SMTL ID : 7vzr.1

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the smaller form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.22 Å

Oligo State

hetero-2-1-2-2-2-2-1-mer

Ligands

2 x 2GO: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc(Non-covalent)

2GO.1: 24 residues within 4Å: Chain A: Y.426, L.657, G.661, K.722, S.725, A.726, W.729, I.736, V.759, M.763, T.767, L.780, H.784, W.787, F.845, T.849, L.852, V.853, Y.856 Chain G: F.760, M.763 Ligands: CLA.10, CLA.31, 2GO.42 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Y.426, A:L.657, A:A.726, A:W.729, A:I.736, A:V.759, A:M.763, A:T.767, A:L.780, A:W.787, A:W.787, A:Y.856 Metal complexes: A:H.784 2GO.42: 25 residues within 4Å: Chain A: F.760, M.763, W.764 Chain G: Y.426, I.721, K.722, P.723, S.725, A.726, W.729, I.736, V.759, M.763, W.764, T.767, H.784, W.787, F.845, T.849, L.852, V.853, Y.856 Ligands: 2GO.1, CLA.10, CLA.31 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain G, Hydrophobic interactions: A:F.760, G:Y.426, G:A.726, G:W.729, G:I.736, G:V.759, G:T.767, G:W.787, G:W.787, G:Y.856 Hydrogen bonds: G:T.849 Metal complexes: G:H.784

