SMTL ID : 8gbt.1

Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase

Coordinates

PDB Format Compare

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: 33 residues within 4Å: Chain A: L.20, A.24, 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 33 PLIP interactions: 33 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:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, 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:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 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, 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: CMO.8 34 PLIP interactions: 29 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:T.316, A:V.320, A:F.348, A:T.349, 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: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, CMO.8 HEA.31: 32 residues within 4Å: Chain N: 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, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 34 PLIP interactions: 34 interactions with chain N, Hydrophobic interactions: N:T.31, N:A.62, N:M.65, N:I.66, N:V.70, N:I.73, N:V.374, N:F.377, 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: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:Y.371, N:Q.428, N:R.439, N:Y.440 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.32: 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: CMO.40 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:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:F.348, 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, O:I.34, O:I.34, O:P.69, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Salt bridges: N:H.368, N:R.438 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, CMO.40

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.33: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CMO.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.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.198, B:E.198, A:H.368, A:D.369, A:D.369 MG.34: 5 residues within 4Å: Chain N: H.368, D.369 Chain O: D.173, S.197, E.198 4 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.7

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.45 NA.35: 7 residues within 4Å: Chain N: E.40, L.41, Q.43, G.45, S.441, D.442, Y.443 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40, N:E.40, N:D.442

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.6: 12 residues within 4Å: Chain A: W.334, K.411, A.415 Chain B: I.42, T.47, K.49 Chain D: T.75, E.77, W.78, V.81 Chain I: R.16, H.20 9 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:A.415, D:E.77, D:V.81, B:I.42 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:W.78 TGL.25: 11 residues within 4Å: Chain A: V.350, N.422, F.426, L.433 Chain B: G.8, H.24, L.28, S.35, L.39 Chain I: F.31, R.43 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: A:V.350, A:N.422, A:F.426, I:F.31, B:L.39 Salt bridges: I:R.43, B:H.24 Water bridges: B:G.8 TGL.28: 18 residues within 4Å: Chain A: F.2, T.17, L.21, W.25, W.81, L.113, F.393, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain L Hydrophobic interactions: A:T.17, A:L.21, A:W.25, A:W.25, A:W.25, A:W.81, A:L.113, A:F.393, A:I.472, L:I.11, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29 TGL.36: 10 residues within 4Å: Chain N: W.334, K.411 Chain O: I.42, L.46, K.49 Chain Q: S.74, T.75, E.77, W.78, M.86 6 PLIP interactions: 2 interactions with chain O, 2 interactions with chain Q, 2 interactions with chain N Hydrophobic interactions: O:I.42, O:K.49, Q:W.78, N:W.334 Hydrogen bonds: Q:W.78 Salt bridges: N:K.411 TGL.38: 14 residues within 4Å: Chain N: V.350, N.422, F.426, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, L.39 Chain V: F.31, R.43 13 PLIP interactions: 5 interactions with chain O, 2 interactions with chain V, 6 interactions with chain N Hydrophobic interactions: O:L.28, O:V.31, O:F.32, O:L.39, V:F.31, N:V.350, N:F.426, N:F.426, N:F.426, N:F.430, N:L.433 Salt bridges: O:H.24, V:R.43 TGL.57: 15 residues within 4Å: Chain N: F.2, T.17, L.20, 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 12 PLIP interactions: 6 interactions with chain N, 6 interactions with chain Y Hydrophobic interactions: N:T.17, N:L.20, N:L.21, N:W.25, N:W.25, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.29

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

PGV.7: 20 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155 Chain C: H.9, V.11, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, G.82, F.86 Ligands: PGV.13, PEK.19 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.31, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, A:V.155, A:V.155 Hydrogen bonds: C:H.9, C:W.57, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.13: 23 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, S.65, T.66, H.71, 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.7, CDL.15, DMU.20 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:L.206, C:I.210, C:T.213, 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 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.14: 9 residues within 4Å: Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: N.22 Ligands: CHD.11, PEK.53, CDL.54 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:W.99 Hydrogen bonds: H:N.22 PGV.29: 15 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16 12 PLIP interactions: 4 interactions with chain M, 2 interactions with chain D, 4 interactions with chain A, 2 interactions with chain K Hydrophobic interactions: M:P.12, M:P.12, M:A.16, D:T.80, D:F.87, A:T.408, A:W.409, A:W.409, K:F.9 Hydrogen bonds: M:A.3, A:T.408 Salt bridges: K:H.10 PGV.37: 19 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, V.155 Chain P: H.9, G.20, M.27, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82 Ligands: PEK.44, PGV.45 9 PLIP interactions: 5 interactions with chain N, 4 interactions with chain P Hydrophobic interactions: N:V.155, P:W.57 Hydrogen bonds: N:R.96, N:R.96, N:M.97, P:H.9, P:E.64, P:H.71 Salt bridges: N:R.96 PGV.45: 24 residues within 4Å: Chain P: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.209, I.210, T.213, F.214, R.221, H.226, F.227, H.231, H.232, F.233, G.234 Ligands: PGV.37, PEK.44, CDL.46 20 PLIP interactions: 19 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:W.58, P:I.62, P:F.86, P:I.209, P:I.210, P:I.210, 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:R.221, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.55: 11 residues within 4Å: Chain G: A.1 Chain N: F.237, D.298 Chain P: T.95, W.99, Y.102, H.103 Chain U: N.22, N.24 Ligands: CDL.22, CHD.43 7 PLIP interactions: 3 interactions with chain P, 2 interactions with chain U, 2 interactions with chain N Hydrophobic interactions: P:T.95, P:W.99, P:W.99, N:F.237 Hydrogen bonds: U:N.22, U:N.24 Water bridges: N:D.298 PGV.58: 17 residues within 4Å: Chain N: N.406, T.408, W.409, R.480 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.5, A.6, P.12, Q.15, A.16, S.20 13 PLIP interactions: 2 interactions with chain X, 4 interactions with chain Z, 4 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: X:F.9, Z:P.12, Z:P.12, Z:A.16, N:T.408, N:W.409, Q:T.80, Q:A.84, Q:F.87 Salt bridges: X:H.10 Hydrogen bonds: Z:A.6, N:N.406, N:T.408

