SMTL ID : 6lu1.1

Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A Resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

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

Ligands

82 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 20 residues within 4Å: Chain A: Y.459, F.544, Y.603, N.604, F.611, W.649, L.654, A.658, F.676, H.680, W.683, Y.735, T.742, T.743, F.746 Chain B: L.627, W.632 Ligands: CLA.2, CLA.59, CLA.66 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.544, A:W.649, A:L.654, A:A.658, A:W.683, A:W.683, A:W.683, A:T.742, A:F.746, B:L.627 Hydrogen bonds: A:Y.735 pi-Stacking: A:F.676 CLA.2: 23 residues within 4Å: Chain A: F.456, D.463, F.544, F.600, W.601, N.604, I.646, L.650, Y.735 Chain B: W.655, L.658, F.659, H.661, L.662, W.664, A.665 Ligands: CLA.1, CLA.60, CLA.66, CLA.72, CLA.73, BCR.103, BCR.110 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:W.655, B:F.659, B:L.662, B:A.665, A:F.456, A:D.463, A:F.544, A:W.601 CLA.3: 8 residues within 4Å: Chain A: I.48, W.49, H.52 Ligands: CLA.4, CLA.11, CLA.40, PQN.43, BCR.61 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:W.49 CLA.4: 16 residues within 4Å: Chain A: W.28, H.33, F.34, L.51, A.55, H.56, F.58, H.61, A.75, G.78, H.79, V.82 Ligands: CLA.3, CLA.5, CLA.6, CLA.11 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.28, A:L.51, A:A.55, A:F.58, A:V.82 Salt bridges: A:H.33 CLA.5: 21 residues within 4Å: Chain A: H.56, F.58, I.72, A.75, H.76, H.79, L.80, V.83, F.84, L.87, W.352, H.353, L.356, N.359, L.360 Ligands: CLA.4, CLA.6, CLA.13, CLA.25, CLA.30, BCR.46 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:F.58, A:I.72, A:I.72, A:A.75, A:H.79, A:L.80, A:V.83, A:L.87, A:W.352, A:L.356 Salt bridges: A:H.79 CLA.6: 14 residues within 4Å: Chain A: H.56, H.79, W.86, F.403, L.404 Ligands: CLA.4, CLA.5, CLA.8, CLA.11, CLA.28, CLA.29, CLA.30, BCR.46, LHG.50 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:W.86, A:F.403 Salt bridges: A:H.56 CLA.7: 13 residues within 4Å: Chain A: I.85, W.86, S.88, G.89, F.92, H.93, F.97, Q.115, V.116, W.118 Ligands: CLA.8, CLA.9, BCR.61 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.97, A:Q.115 CLA.8: 17 residues within 4Å: Chain A: V.82, W.86, M.90, A.114, Q.115, Q.138, I.139, T.140, S.141, L.143, A.671, Y.672, W.744 Ligands: CLA.6, CLA.7, CLA.9, CLA.28 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:V.82, A:A.671, A:Y.672, A:W.744 Hydrogen bonds: A:T.140, A:S.141 CLA.9: 13 residues within 4Å: Chain A: Q.115, V.116, V.117, W.118, I.120, V.121, Q.123, L.126, I.137 Chain B: F.450 Ligands: CLA.7, CLA.8, CLA.28 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.117, A:V.121, A:I.137, B:F.450 Hydrogen bonds: A:W.118, A:Q.123 CLA.10: 11 residues within 4Å: Chain A: V.14, V.16, F.77, F.174, A.175, F.178, H.179, R.183 Ligands: CLA.12, CLA.13, BCR.54 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:V.14, A:F.77, A:F.77, A:F.174, A:A.175, A:F.178 CLA.11: 20 residues within 4Å: Chain A: V.21, P.22, T.23, S.24, F.25, K.27, W.28, H.33, K.71, S.74, V.82, L.173, G.176, W.177, Y.180, H.181 Ligands: CLA.3, CLA.4, CLA.6, LHG.50 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.21, A:T.23, A:F.25, A:W.28, A:W.28, A:V.82, A:W.177, A:Y.180 Salt bridges: A:K.27, A:H.33 CLA.12: 13 residues within 4Å: Chain A: V.12, R.13, V.14, W.189, N.192, S.195, H.199, T.317, W.319 Ligands: CLA.10, CLA.13, CLA.20, BCR.54 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:V.14, A:T.317, A:W.319 Hydrogen bonds: A:S.195 CLA.13: 19 residues within 4Å: Chain A: F.73, H.76, F.77, L.80, F.84, M.168, L.171, M.172, W.189, N.192, S.195, M.196, H.199, H.200, L.204 Ligands: CLA.5, CLA.10, CLA.12, CLA.25 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.73, A:F.84, A:L.171, A:W.189, A:W.189, A:M.196, A:H.199, A:L.204 Salt bridges: A:H.76 CLA.14: 13 residues within 4Å: Chain A: G.151, I.152, Q.157, T.161, A.211, W.212, G.214, H.215, V.219, P.239, I.243 Ligands: CLA.16, BCR.45 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:A.211, A:W.212, A:H.215, A:V.219, A:I.243 CLA.15: 13 residues within 4Å: Chain A: L.210, A.213, G.214, I.217, H.218, I.243, W.258, G.259, F.261, S.262, V.264, Y.275 Ligands: BCR.44 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:I.217, A:I.243, A:W.258, A:Y.275 Hydrogen bonds: A:G.259 Salt bridges: A:H.218 CLA.16: 8 residues within 4Å: Chain A: F.156, C.160, H.240, I.243, L.244 Ligands: CLA.14, BCR.45, BCR.57 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:H.240, A:I.243, A:L.244 CLA.17: 13 residues within 4Å: Chain A: F.270, W.272, A.273, Y.275, L.279, F.281, H.299, L.302, A.303, V.306 Ligands: CLA.18, CLA.36, BCR.55 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.270, A:W.272, A:L.279, A:F.281, A:L.302, A:A.303, A:V.306 Salt bridges: A:H.299 pi-Stacking: A:W.272 CLA.18: 16 residues within 4Å: Chain A: F.281, G.283, G.284, L.292, D.296, H.299, H.300, A.303, I.304, H.373, M.377, A.509 Ligands: CLA.17, CLA.19, CLA.27, CLA.35 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.281, A:F.281, A:L.292, A:H.300, A:A.303, A:I.304 pi-Stacking: A:H.373 CLA.19: 19 residues within 4Å: Chain A: L.205, G.208, S.209, W.212, T.297, H.300, H.301, I.304, L.366, V.370, H.373, M.374, P.379, Y.380 Ligands: CLA.18, CLA.27, CLA.29, CLA.35, BCR.46 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:W.212, A:T.297, A:I.304, A:L.366, A:V.370, A:P.379 pi-Stacking: A:W.212, A:H.300 CLA.20: 9 residues within 4Å: Chain A: N.198, A.202, I.309, H.313, Y.315, T.317, I.321 Ligands: CLA.12, BCR.44 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:N.198, A:I.309, A:I.321 Hydrogen bonds: A:N.198 CLA.21: 17 residues within 4Å: Chain A: L.197, L.201, L.205, F.308, A.311, M.314, Y.315, L.325, I.328, I.358, L.430 Ligands: CLA.23, CLA.24, CLA.25, CLA.27, BCR.47, BCR.48 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:L.197, A:L.201, A:L.205, A:F.308, A:A.311, A:I.358, A:L.430 CLA.22: 9 residues within 4Å: Chain A: I.310, H.313, M.314, I.321, G.322, H.323 Ligands: CLA.23, BCR.44, BCR.56 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:I.310 Hydrogen bonds: A:G.322 Salt bridges: A:H.323 CLA.23: 10 residues within 4Å: Chain A: M.314, H.323, I.328, A.331, H.332 Ligands: CLA.21, CLA.22, CLA.42, BCR.56, BCR.58 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:I.328 Hydrogen bonds: A:H.323 CLA.24: 13 residues within 4Å: Chain A: I.328, L.329, H.332, H.341, V.429 Ligands: CLA.21, CLA.26, CLA.31, CLA.32, CLA.39, BCR.47, BCR.48, LHG.51 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:V.429 Salt bridges: A:H.332 CLA.25: 21 residues within 4Å: Chain A: F.190, V.193, M.196, L.197, H.200, L.201, L.348, T.349, T.350, S.351, W.352, Q.355, I.358, N.359, M.363 Ligands: CLA.5, CLA.13, CLA.21, CLA.27, CLA.29, BCR.47 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.193, A:L.197, A:L.197, A:L.197, A:L.348, A:W.352, A:Q.355, A:I.358 Hydrogen bonds: A:H.200 Salt bridges: A:H.200 CLA.26: 13 residues within 4Å: Chain A: I.368, I.369, Q.372, M.398, V.405, I.546, V.550 Ligands: CLA.24, CLA.27, CLA.37, CLA.38, CLA.39, BCR.48 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:I.368, A:I.368, A:V.405, A:V.550 CLA.27: 16 residues within 4Å: Chain A: L.366, I.369, Q.372, H.373, A.376, M.377, S.510, F.513 Ligands: CLA.18, CLA.19, CLA.21, CLA.25, CLA.26, CLA.35, CLA.37, BCR.48 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.366, A:A.376, A:F.513, A:F.513 CLA.28: 18 residues within 4Å: Chain A: W.86, M.90, T.140, S.141, S.392, T.395, H.396, W.399, I.400, L.675, W.744 Chain H: I.27 Ligands: CLA.6, CLA.8, CLA.9, CLA.29, CLA.30, BCR.49 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain H, Hydrophobic interactions: A:H.396, A:W.399, A:I.400, A:L.675, H:I.27 pi-Stacking: A:W.744 CLA.29: 16 residues within 4Å: Chain A: L.87, S.141, G.142, S.367, V.370, M.374, Y.380, L.393, H.396, H.397, I.400 Ligands: CLA.6, CLA.19, CLA.25, CLA.28, BCR.46 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:V.370, A:L.393, A:I.400 pi-Stacking: A:H.396 CLA.30: 21 residues within 4Å: Chain A: H.52, A.53, H.56, D.57, L.356, L.360, F.403, G.407, A.410, H.411, I.414, R.418, F.574, R.575, W.592 Ligands: CLA.5, CLA.6, CLA.28, CLA.41, BCR.49, LHG.50 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:L.356, A:L.356, A:L.360, A:L.360, A:A.410 Hydrogen bonds: A:H.56, A:R.575 Salt bridges: A:H.56, A:R.418, A:R.575 CLA.31: 15 residues within 4Å: Chain A: F.336, T.337, R.432, V.433, H.436, A.439, H.443 Chain I: V.6, T.20, P.21 Ligands: CLA.24, CLA.32, CLA.39, CLA.42, LHG.51 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:H.443, I:T.20 Salt bridges: A:R.432, A:H.436 pi-Cation interactions: A:H.436 CLA.32: 15 residues within 4Å: Chain A: A.439, H.443 Chain B: W.687, P.693 Chain I: H.17, T.20, I.22, S.23, V.28, I.32 Ligands: CLA.24, CLA.31, CLA.64, BCR.111, CLA.113 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain I, Hydrophobic interactions: B:W.687, I:I.22, I:I.22, I:V.28, I:I.32 CLA.33: 14 residues within 4Å: Chain A: W.446, I.449, F.450, F.453, H.454 Chain I: L.66 Ligands: CLA.34, CLA.64, CLA.96, PQN.98, BCR.103, BCR.110, BCR.111, BCR.115 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain A, Hydrophobic interactions: I:L.66, A:F.450, A:F.450, A:F.453 CLA.34: 21 residues within 4Å: Chain A: F.453, G.457, L.458, V.460, H.461, T.464, M.465, R.470, D.473, F.475 Chain I: P.62, W.63, L.66, G.67, P.68, R.70 Ligands: CLA.33, CLA.73, BCR.110, BCR.111, CLA.114 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain I, Hydrophobic interactions: A:L.458, A:V.460, A:T.464, A:F.475, I:P.62, I:P.62, I:W.63 Hydrogen bonds: A:R.470 Salt bridges: A:R.470 CLA.35: 12 residues within 4Å: Chain A: V.490, L.493, H.494, A.497, T.501 Ligands: CLA.18, CLA.19, CLA.27, CLA.36, CLA.37, BCR.48, BCR.52 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:V.490, A:V.490 Hydrogen bonds: A:T.501 CLA.36: 8 residues within 4Å: Chain A: T.501, A.502, P.503, N.504 Ligands: CLA.17, CLA.35, BCR.48, BCR.52 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:T.501, A:P.503 Hydrogen bonds: A:N.504, A:N.504 CLA.37: 17 residues within 4Å: Chain A: Q.372, Y.375, F.486, A.487, V.490, Q.491, F.513, H.539, H.542, V.609, H.612, F.613 Ligands: CLA.26, CLA.27, CLA.35, CLA.38, CLA.39 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.486, A:F.486, A:A.487, A:H.542, A:V.609, A:F.613 Hydrogen bonds: A:Q.491 CLA.38: 13 residues within 4Å: Chain A: L.451, P.484, V.485, F.486, A.487, D.535, F.536, H.539, H.540, A.543 Ligands: CLA.26, CLA.37, CLA.39 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.451, A:L.451, A:F.486, A:F.486, A:F.536, A:H.539, A:A.543 Hydrogen bonds: A:F.486, A:A.487 Salt bridges: A:H.539 pi-Stacking: A:F.536 CLA.39: 11 residues within 4Å: Chain A: L.444, V.447, A.543, I.546, H.547, V.550 Ligands: CLA.24, CLA.26, CLA.31, CLA.37, CLA.38 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.444, A:V.447, A:I.546, A:V.550 Salt bridges: A:H.547 CLA.40: 13 residues within 4Å: Chain A: T.45, W.49, V.705, V.713, P.715, I.717, P.719, R.720 Chain F: G.104, L.108 Ligands: CLA.3, PQN.43, CLA.63 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F, Hydrophobic interactions: A:T.45, A:W.49, A:V.705, A:P.715, A:P.715, A:I.717, A:P.719, F:L.108 CLA.41: 11 residues within 4Å: Chain A: F.685, Q.726, A.729, V.730, A.733, H.734 Ligands: CLA.30, PQN.43, BCR.49, LHG.50, CLA.62 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.685 Hydrogen bonds: A:Q.726 CLA.42: 9 residues within 4Å: Chain A: K.333, G.334, P.335 Ligands: CLA.23, CLA.31, BCR.47, LHG.51, BCR.56, BCR.58 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:P.335 CLA.59: 17 residues within 4Å: Chain A: L.674, L.677, H.680, F.681, A.684 Chain B: V.442, D.445, F.588, W.589, N.592, W.596, L.623, L.627 Ligands: CLA.1, BCR.49, CLA.62, CLA.66 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:V.442, B:W.589, B:L.623, B:L.623, A:F.681, A:A.684 pi-Stacking: B:W.596 CLA.60: 21 residues within 4Å: Chain A: N.445, C.448, G.452, F.453, F.456, V.460, F.544, L.551, F.600, W.601 Chain B: A.665, T.666, F.668, M.669, S.673, Y.677, W.678, L.681 Ligands: CLA.2, BCR.103, BCR.110 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:F.456, A:V.460, A:F.600, B:A.665, B:F.668, B:Y.677, B:W.678, B:W.678 pi-Stacking: A:W.601, A:W.601 CLA.62: 25 residues within 4Å: Chain A: F.681, A.684, F.685, L.687, M.688, F.691, S.692, Y.696, W.697, L.700 Chain B: S.427, S.430, L.431, G.434, F.435, L.438, L.532, L.539, I.540, F.588, W.589 Ligands: CLA.41, BCR.49, CLA.59, BCR.108 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A, Hydrophobic interactions: B:F.435, B:L.438, B:I.540, B:F.588, A:F.681, A:A.684, A:F.685, A:L.687, A:M.688, A:F.691, A:Y.696, A:W.697 pi-Stacking: B:W.589 Hydrogen bonds: A:Y.696 CLA.63: 17 residues within 4Å: Chain A: I.704, A.707, H.708, L.711, V.713 Chain B: S.424, S.427, W.428, L.431, F.435 Chain F: I.100, G.104 Ligands: CLA.40, PQN.43, CLA.88, CLA.89, BCR.108 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 1 interactions with chain F, Hydrophobic interactions: A:I.704, A:I.704, A:L.711, A:V.713, B:F.435, F:I.100 CLA.64: 13 residues within 4Å: Chain A: S.442, W.446, I.449 Chain B: L.685, A.688, H.689, V.698 Ligands: CLA.32, CLA.33, CLA.96, BCR.103, BCR.111, CLA.113 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.685, B:V.698 pi-Cation interactions: B:H.689 CLA.66: 25 residues within 4Å: Chain A: L.650, L.654, W.655 Chain B: T.437, L.438, Y.441, V.526, A.529, L.532, W.596, F.599, L.623, L.631, S.635, I.639, F.657, H.661, W.664, Y.724, T.727, Y.728, F.731 Ligands: CLA.1, CLA.2, CLA.59 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:T.437, B:L.438, B:Y.441, B:V.526, B:L.532, B:F.599, B:L.623, B:L.631, B:I.639, B:F.657, B:W.664, B:W.664, B:F.731, A:L.650, A:L.654, A:L.654 CLA.67: 18 residues within 4Å: Chain B: F.8, A.24, I.25, A.28, H.29, F.31, H.34, S.49, I.56 Chain J: S.26, L.29, Y.30, K.31 Ligands: CLA.68, CLA.69, LMG.104, BCR.115, BCR.116 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain J, Hydrophobic interactions: B:I.25, B:A.28, B:F.31, B:I.56, J:L.29, J:L.29 CLA.68: 19 residues within 4Å: Chain B: H.29, F.31, I.46, S.49, H.50, H.53, L.54, R.174, L.334, Q.337, L.338, H.341, L.342, L.345 Ligands: CLA.67, CLA.69, CLA.76, CLA.86, BCR.100 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:F.31, B:I.46, B:H.53, B:L.334, B:L.334, B:L.338, B:L.345 Salt bridges: B:H.53 CLA.69: 11 residues within 4Å: Chain B: H.53, I.57, W.60 Ligands: CLA.67, CLA.68, CLA.71, CLA.84, CLA.85, CLA.86, BCR.100, LMG.104 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:I.57, B:W.60 Salt bridges: B:H.29 CLA.70: 21 residues within 4Å: Chain B: L.59, S.62, G.63, F.66, H.67, W.70, Q.71, H.89, A.90 Chain G: L.10, P.11, F.14, I.15, V.18 Chain J: L.12, A.15 Ligands: CLA.71, CLA.72, LMG.104, BCR.110, BCR.116 10 PLIP interactions: 2 interactions with chain G, 6 interactions with chain B, 2 interactions with chain J, Hydrophobic interactions: G:F.14, G:I.15, B:L.59, B:F.66, B:F.66, B:W.70, J:L.12, J:A.15 Hydrogen bonds: B:Q.71 Salt bridges: B:H.67 CLA.71: 16 residues within 4Å: Chain B: A.88, H.89, D.114, I.115, A.116, Y.117, S.118, W.653, M.656 Ligands: CLA.69, CLA.70, CLA.72, CLA.84, CLA.86, BCR.103, BCR.110 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:A.88, B:W.653 Hydrogen bonds: B:Y.117, B:S.118, B:S.118 CLA.72: 23 residues within 4Å: Chain A: A.467, F.468 Chain B: H.89, A.90, I.91, W.92, D.93, Q.95, F.96, D.114, V.652 Chain G: I.15, C.19, P.23, V.26, M.27 Ligands: CLA.2, CLA.70, CLA.71, CLA.73, CLA.86, BCR.103, BCR.110 8 PLIP interactions: 2 interactions with chain G, 4 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: G:P.23, G:V.26, B:I.91, B:F.96, B:F.96, A:F.468, A:F.468 Hydrogen bonds: B:W.92 CLA.73: 12 residues within 4Å: Chain B: P.94, Q.95 Chain G: C.19, W.20 Chain I: W.63, P.68, S.82 Ligands: CLA.2, CLA.34, CLA.72, BCR.110, BCR.111 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:P.94, G:W.20 CLA.74: 11 residues within 4Å: Chain B: F.47, F.51, F.151, A.152, L.155, H.156, F.161, P.163 Ligands: CLA.75, CLA.76, BCR.105 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.47, B:F.51, B:F.151, B:A.152, B:L.155, B:P.163 CLA.75: 7 residues within 4Å: Chain B: W.167, N.170, S.173, H.177 Ligands: CLA.74, CLA.76, BCR.105 2 PLIP interactions: 2 interactions with chain B, Hydrogen bonds: B:S.173 pi-Stacking: B:H.177 CLA.76: 19 residues within 4Å: Chain B: F.47, H.50, F.51, W.123, W.167, S.173, R.174, H.177, H.178, G.181, L.182, F.183, Y.362 Ligands: CLA.68, CLA.74, CLA.75, CLA.81, CLA.85, BCR.100 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:W.123, B:W.167, B:R.174, B:F.183 Salt bridges: B:H.50 CLA.77: 22 residues within 4Å: Chain B: I.127, G.128, M.129, D.134, Q.137, F.141, L.145, S.186, A.189, W.190, G.192, H.193, H.196, V.197, V.207, G.208, W.209, F.212 