16 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 18 residues within 4Å: Chain A: L.18, M.22, R.26, I.27, A.30, H.31, M.33, L.34, G.37, C.40, L.41, Y.133, F.304, H.307 Ligands: BCL.7, CLA.12, LYC.13, UNL.21 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:I.27, A:A.30, A:M.33, A:H.307 Hydrogen bonds: A:H.307 Salt bridges: A:R.26 pi-Stacking: A:F.304 Metal complexes: A:H.31 BCL.3: 21 residues within 4Å: Chain A: H.296, A.302, H.305, T.309, A.310, Y.313, F.316, A.317, V.374, G.377, Y.380, L.381, F.397, I.398, F.401 Chain C: L.12, Y.15 Ligands: BCL.7, UNL.19, UNL.27, UNL.37 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:Y.313, A:Y.313, A:Y.313, A:F.316, A:A.317, A:V.374, A:L.381, A:F.397, C:L.12, C:Y.15, C:Y.15 Hydrogen bonds: A:T.309 Salt bridges: A:H.296 Metal complexes: A:H.305 BCL.4: 16 residues within 4Å: Chain A: F.28, M.32, Y.127, A.128, A.131, H.132, V.173, G.174, L.175, P.176, F.180, T.183, W.185, Y.202 Ligands: BCL.5, UNL.24 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:F.28, A:F.28, A:A.128, A:A.131, A:F.180, A:F.180, A:T.183, A:W.185, A:W.185 Metal complexes: A:H.132 BCL.5: 20 residues within 4Å: Chain A: P.24, I.27, F.28, H.31, F.180, I.187, L.188, R.189, R.190, Y.192, A.195, P.198, H.199, Y.202, L.206 Ligands: BCL.4, BCL.7, CLA.11, LYC.13, UNL.24 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.27, A:F.180, A:Y.192, A:P.198, A:Y.202, A:Y.202 Hydrogen bonds: A:H.31, A:R.189 Salt bridges: A:H.31 pi-Stacking: A:F.28, A:F.28 Metal complexes: A:H.199 BCL.6: 21 residues within 4Å: Chain A: P.64, R.65, S.68, F.207, M.260, N.261, T.262, I.263, G.265, E.266, M.269, C.270, W.273, A.325, L.326, H.329, S.331, Y.332 Ligands: BCL.9, CLA.11, 84Q.36 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:R.65, A:F.207, A:W.273, A:L.326, A:L.326 Hydrogen bonds: A:S.68, A:S.331 pi-Cation interactions: A:R.65 Metal complexes: A:E.266 BCL.7: 21 residues within 4Å: Chain A: Y.192, A.193, A.195, L.196, H.199, T.200, I.203, I.294, L.297, E.298, V.303, V.306, H.307, I.311 Ligands: BCL.2, BCL.3, BCL.5, CLA.11, LYC.13, UNL.20, UNL.26 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:Y.192, A:L.196, A:L.196, A:I.203, A:I.294, A:V.303, A:V.306, A:I.311 Metal complexes: A:H.307 BCL.8: 17 residues within 4Å: Chain A: Y.45, Y.57, V.58, T.61, M.357, I.358, F.360, N.361, Q.364, Y.846, T.847, F.850, F.854, F.857 Ligands: BCL.9, LYC.13, CLA.33 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:T.61, A:M.357, A:F.360, A:N.361, A:Q.364, A:Y.846, A:Y.846, A:T.847, A:F.854, A:F.854, A:F.857 BCL.9: 15 residues within 4Å: Chain A: L.38, I.42, T.61, L.62, S.315, L.318, N.361, H.362, V.365, Y.369 Ligands: BCL.6, BCL.8, CLA.11, LYC.13, 84Q.36 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.38, A:L.38, A:L.62, A:L.318 Metal complexes: A:H.362 BCL.43: 22 residues within 4Å: Chain G: L.18, M.22, R.26, I.27, A.30, H.31, M.33, L.34, C.40, L.41, Y.133, T.300, V.303, F.304, H.307 Chain H: V.1, T.4 Ligands: BCL.48, BCL.50, CLA.53, UNL.64, LYC.74 10 PLIP interactions: 2 interactions with chain H, 8 interactions with chain G, Hydrophobic