SMTL ID : 7vzg.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-2-2-2-2-1-1-1-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.419, L.650, G.654, K.715, S.718, A.719, W.722, I.729, V.752, M.756, T.760, L.773, H.777, W.780, F.838, T.842, L.845, V.846, Y.849 Chain G: F.753, M.756 Ligands: CLA.10, CLA.31, 2GO.42 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Y.419, A:L.650, A:A.719, A:W.722, A:I.729, A:V.752, A:M.756, A:T.760, A:L.773, A:W.780, A:W.780, A:Y.849 Metal complexes: A:H.777 2GO.42: 25 residues within 4Å: Chain A: F.753, M.756, W.757 Chain G: Y.419, I.714, K.715, P.716, S.718, A.719, W.722, I.729, V.752, M.756, W.757, T.760, H.777, W.780, F.838, T.842, L.845, V.846, Y.849 Ligands: 2GO.1, CLA.10, CLA.31 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain A, Hydrophobic interactions: G:Y.419, G:A.719, G:W.722, G:I.729, G:V.752, G:T.760, G:W.780, G:W.780, G:Y.849, A:F.753 Metal complexes: G:H.777

16 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 18 residues within 4Å: Chain A: L.11, M.15, R.19, I.20, A.23, H.24, M.26, L.27, G.30, C.33, L.34, Y.126, F.297, H.300 Ligands: BCL.7, CLA.12, LYC.13, UNL.21 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:I.20, A:A.23, A:M.26, A:H.300 Salt bridges: A:R.19 pi-Stacking: A:F.297 Metal complexes: A:H.24 BCL.3: 21 residues within 4Å: Chain A: H.289, A.295, H.298, T.302, A.303, Y.306, F.309, A.310, V.367, G.370, Y.373, L.374, F.390, I.391, F.394 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.306, A:Y.306, A:Y.306, A:F.309, A:A.310, A:V.367, A:L.374, A:F.390, C:L.12, C:Y.15, C:Y.15 Hydrogen bonds: A:Y.306 Salt bridges: A:H.289 Metal complexes: A:H.298 BCL.4: 16 residues within 4Å: Chain A: F.21, M.25, Y.120, A.121, A.124, H.125, V.166, G.167, L.168, P.169, F.173, T.176, W.178, Y.195 Ligands: BCL.5, UNL.24 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:F.21, A:F.21, A:A.121, A:A.124, A:F.173, A:F.173, A:T.176, A:W.178, A:W.178 pi-Stacking: A:F.21 Metal complexes: A:H.125 BCL.5: 20 residues within 4Å: Chain A: P.17, I.20, F.21, H.24, F.173, I.180, L.181, R.182, R.183, Y.185, A.188, P.191, H.192, Y.195, L.199 Ligands: BCL.4, BCL.7, CLA.11, LYC.13, UNL.24 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:I.20, A:F.173, A:Y.185, A:P.191, A:Y.195, A:Y.195 Hydrogen bonds: A:R.182 Salt bridges: A:H.24 pi-Stacking: A:F.21, A:Y.195 Metal complexes: A:H.192 BCL.6: 21 residues within 4Å: Chain A: P.57, R.58, S.61, F.200, M.253, N.254, T.255, I.256, G.258, E.259, M.262, C.263, W.266, A.318, L.319, H.322, S.324, Y.325 Ligands: BCL.9, CLA.11, 84Q.36 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:R.58, A:F.200, A:W.266, A:L.319, A:L.319 Hydrogen bonds: A:S.61, A:S.324 Metal complexes: A:E.259 BCL.7: 21 residues within 4Å: Chain A: Y.185, A.186, A.188, L.189, H.192, T.193, I.196, I.287, L.290, E.291, V.296, V.299, H.300, I.304 Ligands: BCL.2, BCL.3, BCL.5, CLA.11, LYC.13, UNL.20, UNL.26 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:Y.185, A:L.189, A:L.189, A:I.196, A:I.287, A:V.296, A:V.299, A:I.304 Hydrogen bonds: A:H.192 Metal complexes: A:H.300 BCL.8: 17 residues within 4Å: Chain A: Y.38, Y.50, V.51, T.54, M.350, I.351, F.353, N.354, Q.357, Y.839, T.840, F.843, F.847, F.850 Ligands: BCL.9, LYC.13, CLA.33 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:T.54, A:M.350, A:F.353, A:N.354, A:Q.357, A:Y.839, A:Y.839, A:T.840, A:F.847, A:F.847, A:F.850 Hydrogen bonds: A:Y.38 BCL.9: 15 residues within 4Å: Chain