Ligands: CLA.85, BCR.100, BCR.101, BCR.105 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:I.127, B:F.141, B:W.190, B:W.190, B:H.193, B:H.196, B:V.197, B:W.209, B:F.212 pi-Stacking: B:W.209 CLA.78: 12 residues within 4Å: Chain B: L.188, G.192, I.195, H.196, L.213, M.216, P.217, G.221, L.222, L.278 Ligands: BCR.99, BCR.101 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:I.195, B:P.217, B:L.222, B:L.222, B:L.278 CLA.79: 11 residues within 4Å: Chain B: F.225, G.228, W.230, A.234, L.255, F.257, H.275, L.278, A.279, V.499 Ligands: CLA.80 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:F.225, B:W.230, B:W.230, B:W.230, B:W.230, B:L.255, B:L.278, B:L.278, B:A.279 Salt bridges: B:H.275 CLA.80: 16 residues within 4Å: Chain B: F.257, G.260, L.268, D.272, H.275, H.276, I.280, H.355, L.359, W.500, W.504 Ligands: CLA.79, CLA.81, CLA.83, CLA.91, CLA.92 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:F.257, B:L.268, B:H.275, B:H.276, B:I.280 Hydrogen bonds: B:G.260, B:H.355 CLA.81: 17 residues within 4Å: Chain B: W.123, I.127, F.183, S.186, S.187, W.190, M.273, H.276, H.277, I.280, V.352, M.356, P.361, Y.362 Ligands: CLA.76, CLA.80, CLA.85 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:W.190, B:W.190, B:I.280, B:V.352, B:P.361 pi-Stacking: B:W.190, B:H.276 CLA.82: 13 residues within 4Å: Chain B: V.347, S.350, L.351, Q.354, Q.380, M.387, L.534, T.538, I.594 Ligands: CLA.83, CLA.93, CLA.95, BCR.102 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:T.538, B:I.594 Hydrogen bonds: B:S.350, B:Q.354, B:Q.380 CLA.83: 12 residues within 4Å: Chain B: L.351, Q.354, H.355, S.358, L.359, L.515, F.516 Ligands: CLA.80, CLA.82, CLA.91, CLA.93, BCR.102 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.351, B:L.351, B:L.359, B:L.515, B:F.516 pi-Cation interactions: B:H.355 CLA.84: 15 residues within 4Å: Chain B: W.60, Y.117, S.118, H.378, Y.381, I.382, M.656, I.725, L.726, A.729, I.733 Ligands: CLA.69, CLA.71, CLA.85, LMG.104 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:H.378, B:Y.381, B:I.382, B:L.726, B:A.729 CLA.85: 21 residues within 4Å: Chain B: W.60, V.61, S.118, G.119, W.123, A.189, T.349, V.352, M.356, Y.362, L.375, H.378, H.379, I.382 Ligands: CLA.69, CLA.76, CLA.77, CLA.81, CLA.84, BCR.100, BCR.101 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.61, B:W.123, B:A.189, B:T.349, B:V.352, B:L.375, B:I.382 Hydrogen bonds: B:Y.362 pi-Stacking: B:H.378 CLA.86: 20 residues within 4Å: Chain B: A.26, H.29, D.30, L.338, L.342, F.385, G.389, H.393, I.396, R.400, Y.562, W.580, F.583, V.722 Ligands: CLA.68, CLA.69, CLA.71, CLA.72, CLA.97, LMG.104 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:A.26, B:L.338, B:L.338, B:L.342, B:F.583, B:V.722 Salt bridges: B:H.29, B:R.400 CLA.87: 9 residues within 4Å: Chain B: V.411, R.414, V.415, Q.417, H.418, I.422, H.425 Ligands: CLA.88, CLA.95 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:V.411, B:V.415, B:I.422 Salt bridges: B:R.414, B:H.418 CLA.88: 6 residues within 4Å: Chain A: W.706 Chain B: A.421, H.425, W.428 Ligands: CLA.63, CLA.87 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:W.706 pi-Stacking: B:H.425 CLA.89: 14 residues within 4Å: Chain B: W.428, L.431, F.432, F.435, H.436 Chain F: S.90, F.93, L.94, A.97 Ligands: CLA.63, CLA.90, CLA.94, BCR.108, BCR.109 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain B, Hydrophobic interactions: F:F.93, F:L.94, F:L.94, F:A.97, B:F.432, B:F.435 pi-Stacking: F:F.93 Salt bridges: B:H.436 CLA.90: 8 residues within 4Å: Chain B: G.439, V.442, H.443, V.446, K.455 Ligands: BCR.49, CLA.89, BCR.109 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:V.442 Hydrogen bonds: B:K.455 Salt bridges: B:K.455 pi-Cation interactions: B:H.443 CLA.91: 11 residues within 4Å: Chain B: I.467, A.470, H.471, L.481, L.482, W.504 Ligands: CLA.80, CLA.83, CLA.92, CLA.93, BCR.102 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:I.467, B:L.481, B:L.482 pi-Stacking: B:H.471 CLA.92: 9 residues within 4Å: Chain B: L.481, I.488, A.489, P.494, N.495, W.500 Ligands: CLA.80, CLA.91, BCR.102 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.481, B:I.488, B:W.500 Hydrogen bonds: B:N.495 CLA.93: 20 residues within 4Å: Chain B: Q.354, Y.357, Y.376, A.464, I.467, Q.468, F.516, L.517, I.519, H.527, I.530, V.597, Y.600, W.601, K.604 Ligands: CLA.82, CLA.83, CLA.91, CLA.94, CLA.95 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:A.464, B:I.519, B:I.530, B:V.597, B:Y.600, B:Y.600, B:K.604 Hydrogen bonds: B:Q.468 CLA.94: 15 residues within 4Å: Chain B: V.429, F.432, L.433, E.460, P.461, V.462, F.463, A.464, F.524, H.527, H.528 Ligands: CLA.89, CLA.93, CLA.95, BCR.109 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:V.429, B:F.432, B:L.433, B:V.462, B:F.463, B:F.463, B:F.524 Hydrogen bonds: B:F.463, B:A.464 Salt bridges: B:H.527 pi-Stacking: B:F.524 CLA.95: 11 residues within 4Å: Chain B: I.422, L.426, V.429, A.531, L.534, H.535 Ligands: CLA.82, CLA.87, CLA.93, CLA.94, BCR.102 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.426, B:V.429, B:L.534 Salt bridges: B:H.535 CLA.96: 21 residues within 4Å: Chain B: T.18, I.21, W.22, H.689, R.699, W.700, K.701, P.704, V.705 Chain G: W.20, F.31, E.35 Chain I: L.86, V.100, S.101 Ligands: CLA.33, CLA.64, PQN.98, BCR.110, BCR.111, BCR.115 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain G, 1 interactions with chain I, Hydrophobic interactions: B:I.21, B:W.700, B:P.704, B:P.704, G:F.31, I:L.86 Hydrogen bonds: B:K.701 CLA.97: 15 residues within 4Å: Chain B: W.22, F.659, L.662, V.663, T.666, M.669, F.670, L.714, V.715, A.718, H.719 Ligands: CLA.86, PQN.98, BCR.103, LMG.104 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.659, B:L.662, B:V.663, B:T.666, B:V.715 CLA.112: 6 residues within 4Å: Chain I: F.31, N.34, R.39, E.50, M.53 Ligands: CLA.113 2 PLIP interactions: 2 interactions with chain I, Hydrophobic interactions: I:F.31, I:N.34 CLA.113: 15 residues within 4Å: Chain B: P.693, L.694, L.697 Chain I: L.35, P.36, V.51, A.54, H.55, F.58 Ligands: CLA.32, CLA.64, BCR.111, CLA.112, CLA.114, BCR.115 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain I, Hydrophobic interactions: B:P.693, B:L.694, B:L.697, I:A.54, I:F.58 CLA.114: 8 residues within 4Å: Chain I: Y.57, F.58, G.61, P.62, V.64, K.65 Ligands: CLA.34, CLA.113 5 PLIP interactions: 5 interactions with chain I, Hydrophobic interactions: I:F.58, I:P.62, I:V.64, I:K.65 Hydrogen bonds: I:Y.57

2 x PQN: PHYLLOQUINONE(Non-covalent)