interactions: H:V.1, H:T.4, G:I.27, G:I.27, G:A.30, G:L.41, G:V.303 Salt bridges: G:R.26 pi-Stacking: G:F.304 Metal complexes: G:H.31 BCL.44: 24 residues within 4Å: Chain G: H.296, A.302, H.305, V.306, T.309, A.310, Y.313, A.317, V.374, G.377, Y.380, L.381, F.397, I.398, F.401, L.670, F.674 Chain I: L.12, Y.15 Ligands: BCL.48, UNL.62, UNL.69, UNL.70, UNL.77 13 PLIP interactions: 3 interactions with chain I, 10 interactions with chain G, Hydrophobic interactions: I:L.12, I:Y.15, I:Y.15, G:V.306, G:V.306, G:Y.313, G:A.317, G:V.374, G:F.397, G:L.670 Hydrogen bonds: G:Y.313 Salt bridges: G:H.296 Metal complexes: G:H.305 BCL.45: 14 residues within 4Å: Chain G: F.28, M.32, W.124, A.131, H.132, V.173, G.174, P.176, F.180, T.183, W.185, Y.202 Ligands: BCL.46, UNL.67 10 PLIP interactions: 10 interactions with chain G, Hydrophobic interactions: G:F.28, G:F.28, G:W.124, G:V.173, G:T.183, G:W.185, G:W.185 Hydrogen bonds: G:Y.202 pi-Stacking: G:F.28 Metal complexes: G:H.132 BCL.46: 23 residues within 4Å: Chain G: P.24, I.27, F.28, H.31, M.32, I.35, F.180, I.187, L.188, R.189, R.190, T.191, Y.192, A.195, P.198, H.199, Y.202, L.206 Ligands: BCL.45, BCL.48, CLA.52, UNL.67, LYC.74 16 PLIP interactions: 16 interactions with chain G, Hydrophobic interactions: G:I.27, G:F.28, G:F.28, G:I.35, G:F.180, G:I.187, G:Y.192, G:A.195, G:P.198, G:Y.202, G:Y.202, G:Y.202, G:Y.202 Hydrogen bonds: G:R.189 pi-Stacking: G:F.28 Metal complexes: G:H.199 BCL.47: 25 residues within 4Å: Chain G: P.64, R.65, S.68, F.207, M.260, N.261, T.262, I.263, G.265, E.266, M.269, C.270, W.273, F.277, L.318, L.326, H.329, S.331, Y.332 Chain I: M.1, L.5 Ligands: BCL.50, CLA.52, 84Q.60, UNL.69 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain I, Hydrophobic interactions: G:R.65, G:F.207, G:E.266, G:W.273, G:W.273, G:W.273, G:F.277, G:L.326, G:Y.332, I:L.5 Hydrogen bonds: G:S.68, G:S.331 pi-Cation interactions: G:R.65 Metal complexes: G:E.266 BCL.48: 21 residues within 4Å: Chain G: Y.192, A.193, A.195, L.196, H.199, T.200, I.203, W.210, I.294, L.297, E.298, V.306, H.307, I.311 Ligands: BCL.43, BCL.44, BCL.46, CLA.52, UNL.63, UNL.69, LYC.74 10 PLIP interactions: 10 interactions with chain G, Hydrophobic interactions: G:L.196, G:L.196, G:W.210, G:I.294, G:L.297, G:V.306, G:H.307 Hydrogen bonds: G:H.199 Salt bridges: G:H.307 Metal complexes: G:H.307 BCL.49: 21 residues within 4Å: Chain G: Y.45, Y.57, V.58, T.61, L.62, M.357, I.358, F.360, N.361, Q.364, L.368, T.842, V.843, Y.846, T.847, F.850, F.854, F.857 Ligands: BCL.50, CLA.54, LYC.74 17 PLIP interactions: 17 interactions with chain G, Hydrophobic interactions: G:Y.57, G:T.61, G:M.357, G:I.358, G:N.361, G:Q.364, G:L.368, G:V.843, G:Y.846, G:Y.846, G:T.847, G:F.854, G:F.854, G:F.854, G:F.857 Hydrogen bonds: G:Y.45, G:Q.364 BCL.50: 18 residues within 4Å: Chain G: L.38, L.41, I.42, T.61, L.62, S.315, L.318, I.358, N.361, H.362, V.365, Y.369 Ligands: BCL.43, BCL.47, BCL.49, CLA.52, 84Q.60, LYC.74 5 PLIP interactions: 5 interactions with chain G, Hydrophobic interactions: G:L.38, G:L.41, G:L.62 Hydrogen bonds: G:Y.369 Metal complexes: G:H.362