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

CMO.8: 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.40: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.32, CU.33 No protein-ligand interaction detected (PLIP)

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

CUA.9: 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

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.10: 11 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.21, G.22 Ligands: PEK.51 9 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 3 interactions with chain T Hydrogen bonds: B:Q.59, B:E.62 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 Water bridges: T:R.17 Salt bridges: T:R.14, T:R.17 CHD.11: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.14, CDL.54 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:W.288, A:T.301, A:Y.304 CHD.16: 6 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164 Chain J: F.1 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:Q.161, C:F.164, J:F.1 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.23: 12 residues within 4Å: Chain G: R.14, 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.21 12 PLIP interactions: 4 interactions with chain N, 4 interactions with chain O, 4 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:E.62, O:E.62, O:T.63 Water bridges: G:R.14, G:R.17 Salt bridges: G:R.14 CHD.27: 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:R.33, J:T.37, J:L.40, A:I.3 CHD.39: 6 residues within 4Å: Chain N: I.3, F.8 Chain W: Y.32, R.33, M.36, T.37 2 PLIP interactions: 2 interactions with chain W Hydrophobic interactions: W:Y.32, W:R.33 CHD.43: 9 residues within 4Å: Chain N: H.233, W.288, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: CDL.22, PGV.55 8 PLIP interactions: 6 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:W.288, N:W.288, N:Y.304 Hydrogen bonds: N:T.301, N:T.301, P:W.99 Salt bridges: N:H.233, P:H.103 CHD.47: 3 residues within 4Å: Chain P: R.156, F.164 Chain W: F.1 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:F.164, P:F.164, P:F.164 Salt bridges: P:R.156

2 x OH: HYDROXIDE ION(Non-covalent)

OH.12: 4 residues within 4Å: Chain C: H.148, M.152, H.232, E.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.236, C:E.236 OH.42: 4 residues within 4Å: Chain P: H.148, M.152, H.232, E.236 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:H.148

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 15 residues within 4Å: Chain C: M.51, M.54, Y.55, W.58, R.59, R.63, F.67, I.216, V.217, R.221, K.224, H.226 Chain J: K.8, T.27 Ligands: PGV.13 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:M.54, C:Y.55, C:W.58, C:R.59, C:I.216, C:V.217 Hydrogen bonds: C:Y.55 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.22: 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 Chain N: F.282, L.283, I.286, D.300, Y.304, S.307, I.311 Chain O: L.78, Y.85 Ligands: PEK.21, PEK.24, CHD.43, PGV.55 17 PLIP interactions: 4 interactions with chain C, 7 interactions with chain G, 5 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: C:L.131, C:L.131, C:L.138, C:V.142, G:L.30, G:L.30, G:L.37, N:F.282, N:F.282, N:L.283, N:I.286, N:I.311 Hydrogen bonds: G:N.34, G:H.38, G:H.38, O:Y.85 Salt bridges: G:H.38 CDL.46: 18 residues within 4Å: Chain P: M.51, 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 W: K.8, F.12, T.27, L.31 Ligands: PGV.45 15 PLIP interactions: 12 interactions with chain P, 3 interactions with chain W Hydrophobic interactions: P:Y.55, P:Y.55, P:W.58, P:I.62, P:I.216, P:F.220, W:L.31 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, W:K.8 CDL.54: 27 residues within 4Å: Chain A: F.282, I.286, 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, S.135, V.254 Chain T: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Ligands: CHD.11, PGV.14, PEK.51, PEK.53 18 PLIP interactions: 8 interactions with chain T, 4 interactions with chain A, 3 interactions with chain B, 3 interactions with chain P Hydrophobic interactions: T:L.23, T:L.30, T:L.37, A:F.282, A:F.282, A:I.286, A:I.311, B:A.70, B:A.77, B:L.81, P:L.131, P:L.131, P:V.254 Hydrogen bonds: T:N.34, T:H.38, T:H.38, T:R.42 Salt bridges: T:H.38