A: L.31, I.35, T.54, L.55, S.308, L.311, N.354, H.355, V.358, Y.362 Ligands: BCL.6, BCL.8, CLA.11, LYC.13, 84Q.36 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:L.31, A:L.31, A:L.55, A:L.311 Hydrogen bonds: A:Y.362 Metal complexes: A:H.355 BCL.43: 22 residues within 4Å: Chain G: L.11, M.15, R.19, I.20, A.23, H.24, M.26, L.27, C.33, L.34, Y.126, T.293, V.296, F.297, H.300 Chain H: V.1, T.4 Ligands: BCL.48, BCL.50, CLA.53, UNL.64, LYC.74 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain H, Hydrophobic interactions: G:I.20, G:I.20, G:A.23, G:L.34, G:V.296, H:V.1, H:T.4 Hydrogen bonds: G:Y.126, G:H.300 Salt bridges: G:R.19 pi-Stacking: G:F.297 Metal complexes: G:H.24 BCL.44: 24 residues within 4Å: Chain G: H.289, A.295, H.298, V.299, T.302, A.303, Y.306, A.310, V.367, G.370, Y.373, L.374, F.390, I.391, F.394, L.663, F.667 Chain I: L.12, Y.15 Ligands: BCL.48, UNL.62, UNL.69, UNL.70, UNL.77 11 PLIP interactions: 2 interactions with chain I, 9 interactions with chain G, Hydrophobic interactions: I:L.12, I:Y.15, G:V.299, G:V.299, G:Y.306, G:A.310, G:V.367, G:F.390, G:L.663 Salt bridges: G:H.289 Metal complexes: G:H.298 BCL.45: 14 residues within 4Å: Chain G: F.21, M.25, W.117, A.124, H.125, V.166, G.167, P.169, F.173, T.176, W.178, Y.195 Ligands: BCL.46, UNL.67 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:F.21, G:F.21, G:W.117, G:V.166, G:T.176, G:W.178, G:W.178 pi-Stacking: G:F.21 Metal complexes: G:H.125 BCL.46: 23 residues within 4Å: Chain G: P.17, I.20, F.21, H.24, M.25, I.28, F.173, I.180, L.181, R.182, R.183, T.184, Y.185, A.188, P.191, H.192, Y.195, L.199 Ligands: BCL.45, BCL.48, CLA.52, UNL.67, LYC.74 17 PLIP interactions: 17 interactions with chain G, Hydrophobic interactions: G:I.20, G:F.21, G:I.28, G:F.173, G:I.180, G:Y.185, G:A.188, G:P.191, G:Y.195, G:Y.195, G:Y.195, G:Y.195 Hydrogen bonds: G:H.24, G:R.182 pi-Stacking: G:F.21, G:Y.195 Metal complexes: G:H.192 BCL.47: 25 residues within 4Å: Chain G: P.57, R.58, S.61, F.200, M.253, N.254, T.255, I.256, G.258, E.259, M.262, C.263, W.266, F.270, L.311, L.319, H.322, S.324, Y.325 Chain I: M.1, L.5 Ligands: BCL.50, CLA.52, 84Q.60, UNL.69 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain I, Hydrophobic interactions: G:R.58, G:F.200, G:E.259, G:W.266, G:W.266, G:W.266, G:F.270, G:L.319, G:Y.325, I:L.5 Hydrogen bonds: G:S.61, G:S.324 Metal complexes: G:E.259 BCL.48: 21 residues within 4Å: Chain G: Y.185, A.186, A.188, L.189, H.192, T.193, I.196, W.203, I.287, L.290, E.291, V.299, H.300, I.304 Ligands: BCL.43, BCL.44, BCL.46, CLA.52, UNL.63, UNL.69, LYC.74 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:L.189, G:L.189, G:W.203, G:I.287, G:L.290, G:V.299, G:H.300 Salt bridges: G:H.300 Metal complexes: G:H.300 BCL.49: 21 residues within 4Å: Chain G: Y.38, Y.50, V.51, T.54, L.55, M.350, I.351, F.353, N.354, Q.357, L.361, T.835, V.836, Y.839, T.840, F.843, F.847, F.850 Ligands: BCL.50, CLA.54, LYC.74 16 PLIP interactions: 16 interactions with chain G, Hydrophobic interactions: G:Y.50, G:T.54, G:M.350, G:I.351, G:N.354, G:Q.357, G:L.361, G:V.836, G:Y.839, G:Y.839, G:T.840, G:F.847, G:F.847, G:F.847, G:F.850 Hydrogen bonds: G:Q.357 BCL.50: 18 residues within 4Å: Chain G: L.31, L.34, I.35, T.54, L.55, S.308, L.311, I.351, N.354, H.355, V.358, Y.362 Ligands: BCL.43, BCL.47, BCL.49, CLA.52, 84Q.60, LYC.74 4 PLIP interactions: 4 interactions with chain G, Hydrophobic interactions: G:L.31, G:L.34, G:L.55 Metal complexes: G:H.355