10 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.10: 24 residues within 4Å: Chain A: L.781, L.782, H.784, L.785, W.787, F.788, F.791 Chain G: V.423, Y.426, G.427, C.430, L.439, F.441, F.719, K.722, M.739, F.760, M.763, F.845 Chain J: T.18 Ligands: 2GO.1, CLA.40, 2GO.42, 85N.79 21 PLIP interactions: 11 interactions with chain A, 10 interactions with chain G, Hydrophobic interactions: A:L.781, A:L.782, A:L.785, A:W.787, A:F.788, A:F.788, A:F.788, A:F.788, A:F.791, G:Y.426, G:Y.426, G:L.439, G:F.441, G:F.719, G:K.722, G:K.722, G:F.760, G:F.845 Salt bridges: A:H.784 pi-Stacking: A:F.788 Hydrogen bonds: G:Y.426 CLA.11: 19 residues within 4Å: Chain A: I.35, A.39, I.42, F.46, R.65, L.66, W.114, F.117, H.118, L.121, I.203, F.207, W.210, V.213 Ligands: BCL.5, BCL.6, BCL.7, BCL.9, UNL.20 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.39, A:I.42, A:F.117, A:F.117, A:L.121, A:I.203, A:F.207, A:W.210, A:W.210, A:V.213 Salt bridges: A:R.65 Metal complexes: A:H.118 CLA.12: 16 residues within 4Å: Chain A: Y.15, Q.16, K.17, L.18, E.19, F.304, L.368, Y.369, A.372, F.375, H.376, Q.379, Q.710, L.713, I.717 Ligands: BCL.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.304, A:Y.369, A:A.372, A:F.375, A:F.375, A:L.713, A:I.717 Hydrogen bonds: A:Q.16, A:K.17, A:L.18, A:Q.379 Metal complexes: A:H.376 CLA.31: 24 residues within 4Å: Chain A: Y.426, G.427, C.430, T.433, L.439, F.441, L.718, F.719, K.722, M.739, F.760, M.763, W.787, F.845 Chain D: T.18 Chain G: L.781, L.782, H.784, L.785, F.788, F.791 Ligands: 2GO.1, 2GO.42, CLA.51 22 PLIP interactions: 10 interactions with chain A, 12 interactions with chain G, Hydrophobic interactions: A:Y.426, A:Y.426, A:Y.426, A:L.439, A:F.441, A:F.719, A:K.722, A:F.760, A:W.787, A:F.845, G:L.781, G:L.781, G:L.782, G:H.784, G:L.785, G:F.788, G:F.788, G:F.788, G:F.788, G:F.791 Salt bridges: G:H.784 pi-Stacking: G:F.788 CLA.33: 19 residues within 4Å: Chain A: G.56, Y.57, I.342, Y.343, H.775, M.779, L.782, F.854 Chain B: G.18, G.19, F.21, V.22 Chain G: N.440, F.441 Chain L: X.3, X.4, X.5, X.6 Ligands: BCL.8 11 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A, 1 interactions with chain G, Hydrogen bonds: B:G.19, B:F.21, A:Y.57, A:V.58 Hydrophobic interactions: A:Y.57, A:Y.343, A:L.782, A:F.854, G:F.441 Salt bridges: A:H.775 Metal complexes: A:H.775 CLA.40: 25 residues within 4Å: Chain A: F.788, F.791, A.792, D.797, S.800, R.801, G.804, G.805, Q.808 Chain G: M.415, S.418, F.419, V.422, V.423, Y.426, I.667, R.671, F.715, F.719 Chain J: T.21, L.22 Chain L: X.1 Ligands: CLA.10, 85I.16, 85I.17 19 PLIP interactions: 10 interactions with chain G, 3 interactions with chain J, 5 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: G:F.419, G:F.419, G:V.422, G:V.422, G:V.423, G:Y.426, G:F.715, G:F.719, J:T.21, J:L.22, J:L.22, A:F.788, A:F.788, A:A.792, A:D.797, A:R.801 Hydrogen bonds: G:R.671 pi-Stacking: G:F.719 Metal complexes: H2O.1 CLA.51: 25 residues within 4Å: Chain A: M.415, S.418, F.419, V.422, F.664, R.671, F.715, F.719 Chain D: T.18, T.21, L.22 Chain F: X.1 Chain G: L.785, F.788, F.791, A.792, D.797, S.800, R.801, G.804, G.805, Q.808 Ligands: CLA.31, 85I.58, 85I.59 16 PLIP interactions: 7 interactions with chain G, 6 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: G:L.785, G:F.788, G:F.788, G:F.788, G:A.792, G:D.797, G:R.801, A:V.422, A:F.664, A:F.715, A:F.719, D:T.21, D:L.22 Hydrogen bonds: A:R.671 pi-Stacking: A:F.719 Metal complexes: H2O.1 CLA.52: 25 residues within 4Å: Chain G: I.35, L.38, A.39, I.42, F.46, L.62, R.65, L.66, I.71, W.114, F.117, H.118, L.121, L.125, I.203, L.206, F.207, W.210, V.213, L.318 Ligands: BCL.46, BCL.47, BCL.48, BCL.50, UNL.69 18 PLIP interactions: 18 interactions with chain G, Hydrophobic interactions: G:I.35, G:L.38, G:A.39, G:I.42, G:I.71, G:W.114, G:F.117, G:L.121, G:L.125, G:I.203, G:F.207, G:W.210, G:W.210, G:V.213, G:L.318 Hydrogen bonds: G:R.65 pi-Stacking: G:F.117 Metal complexes: G:H.118 CLA.53: 16 residues within 4Å: Chain G: Y.15, Q.16, K.17, L.18, E.19, L.20, F.304, L.308, Y.369, A.372, F.375, H.376, Q.379, Q.710, W.714 Ligands: BCL.43 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:L.20, G:F.304, G:L.308, G:Y.369, G:A.372, G:F.375, G:W.714 Hydrogen bonds: G:K.17, G:L.18, G:Q.379 Salt bridges: G:H.376 Metal complexes: G:H.376 CLA.54: 21 residues within 4Å: Chain A: N.440, F.441 Chain F: X.3, X.4, X.5 Chain G: G.56, Y.57, I.342, Y.343, H.775, A.778, M.779, L.782, F.854 Chain H: M.2, A.3, C.6, F.7, V.8 Ligands: BCL.49, UNL.76 10 PLIP interactions: 2 interactions with chain H, 7 interactions with chain G, 1 interactions with chain A, Hydrophobic interactions: H:M.2, G:Y.343, G:A.778, G:L.782, G:F.854, A:F.441 Hydrogen bonds: H:F.7, G:Y.57 Salt bridges: G:H.775 Metal complexes: G:H.775