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.17: 12 residues within 4Å: Chain A: F.321 Chain B: L.37, I.41, H.52, M.56, D.57, I.64, W.65 Chain E: T.7, D.8 Chain I: R.10, L.17 11 PLIP interactions: 1 interactions with chain E, 7 interactions with chain B, 1 interactions with chain I, 2 interactions with chain A Salt bridges: E:D.8 Hydrophobic interactions: B:L.37, B:I.41, B:I.41, B:I.64, B:W.65, B:W.65, I:L.17, A:F.321, A:F.321 Hydrogen bonds: B:D.57 PSC.49: 20 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: L.37, I.41, M.45, H.52, T.55, M.56, D.57, V.61, L.68 Chain R: E.6, T.7, D.8, F.11, L.41 Chain V: R.10, A.14, R.18 12 PLIP interactions: 8 interactions with chain O, 3 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:L.68, N:F.321, N:F.321, N:H.328 Salt bridges: O:H.52, O:H.52, R:D.8

2 x ZN: ZINC ION(Non-covalent)

ZN.18: 5 residues within 4Å: Chain F: C.60, C.62, C.82, C.85, T.87 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

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.19: 26 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, F.35, A.178, 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, DMU.20 17 PLIP interactions: 4 interactions with chain A, 5 interactions with chain G, 8 interactions with chain C Hydrophobic interactions: A:V.155, A:A.203, A:L.210, A:L.215, G:F.69, C:W.34, C:F.35, C:A.178, C:F.203, C:F.203 Hydrogen bonds: G:T.68, G:F.69, G:F.70, G:N.76, C:Y.181, C:A.184, C:I.188 PEK.21: 12 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain G: R.17, F.21 Chain N: S.279, I.314 Chain O: Q.59 Ligands: CDL.22, CHD.23 10 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G, 1 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: C:T.168, C:Y.172, G:F.21, N:I.314 Hydrogen bonds: C:K.157, C:K.157, G:R.17, O:Q.59 Salt bridges: G:R.17, G:R.17 PEK.24: 13 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Chain P: Y.81, I.84, L.85, V.91, W.240, F.244, V.247 Ligands: CDL.22 9 PLIP interactions: 7 interactions with chain P, 2 interactions with chain G Hydrophobic interactions: P:Y.81, P:I.84, P:L.85, P:V.91, P:W.240, P:W.240, P:V.247, G:A.3, G:K.5 PEK.44: 22 residues within 4Å: Chain N: H.151, A.203, T.207, L.215 Chain P: F.35, T.174, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, F.203 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.37, PGV.45 13 PLIP interactions: 4 interactions with chain P, 7 interactions with chain T, 2 interactions with chain N Hydrophobic interactions: P:F.35, P:Y.181, T:W.62, T:F.69, T:F.69, N:A.203, N:L.215 Hydrogen bonds: P:Y.181, P:I.188, T:T.68, T:F.70, T:N.76 Water bridges: T:F.69 PEK.51: 13 residues within 4Å: Chain A: W.275, L.283 Chain B: Q.59, T.66 Chain P: K.157, H.158, Q.161, Y.172 Chain S: A.1 Chain T: R.17, F.21 Ligands: CHD.10, CDL.54 10 PLIP interactions: 4 interactions with chain P, 1 interactions with chain B, 2 interactions with chain A, 3 interactions with chain T Hydrophobic interactions: P:Y.172, P:Y.172, B:T.66, A:W.275, A:L.283, T:F.21 Hydrogen bonds: P:K.157, T:R.17 Water bridges: P:Q.161 Salt bridges: T:R.17 PEK.53: 15 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, V.91, W.240, V.247 Chain T: S.2, A.3, K.5, G.6, H.8, L.19 Ligands: PGV.14, CDL.54 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain T Hydrophobic interactions: C:Y.81, C:I.84, C:I.84, C:I.84, C:V.91, C:W.240, T:A.3, T:K.5, T:K.5, T:L.19 Salt bridges: C:K.77, C:R.80

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

DMU.20: 7 residues within 4Å: Chain C: W.34, M.40 Chain G: W.62, G.63, F.69 Ligands: PGV.13, PEK.19 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.63 DMU.30: 11 residues within 4Å: Chain A: F.459 Chain D: L.95, W.98 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 4 interactions with chain M, 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: M:A.30, M:L.34, D:L.95, D:W.98, D:W.98, A:F.459, A:F.459 Hydrogen bonds: M:W.32, M:Y.35 DMU.48: 11 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, L.34, Y.35, H.36 8 PLIP interactions: 3 interactions with chain Z, 4 interactions with chain Q, 1 interactions with chain N Hydrophobic interactions: Z:L.27, Z:L.34, Q:L.95, Q:W.98, Q:W.98, N:F.459 Hydrogen bonds: Z:W.32, Q:Y.102 DMU.52: 3 residues within 4Å: Chain P: M.40 Chain T: W.62, F.69 No protein-ligand interaction detected (PLIP)

2 x SAC: N-ACETYL-SERINE(Non-covalent)

SAC.26: 1 residues within 4Å: Chain I: T.2 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.2 SAC.56: 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., Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography. J.Am.Chem.Soc. (2023)

Release Date

2023-09-20

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