10 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.10: 23 residues within 4Å: Chain A: L.774, L.775, H.777, L.778, W.780, F.781 Chain G: V.415, V.416, Y.419, G.420, C.423, F.434, F.657, F.712, K.715, M.732, F.753, M.756, F.838 Chain J: T.18 Ligands: 2GO.1, CLA.40, 2GO.42 17 PLIP interactions: 7 interactions with chain G, 9 interactions with chain A, 1 interactions with chain J, Hydrophobic interactions: G:V.415, G:Y.419, G:F.434, G:F.657, G:F.712, G:F.753, G:F.838, A:L.774, A:L.775, A:W.780, A:F.781, A:F.781, A:F.781, A:F.781, A:F.781, J:T.18 Salt bridges: A:H.777 CLA.11: 19 residues within 4Å: Chain A: I.28, A.32, I.35, F.39, R.58, L.59, W.107, F.110, H.111, L.114, I.196, F.200, W.203, V.206 Ligands: BCL.5, BCL.6, BCL.7, BCL.9, UNL.20 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.32, A:I.35, A:F.110, A:F.110, A:L.114, A:I.196, A:F.200, A:W.203, A:W.203, A:V.206 Salt bridges: A:R.58 Metal complexes: A:H.111 CLA.12: 16 residues within 4Å: Chain A: Y.8, Q.9, K.10, L.11, E.12, F.297, L.361, Y.362, A.365, F.368, H.369, Q.372, Q.703, L.706, I.710 Ligands: BCL.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.297, A:Y.362, A:A.365, A:F.368, A:F.368, A:L.706, A:I.710 Hydrogen bonds: A:Q.9, A:K.10, A:L.11, A:Q.372 Metal complexes: A:H.369 CLA.31: 24 residues within 4Å: Chain A: Y.419, G.420, C.423, T.426, L.432, F.434, L.711, F.712, K.715, M.732, F.753, M.756, W.780, F.838 Chain D: T.18 Chain G: L.774, L.775, H.777, L.778, F.781, F.784 Ligands: 2GO.1, 2GO.42, CLA.51 22 PLIP interactions: 11 interactions with chain A, 11 interactions with chain G, Hydrophobic interactions: A:Y.419, A:Y.419, A:Y.419, A:L.432, A:F.434, A:F.712, A:K.715, A:F.753, A:W.780, A:F.838, G:L.774, G:L.774, G:L.775, G:H.777, G:L.778, G:F.781, G:F.781, G:F.781, G:F.781, G:F.784 Hydrogen bonds: A:Y.419 Salt bridges: G:H.777 CLA.33: 19 residues within 4Å: Chain A: G.49, Y.50, I.335, Y.336, H.768, M.772, L.775, F.847 Chain B: G.4, G.5, F.7, V.8 Chain G: N.433, F.434 Chain L: X.3, X.4, X.5, X.6 Ligands: BCL.8 12 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: A:Y.50, A:Y.336, A:L.775, A:F.847, G:F.434 Hydrogen bonds: A:Y.50, A:V.51, B:G.5, B:F.7 Salt bridges: A:H.768 pi-Stacking: A:H.768 Metal complexes: A:H.768 CLA.40: 25 residues within 4Å: Chain A: F.781, F.784, A.785, D.790, S.793, R.794, G.797, G.798, Q.801 Chain G: M.408, S.411, F.412, V.415, V.416, Y.419, I.660, R.664, F.708, F.712 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, 5 interactions with chain A, 3 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: G:F.412, G:F.412, G:V.415, G:V.415, G:V.416, G:Y.419, G:F.708, G:F.712, G:F.712, A:F.781, A:F.781, A:A.785, A:D.790, A:R.794, J:T.21, J:L.22, J:L.22 Hydrogen bonds: G:R.664 Metal complexes: H2O.1 CLA.51: 25 residues within 4Å: Chain A: M.408, S.411, F.412, V.415, F.657, R.664, F.708, F.712 Chain D: T.18, T.21, L.22 Chain F: X.1 Chain G: L.778, F.781, F.784, A.785, D.790, S.793, R.794, G.797, G.798, Q.801 Ligands: CLA.31, 85I.58, 85I.59 17 PLIP interactions: 8 interactions with chain G, 6 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: G:L.778, G:F.781, G:F.781, G:F.781, G:A.785, G:D.790, G:R.794, A:V.415, A:F.657, A:F.708, A:F.712, A:F.712, D:T.21, D:L.22 Hydrogen bonds: G:Q.801, A:R.664 Metal complexes: H2O.1 CLA.52: 25 residues within 4Å: Chain G: I.28, L.31, A.32, I.35, F.39, L.55, R.58, L.59, I.64, W.107, F.110, H.111, L.114, L.118, I.196, L.199, F.200, W.203, V.206, L.311 Ligands: BCL.46, BCL.47, BCL.48, BCL.50, UNL.69 18 PLIP interactions: 18 interactions with chain G, Hydrophobic interactions: G:I.28, G:L.31, G:A.32, G:I.35, G:I.64, G:W.107, G:F.110, G:L.114, G:L.118, G:I.196, G:F.200, G:W.203, G:W.203, G:V.206, G:L.311 Hydrogen bonds: G:R.58 pi-Stacking: G:F.110 Metal complexes: G:H.111 CLA.53: 16 residues within 4Å: Chain G: Y.8, Q.9, K.10, L.11, E.12, L.13, F.297, L.301, Y.362, A.365, F.368, H.369, Q.372, Q.703, W.707 Ligands: BCL.43 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:L.13, G:F.297, G:L.301, G:Y.362, G:A.365, G:F.368, G:W.707 Hydrogen bonds: G:K.10, G:L.11, G:Q.372 Salt bridges: G:H.369 Metal complexes: G:H.369 CLA.54: 21 residues within 4Å: Chain A: N.433, F.434 Chain F: X.3, X.4, X.5 Chain G: G.49, Y.50, I.335, Y.336, H.768, A.771, M.772, L.775, F.847 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.336, G:A.771, G:L.775, G:F.847, A:F.434 Hydrogen bonds: H:F.7, G:Y.50 Salt bridges: G:H.768 Metal complexes: G:H.768