2 x LYC: LYCOPENE(Non-covalent)

LYC.13: 13 residues within 4Å: Chain A: H.31, L.34, I.35, Y.45, V.58, Y.192, H.307 Ligands: BCL.2, BCL.5, BCL.7, BCL.8, BCL.9, UNL.35 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.31, A:L.34, A:L.34, A:I.35, A:V.58, A:Y.192, A:Y.192 LYC.74: 15 residues within 4Å: Chain G: H.31, L.34, I.35, L.38, Y.45, Y.192, H.307 Chain H: V.1, M.2, A.3 Ligands: BCL.43, BCL.46, BCL.48, BCL.49, BCL.50 7 PLIP interactions: 2 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:M.2, H:A.3, G:L.34, G:I.35, G:L.38, G:Y.192, G:Y.192

2 x CA: CALCIUM ION(Non-covalent)

CA.14: 5 residues within 4Å: Chain A: D.732, E.766, Y.856, D.859, G.860 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.732, A:E.766, A:Y.856, A:G.860, H2O.1 CA.55: 5 residues within 4Å: Chain G: D.732, E.766, Y.856, D.859, G.860 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.732, G:E.766, G:Y.856, G:G.860, H2O.1

6 x 85I: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate(Non-covalent)

85I.15: 19 residues within 4Å: Chain A: F.316, I.320, F.323, L.324, R.327, L.636, Y.637, S.638, R.645, W.662, F.666, I.727, Y.730, L.731, G.733, Q.863 Chain C: F.10, G.14, Y.15 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.316, A:F.316, A:I.320, A:F.323, A:W.662, A:F.666, A:I.727, A:L.731, C:F.10, C:Y.15 Hydrogen bonds: A:Y.637, A:S.638, A:S.638 Salt bridges: A:R.327, A:R.645 85I.16: 15 residues within 4Å: Chain A: A.792, L.793, R.801, Q.808, F.829, P.830, V.831, S.832, F.844 Chain G: F.419 Chain J: L.22, F.23, I.25 Ligands: 85I.17, CLA.40 8 PLIP interactions: 1 interactions with chain G, 4 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: G:F.419, A:F.844, J:L.22, J:F.23, J:I.25 Hydrogen bonds: A:S.832, A:S.832 Salt bridges: A:R.801 85I.17: 15 residues within 4Å: Chain A: K.12, P.830, V.831, S.832, N.833, T.836, W.840 Chain J: I.25, V.26, V.28, S.29, L.32, S.33 Ligands: 85I.16, CLA.40 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain J Hydrophobic interactions: A:P.830, J:I.25, J:V.26, J:V.28, J:L.32 Hydrogen bonds: A:N.833, A:N.833, A:T.836, J:S.33 85I.57: 24 residues within 4Å: Chain G: F.316, I.320, F.323, L.324, R.327, L.552, L.636, Y.637, S.638, R.645, F.654, F.655, M.658, W.662, L.663, F.666, I.727, Y.730, L.731, Q.863 Chain I: A.7, F.10, V.11, Y.15 19 PLIP interactions: 16 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: G:F.316, G:I.320, G:F.323, G:L.552, G:F.655, G:F.655, G:W.662, G:F.666, G:I.727, G:Y.730, G:L.731, I:A.7, I:V.11, I:Y.15 Hydrogen bonds: G:S.638, G:S.638, G:Y.730 Salt bridges: G:R.327, G:R.645 85I.58: 17 residues within 4Å: Chain A: M.415, F.416, F.419 Chain D: L.22, I.25 Chain G: V.789, L.793, R.801, Q.808, W.811, P.830, V.831, S.832, W.840, F.844 Ligands: CLA.51, 85I.59 13 PLIP interactions: 2 interactions with chain D, 10 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: D:L.22, D:I.25, G:Q.808, G:W.811, G:W.840, G:W.840, G:F.844, A:F.419 Hydrogen bonds: G:P.830, G:S.832, G:S.832 Salt bridges: G:R.801, G:R.801 85I.59: 20 residues within 4Å: Chain D: I.25, V.26, V.28, S.29, L.32, S.33 Chain F: X.1 Chain G: G.10, V.11, L.785, I.786, P.830, V.831, S.832, N.833, T.836, W.840 Ligands: 85N.41, CLA.51, 85I.58 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain D Hydrophobic interactions: G:V.11, G:L.785, G:I.786, D:I.25, D:V.26, D:V.28 Hydrogen bonds: G:V.11, G:S.832, G:N.833, G:N.833, G:T.836, D:S.33

