P:H.226, W:K.8 CDL.52: 23 residues within 4Å: Chain A: F.282, D.300, Y.304, S.307, I.311 Chain B: A.70, A.77, L.78, L.81, Y.85 Chain P: L.127, L.131, V.142, V.254 Chain T: S.27, L.30, C.31, N.34, L.37, H.38 Ligands: CHD.16, PEK.45, PEK.51 13 PLIP interactions: 3 interactions with chain T, 3 interactions with chain A, 3 interactions with chain P, 4 interactions with chain B Hydrophobic interactions: T:L.30, T:L.37, A:F.282, A:Y.304, A:I.311, P:L.131, P:V.142, P:V.254, B:A.70, B:A.77, B:L.78, B:L.81 Salt bridges: T:H.38

2 x ZN: ZINC ION(Non-covalent)

ZN.20: 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.49: 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

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

DMU.21: 6 residues within 4Å: Chain C: W.34, L.43 Chain G: S.61, W.62, G.63, F.69 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.43 Hydrogen bonds: G:S.61, G:G.63 DMU.28: 11 residues within 4Å: Chain A: F.459 Chain D: W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 8 PLIP interactions: 5 interactions with chain M, 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: M:L.27, M:A.30, M:L.34, A:F.459, D:W.98, D:W.98 Hydrogen bonds: M:W.32, M:Y.35 DMU.48: 9 residues within 4Å: Chain N: F.459 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, L.34, Y.35, H.36 10 PLIP interactions: 4 interactions with chain Q, 2 interactions with chain N, 4 interactions with chain Z Hydrophobic interactions: Q:L.95, Q:W.98, Q:W.98, N:F.459, N:F.459, Z:L.27, Z:L.34 Hydrogen bonds: Q:Y.102, Z:L.28, Z:H.36 DMU.50: 4 residues within 4Å: Chain P: W.34 Chain T: W.62, G.63, F.69 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.63

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

2019-03-20

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.
Show / Hide

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

Related Entries With Identical Sequence