2 x LYC: LYCOPENE(Non-covalent)

LYC.13: 13 residues within 4Å: Chain A: H.24, L.27, I.28, Y.38, V.51, Y.185, H.300 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.24, A:L.27, A:L.27, A:I.28, A:V.51, A:Y.185, A:Y.185 LYC.74: 15 residues within 4Å: Chain G: H.24, L.27, I.28, L.31, Y.38, Y.185, H.300 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.27, G:I.28, G:L.31, G:Y.185, G:Y.185

2 x CA: CALCIUM ION(Non-covalent)

CA.14: 5 residues within 4Å: Chain A: D.725, E.759, Y.849, D.852, G.853 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.725, A:E.759, A:Y.849, A:G.853, H2O.1 CA.55: 5 residues within 4Å: Chain G: D.725, E.759, Y.849, D.852, G.853 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.725, G:E.759, G:Y.849, G:G.853, 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.309, I.313, F.316, L.317, R.320, L.629, Y.630, S.631, R.638, W.655, F.659, I.720, Y.723, L.724, G.726, Q.856 Chain C: F.10, G.14, Y.15 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.309, A:F.309, A:I.313, A:F.316, A:W.655, A:F.659, A:I.720, A:L.724, C:F.10, C:Y.15 Hydrogen bonds: A:S.631, A:S.631 Salt bridges: A:R.320, A:R.638 85I.16: 15 residues within 4Å: Chain A: A.785, L.786, R.794, Q.801, F.822, P.823, V.824, S.825, F.837 Chain G: F.412 Chain J: L.22, F.23, I.25 Ligands: 85I.17, CLA.40 8 PLIP interactions: 4 interactions with chain A, 3 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: A:F.837, J:L.22, J:F.23, J:I.25, G:F.412 Hydrogen bonds: A:S.825, A:S.825 Salt bridges: A:R.794 85I.17: 15 residues within 4Å: Chain A: K.5, P.823, V.824, S.825, N.826, T.829, W.833 Chain J: I.25, V.26, V.28, S.29, L.32, S.33 Ligands: 85I.16, CLA.40 8 PLIP interactions: 5 interactions with chain J, 3 interactions with chain A Hydrophobic interactions: J:I.25, J:V.26, J:V.28, J:L.32, A:P.823 Hydrogen bonds: J:S.33, A:N.826, A:N.826 85I.57: 24 residues within 4Å: Chain G: F.309, I.313, F.316, L.317, R.320, L.545, L.629, Y.630, S.631, R.638, F.647, F.648, M.651, W.655, L.656, F.659, I.720, Y.723, L.724, Q.856 Chain I: A.7, F.10, V.11, Y.15 18 PLIP interactions: 15 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: G:F.309, G:I.313, G:F.316, G:L.545, G:F.648, G:F.648, G:W.655, G:F.659, G:I.720, G:Y.723, G:L.724, I:A.7, I:V.11, I:Y.15 Hydrogen bonds: G:S.631, G:S.631 Salt bridges: G:R.320, G:R.638 85I.58: 17 residues within 4Å: Chain A: M.408, F.409, F.412 Chain D: L.22, I.25 Chain G: V.782, L.786, R.794, Q.801, W.804, P.823, V.824, S.825, W.833, F.837 Ligands: CLA.51, 85I.59 13 PLIP interactions: 10 interactions with chain G, 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: G:Q.801, G:W.804, G:W.833, G:W.833, G:F.837, A:F.412, D:L.22, D:I.25 Hydrogen bonds: G:P.823, G:S.825, G:S.825 Salt bridges: G:R.794, G:R.794 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.3, V.4, L.778, I.779, P.823, V.824, S.825, N.826, T.829, W.833 Ligands: 85N.41, CLA.51, 85I.58 11 PLIP interactions: 7 interactions with chain G, 4 interactions with chain D Hydrophobic interactions: G:V.4, G:L.778, G:I.779, D:I.25, D:V.26, D:V.28 Hydrogen bonds: G:V.4, G:S.825, G:N.826, G:N.826, D:S.33