32 x UNL: UNKNOWN LIGAND

UNL.18: 4 residues within 4Å: Chain A: W.554, G.558, Y.561, L.562 Ligand excluded by PLIP UNL.19: 8 residues within 4Å: Chain A: W.400, F.401 Chain C: Y.15, W.19 Ligands: BCL.3, UNL.26, UNL.27, UNL.37 Ligand excluded by PLIP UNL.20: 8 residues within 4Å: Chain A: L.196, L.280, P.289, R.290, S.291 Ligands: BCL.7, CLA.11, UNL.26 Ligand excluded by PLIP UNL.21: 12 residues within 4Å: Chain A: L.18, R.26, A.130, Y.133, R.137, I.145, F.146, W.147, W.163, F.164 Ligands: BCL.2, UNL.25 Ligand excluded by PLIP UNL.22: 4 residues within 4Å: Chain A: V.83, F.109, G.113, W.114 Ligand excluded by PLIP UNL.23: 8 residues within 4Å: Chain A: T.44, W.53 Chain B: C.20, V.22, G.23, S.24 Chain L: X.8, X.9 Ligand excluded by PLIP UNL.24: 7 residues within 4Å: Chain A: G.113, F.117, L.121, W.124, W.185 Ligands: BCL.4, BCL.5 Ligand excluded by PLIP UNL.25: 5 residues within 4Å: Chain A: L.123, Y.127, I.161, Y.171 Ligands: UNL.21 Ligand excluded by PLIP UNL.26: 6 residues within 4Å: Chain A: Y.313, V.314 Ligands: BCL.7, UNL.19, UNL.20, UNL.27 Ligand excluded by PLIP UNL.27: 6 residues within 4Å: Chain A: F.397, W.400, F.401 Ligands: BCL.3, UNL.19, UNL.26 Ligand excluded by PLIP UNL.28: 7 residues within 4Å: Chain A: F.545, R.547, K.548 Chain D: I.8, L.12, F.15 Ligands: UNL.29 Ligand excluded by PLIP UNL.29: 5 residues within 4Å: Chain A: K.548, P.551, W.554 Ligands: UNL.28, UNL.30 Ligand excluded by PLIP UNL.30: 4 residues within 4Å: Chain A: P.551, W.554 Ligands: UNL.29, UNL.38 Ligand excluded by PLIP UNL.35: 5 residues within 4Å: Chain A: T.44 Chain B: G.19, C.20, F.21 Ligands: LYC.13 Ligand excluded by PLIP UNL.37: 9 residues within 4Å: Chain A: I.410, L.663, L.670 Chain C: L.18, W.19, I.22, K.23 Ligands: BCL.3, UNL.19 Ligand excluded by PLIP UNL.38: 4 residues within 4Å: Chain C: L.12, G.13, A.16 Ligands: UNL.30 Ligand excluded by PLIP UNL.61: 4 residues within 4Å: Chain G: W.554, G.558, Y.561 Ligands: UNL.73 Ligand excluded by PLIP UNL.62: 5 residues within 4Å: Chain G: W.400 Chain I: Y.15, W.19 Ligands: BCL.44, UNL.77 Ligand excluded by PLIP UNL.63: 9 residues within 4Å: Chain G: L.196, F.277, W.284, P.289, S.291, N.293, I.294 Ligands: BCL.48, UNL.69 Ligand excluded by PLIP UNL.64: 8 residues within 4Å: Chain G: A.130, Y.134, I.142, I.145, F.146, W.163 Ligands: BCL.43, UNL.68 Ligand excluded by PLIP UNL.65: 4 residues within 4Å: Chain G: F.109, R.110, G.113, W.114 Ligand excluded by PLIP UNL.66: 12 residues within 4Å: Chain F: X.7, X.9 Chain G: T.44, F.47, A.48, W.53, Y.102 Chain H: T.4, C.6, F.7, G.9, A.10 Ligand excluded by PLIP UNL.67: 5 residues within 4Å: Chain G: G.120, L.121, W.124 Ligands: BCL.45, BCL.46 Ligand excluded by PLIP UNL.68: 6 residues within 4Å: Chain G: L.123, W.124, V.126, Y.127, Y.171 Ligands: UNL.64 Ligand excluded by PLIP UNL.69: 10 residues within 4Å: Chain G: A.310, Y.313, V.314, F.397 Ligands: BCL.44, BCL.47, BCL.48, CLA.52, UNL.63, UNL.70 Ligand excluded by PLIP UNL.70: 3 residues within 4Å: Chain G: F.397 Ligands: BCL.44, UNL.69 Ligand excluded by PLIP UNL.71: 7 residues within 4Å: Chain G: F.424, F.545, R.547, K.548, V.549 Chain J: F.15 Ligands: UNL.72 Ligand excluded by PLIP UNL.72: 4 residues within 4Å: Chain G: K.548, W.554 Ligands: UNL.71, UNL.73 Ligand excluded by PLIP UNL.73: 4 residues within 4Å: Chain G: P.551, W.554 Ligands: UNL.61, UNL.72 Ligand excluded by PLIP UNL.76: 6 residues within 4Å: Chain F: X.2, X.3, X.4 Chain H: A.3, C.6 Ligands: CLA.54 Ligand excluded by PLIP UNL.77: 8 residues within 4Å: Chain G: L.406, L.670 Chain I: Y.15, L.18, W.19, I.22 Ligands: BCL.44, UNL.62 Ligand excluded by PLIP UNL.78: 2 residues within 4Å: Chain I: F.10, G.13 Ligand excluded by PLIP

4 x 85N: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium(Covalent)(Non-covalent)

85N.32: 16 residues within 4Å: Chain A: M.815, T.823, L.824, E.826, V.827, R.828 Chain J: G.20, F.23, G.24, I.25, V.26, Y.27, H.30 Chain K: S.10, A.13, W.16 11 PLIP interactions: 6 interactions with chain A, 2 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: A:M.815, A:L.824, A:V.827, K:W.16, J:F.23 Hydrogen bonds: A:T.823, A:R.828, K:S.10 Salt bridges: A:E.826, J:H.30, J:H.30 85N.39: 17 residues within 4Å: Chain A: W.431, Y.444 Chain D: G.6, I.9, S.10, C.13, F.14, L.17 Chain E: I.23, I.26, G.27, F.29, G.30, M.40, F.43 Chain F: X.1, X.2 8 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: A:W.431, A:Y.444, D:F.14, D:L.17, E:I.23, E:F.43, E:F.43 Hydrogen bonds: E:G.30 85N.41: 14 residues within 4Å: Chain D: F.23, G.24, V.26, Y.27, H.30 Chain E: I.9, S.10, A.13, W.16, F.17 Chain G: T.823, E.826, R.828 Ligands: 85I.59 12 PLIP interactions: 1 interactions with chain G, 6 interactions with chain D, 5 interactions with chain E Salt bridges: G:E.826, D:H.30 Hydrophobic interactions: D:F.23, D:F.23, D:V.26, D:Y.27, D:Y.27, E:I.9, E:A.13, E:W.16, E:F.17 Hydrogen bonds: E:S.10 85N.79: 17 residues within 4Å: Chain G: W.431, F.441, I.443, G.540 Chain J: G.6, Q.7, S.10, C.13, F.14 Chain K: I.23, I.26, G.27, F.29, G.30, F.43 Chain L: X.2 Ligands: CLA.10 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: G:W.431, G:F.441, G:I.443, K:F.43, J:Q.7