32 x UNL: UNKNOWN LIGAND

UNL.18: 4 residues within 4Å: Chain A: W.547, G.551, Y.554, L.555 Ligand excluded by PLIP UNL.19: 8 residues within 4Å: Chain A: W.393, F.394 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.189, L.273, P.282, R.283, S.284 Ligands: BCL.7, CLA.11, UNL.26 Ligand excluded by PLIP UNL.21: 12 residues within 4Å: Chain A: L.11, R.19, A.123, Y.126, R.130, I.138, F.139, W.140, W.156, F.157 Ligands: BCL.2, UNL.25 Ligand excluded by PLIP UNL.22: 4 residues within 4Å: Chain A: V.76, F.102, G.106, W.107 Ligand excluded by PLIP UNL.23: 8 residues within 4Å: Chain A: T.37, W.46 Chain B: C.6, V.8, G.9, S.10 Chain L: X.8, X.9 Ligand excluded by PLIP UNL.24: 7 residues within 4Å: Chain A: G.106, F.110, L.114, W.117, W.178 Ligands: BCL.4, BCL.5 Ligand excluded by PLIP UNL.25: 5 residues within 4Å: Chain A: L.116, Y.120, I.154, Y.164 Ligands: UNL.21 Ligand excluded by PLIP UNL.26: 5 residues within 4Å: Chain A: Y.306 Ligands: BCL.7, UNL.19, UNL.20, UNL.27 Ligand excluded by PLIP UNL.27: 6 residues within 4Å: Chain A: F.390, W.393, F.394 Ligands: BCL.3, UNL.19, UNL.26 Ligand excluded by PLIP UNL.28: 7 residues within 4Å: Chain A: F.538, R.540, K.541 Chain D: I.8, L.12, F.15 Ligands: UNL.29 Ligand excluded by PLIP UNL.29: 5 residues within 4Å: Chain A: K.541, P.544, W.547 Ligands: UNL.28, UNL.30 Ligand excluded by PLIP UNL.30: 4 residues within 4Å: Chain A: P.544, W.547 Ligands: UNL.29, UNL.38 Ligand excluded by PLIP UNL.35: 5 residues within 4Å: Chain A: T.37 Chain B: G.5, C.6, F.7 Ligands: LYC.13 Ligand excluded by PLIP UNL.37: 9 residues within 4Å: Chain A: I.403, L.656, L.663 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.547, G.551, Y.554 Ligands: UNL.73 Ligand excluded by PLIP UNL.62: 5 residues within 4Å: Chain G: W.393 Chain I: Y.15, W.19 Ligands: BCL.44, UNL.77 Ligand excluded by PLIP UNL.63: 9 residues within 4Å: Chain G: L.189, F.270, W.277, P.282, S.284, N.286, I.287 Ligands: BCL.48, UNL.69 Ligand excluded by PLIP UNL.64: 8 residues within 4Å: Chain G: A.123, Y.127, I.135, I.138, F.139, W.156 Ligands: BCL.43, UNL.68 Ligand excluded by PLIP UNL.65: 4 residues within 4Å: Chain G: F.102, R.103, G.106, W.107 Ligand excluded by PLIP UNL.66: 12 residues within 4Å: Chain F: X.7, X.9 Chain G: T.37, F.40, A.41, W.46, Y.95 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.113, L.114, W.117 Ligands: BCL.45, BCL.46 Ligand excluded by PLIP UNL.68: 6 residues within 4Å: Chain G: L.116, W.117, V.119, Y.120, Y.164 Ligands: UNL.64 Ligand excluded by PLIP UNL.69: 10 residues within 4Å: Chain G: A.303, Y.306, V.307, F.390 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.390 Ligands: BCL.44, UNL.69 Ligand excluded by PLIP UNL.71: 7 residues within 4Å: Chain G: F.417, F.538, R.540, K.541, V.542 Chain J: F.15 Ligands: UNL.72 Ligand excluded by PLIP UNL.72: 4 residues within 4Å: Chain G: K.541, W.547 Ligands: UNL.71, UNL.73 Ligand excluded by PLIP UNL.73: 4 residues within 4Å: Chain G: P.544, W.547 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.399, L.663 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.808, T.816, L.817, E.819, V.820, R.821 Chain J: G.20, F.23, G.24, I.25, V.26, Y.27, H.30 Chain K: S.3, A.6, W.9 12 PLIP interactions: 3 interactions with chain J, 7 interactions with chain A, 2 interactions with chain K Hydrophobic interactions: J:F.23, A:M.808, A:L.817, A:V.820, K:W.9 Salt bridges: J:H.30, J:H.30, A:E.819 Hydrogen bonds: A:T.816, A:T.816, A:R.821, K:S.3 85N.39: 17 residues within 4Å: Chain A: W.424, Y.437 Chain D: G.6, I.9, S.10, C.13, F.14, L.17 Chain E: I.16, I.19, G.20, F.22, G.23, M.33, F.36 Chain F: X.1, X.2 8 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: E:I.16, E:F.36, E:F.36, A:W.424, A:Y.437, D:F.14, D:L.17 Hydrogen bonds: E:G.23 85N.41: 14 residues within 4Å: Chain D: F.23, G.24, V.26, Y.27, H.30 Chain E: I.2, S.3, A.6, W.9, F.10 Chain G: T.816, E.819, R.821 Ligands: 85I.59 12 PLIP interactions: 5 interactions with chain E, 6 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: E:I.2, E:A.6, E:W.9, E:F.10, D:F.23, D:F.23, D:V.26, D:Y.27, D:Y.27 Hydrogen bonds: E:S.3 Salt bridges: D:H.30, G:E.819 85N.79: 16 residues within 4Å: Chain G: W.424, F.434, I.436, G.533 Chain J: G.6, Q.7, S.10, C.13, F.14 Chain K: I.16, I.19, G.20, F.22, G.23, F.36 Chain L: X.2 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: J:Q.7, G:W.424, G:F.434, G:I.436, K:F.36