2 x HEC: HEME C(Non-covalent)

HEC.34: 25 residues within 4Å: Chain A: W.764 Chain B: N.124, C.125, C.128, H.129, P.138, R.139, S.140, T.141, F.143, W.148, N.152, I.157, S.160, I.161, K.165, A.173, M.174, P.175, Y.177 Chain H: N.102, S.103, G.106, K.115 Ligands: HEC.75 18 PLIP interactions: 3 interactions with chain H, 14 interactions with chain B, 1 interactions with chain A, Hydrogen bonds: H:S.103, H:G.106, B:W.148, B:S.160 Salt bridges: H:K.115, B:K.165, B:K.165 Hydrophobic interactions: B:F.143, B:F.143, B:I.157, B:I.161, B:A.173, B:M.174, B:P.175, B:Y.177, A:W.764 pi-Stacking: B:F.143 Metal complexes: B:H.129 HEC.75: 26 residues within 4Å: Chain B: S.153, G.156, K.165 Chain H: A.72, A.73, C.74, C.77, H.78, I.88, N.89, A.90, T.91, F.93, W.98, N.102, M.107, S.110, I.111, K.115, G.116, V.118, M.119, P.120, Y.122, I.138 Ligands: HEC.34 21 PLIP interactions: 18 interactions with chain H, 3 interactions with chain B, Hydrophobic interactions: H:A.72, H:A.90, H:T.91, H:F.93, H:F.93, H:W.98, H:I.111, H:V.118, H:M.119, H:Y.122, H:I.138 Hydrogen bonds: H:W.98, H:N.102, H:S.110, H:G.116, B:S.153, B:G.156 Salt bridges: H:K.115, H:K.115, B:K.165 Metal complexes: H:H.78

2 x 84Q: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate(Non-covalent)

84Q.36: 12 residues within 4Å: Chain A: H.258, M.260, N.261, W.273, A.317, L.318, G.322, A.325 Chain C: M.1, T.2 Ligands: BCL.6, BCL.9 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:M.260, A:W.273, A:A.317, A:L.318, A:A.325 Salt bridges: A:H.258, A:H.258 Hydrogen bonds: C:M.1, C:T.2 84Q.60: 11 residues within 4Å: Chain G: M.260, N.261, A.317, L.318, V.321, G.322, A.325, H.362 Chain I: M.1 Ligands: BCL.47, BCL.50 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:M.260, G:L.318, G:V.321, G:A.325 Hydrogen bonds: G:A.634, I:M.1 Salt bridges: G:H.258, G:H.258

1 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.56: 11 residues within 4Å: Chain A: C.696, G.698, P.699, C.705, K.796, L.834 Chain G: C.696, G.698, P.699, C.705, L.834 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain A, Metal complexes: G:C.696, G:C.705, A:C.696, A:C.705

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, S. et al., Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c. Nat Commun (2022)

Release Date

2022-12-28

Peptides

Photosynthetic reaction center subunit M: AG
Cytochrome c, mono-and diheme variants: B
PscE: CI
PscF: DJ
PscG: EK
undefined polypeptide: FL
Cytochrome c domain-containing protein: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
a

B
C

C
E

I
e

D
F

J
f

E
G

K
g

F
H

L
h

H
c

Membrane

We predict this structure to be a membrane protein.
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Photosynthetic reaction center subunit M

Cytochrome c, mono-and diheme variants

PscE

PscF

PscG

undefined polypeptide

Cytochrome c domain-containing protein

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