2 x HEC: HEME C(Non-covalent)

HEC.34: 25 residues within 4Å: Chain A: W.757 Chain B: N.110, C.111, C.114, H.115, P.124, R.125, S.126, T.127, F.129, W.134, N.138, I.143, S.146, I.147, K.151, A.159, M.160, P.161, Y.163 Chain H: N.102, S.103, G.106, K.115 Ligands: HEC.75 18 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A, 3 interactions with chain H, Hydrophobic interactions: B:F.129, B:F.129, B:I.143, B:I.147, B:A.159, B:M.160, B:P.161, B:Y.163, A:W.757 Hydrogen bonds: B:W.134, B:S.146, H:S.103, H:G.106 Salt bridges: B:K.151, B:K.151, H:K.115 pi-Stacking: B:F.129 Metal complexes: B:H.115 HEC.75: 26 residues within 4Å: Chain B: S.139, G.142, K.151 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.139, B:G.142 Salt bridges: H:K.115, H:K.115, B:K.151 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.251, M.253, N.254, W.266, A.310, L.311, G.315, A.318 Chain C: M.1, T.2 Ligands: BCL.6, BCL.9 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:M.253, A:W.266, A:A.310, A:L.311, A:A.318 Salt bridges: A:H.251, A:H.251 Hydrogen bonds: C:M.1, C:T.2, C:T.2 84Q.60: 11 residues within 4Å: Chain G: M.253, N.254, A.310, L.311, V.314, G.315, A.318, H.355 Chain I: M.1 Ligands: BCL.47, BCL.50 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:M.253, G:L.311, G:V.314, G:A.318 Hydrogen bonds: G:A.627 Salt bridges: G:H.251, G:H.251

3 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.56: 11 residues within 4Å: Chain A: C.689, G.691, P.692, C.698, K.789, L.827 Chain G: C.689, G.691, P.692, C.698, L.827 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain A, Metal complexes: G:C.689, G:C.698, A:C.689, A:C.698 SF4.80: 12 residues within 4Å: Chain M: I.5, C.10, I.11, G.12, C.13, G.14, F.15, C.16, T.60, C.61, T.63, A.65 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.10, M:C.13, M:C.16, M:C.61 SF4.81: 12 residues within 4Å: Chain M: Y.3, C.20, A.26, I.27, I.44, C.49, I.50, S.51, C.52, S.53, L.54, C.55 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.20, M:C.49, M:C.52, M:C.55

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

2023-02-22

Peptides

PscA: AG
Cytochrome c, mono-and diheme variants: B
PscE: CI
PscF: DJ
PscG: EK
undefined polypeptide: FL
Cytochrome c domain-containing protein: H
Photosystem P840 reaction center iron-sulfur protein: M
PscD': N

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

M
B

N
D

Membrane

We predict this structure to be a membrane protein.
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PscA

Cytochrome c, mono-and diheme variants

PscE

PscF

PscG

undefined polypeptide

Cytochrome c domain-containing protein

Photosystem P840 reaction center iron-sulfur protein

PscD'

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