PQN.43: 12 residues within 4Å: Chain A: M.688, F.689, S.692, R.694, W.697, A.721, L.722 Ligands: CLA.3, CLA.40, CLA.41, CLA.63, BCR.108 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.689, A:F.689, A:R.694, A:W.697, A:W.697, A:L.722, A:L.722 Hydrogen bonds: A:L.722 PQN.98: 15 residues within 4Å: Chain B: W.22, M.669, F.670, S.673, W.674, R.675, W.678, A.706, L.707, S.708, A.712 Ligands: CLA.33, CLA.96, CLA.97, LMG.104 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.22, B:F.670, B:W.678, B:W.678, B:A.712 Hydrogen bonds: B:L.707

26 x BCR: BETA-CAROTENE(Non-covalent)(Non-functional Binders)

BCR.44: 9 residues within 4Å: Chain A: L.210, F.267, V.306, I.309, H.313 Ligands: CLA.15, CLA.20, CLA.22, BCR.45 Ligand excluded by PLIP BCR.45: 8 residues within 4Å: Chain A: F.84, T.161, M.168, A.211 Ligands: CLA.14, CLA.16, BCR.44, BCR.46 Ligand excluded by PLIP BCR.46: 8 residues within 4Å: Chain A: G.203, L.207, G.208 Ligands: CLA.5, CLA.6, CLA.19, CLA.29, BCR.45 Ligand excluded by PLIP BCR.47: 10 residues within 4Å: Chain A: A.357, I.358, G.412, F.415 Ligands: CLA.21, CLA.24, CLA.25, CLA.42, BCR.48, LHG.51 Ligand excluded by PLIP BCR.48: 14 residues within 4Å: Chain A: A.357, A.361, M.362, S.365, V.405, G.408, L.553 Ligands: CLA.21, CLA.24, CLA.26, CLA.27, CLA.35, CLA.36, BCR.47 Ligand excluded by PLIP BCR.49: 13 residues within 4Å: Chain A: L.675, G.678, F.681, I.682, L.737, A.741, W.744 Ligands: CLA.28, CLA.30, CLA.41, CLA.59, CLA.62, CLA.90 Ligand excluded by PLIP BCR.52: 4 residues within 4Å: Chain A: W.489, L.493 Ligands: CLA.35, CLA.36 Ligand excluded by PLIP BCR.53: 2 residues within 4Å: Chain A: W.118 Ligands: BCR.61 Ligand excluded by PLIP BCR.54: 2 residues within 4Å: Ligands: CLA.10, CLA.12 Ligand excluded by PLIP BCR.55: 2 residues within 4Å: Chain A: I.310 Ligands: CLA.17 Ligand excluded by PLIP BCR.56: 4 residues within 4Å: Ligands: CLA.22, CLA.23, CLA.42, BCR.58 Ligand excluded by PLIP BCR.57: 1 residues within 4Å: Ligands: CLA.16 Ligand excluded by PLIP BCR.58: 3 residues within 4Å: Ligands: CLA.23, CLA.42, BCR.56 Ligand excluded by PLIP BCR.61: 7 residues within 4Å: Chain A: W.118, I.120 Chain H: I.27, E.28 Ligands: CLA.3, CLA.7, BCR.53 Ligand excluded by PLIP BCR.99: 8 residues within 4Å: Chain B: L.188, L.222, F.225, V.282, I.285, H.289 Ligands: CLA.78, BCR.101 Ligand excluded by PLIP BCR.100: 12 residues within 4Å: Chain B: L.54, I.57, G.181, L.182, V.185, S.186 Ligands: CLA.68, CLA.69, CLA.76, CLA.77, CLA.85, BCR.105 Ligand excluded by PLIP BCR.101: 11 residues within 4Å: Chain B: L.65, W.123, W.124, M.129, G.138, F.141, L.142 Ligands: CLA.77, CLA.78, CLA.85, BCR.99 Ligand excluded by PLIP BCR.102: 13 residues within 4Å: Chain B: F.336, G.339, A.343, M.387, A.390, F.391, G.394, F.397 Ligands: CLA.82, CLA.83, CLA.91, CLA.92, CLA.95 Ligand excluded by PLIP BCR.103: 9 residues within 4Å: Chain B: F.659, W.678 Ligands: CLA.2, CLA.33, CLA.60, CLA.64, CLA.71, CLA.72, CLA.97 Ligand excluded by PLIP BCR.105: 4 residues within 4Å: Ligands: CLA.74, CLA.75, CLA.77, BCR.100 Ligand excluded by PLIP BCR.108: 10 residues within 4Å: Chain A: W.697 Chain B: L.431, F.435 Chain F: L.92, F.93, I.96 Ligands: PQN.43, CLA.62, CLA.63, CLA.89 Ligand excluded by PLIP BCR.109: 11 residues within 4Å: Chain B: F.432, H.436, L.440, I.459, F.524 Chain F: D.85, I.88, P.89 Ligands: CLA.89, CLA.90, CLA.94 Ligand excluded by PLIP BCR.110: 11 residues within 4Å: Chain G: V.18 Ligands: CLA.2, CLA.33, CLA.34, CLA.60, CLA.70, CLA.71, CLA.72, CLA.73, CLA.96, BCR.111 Ligand excluded by PLIP BCR.111: 11 residues within 4Å: Chain B: L.694 Chain G: W.20 Chain I: W.63 Ligands: CLA.32, CLA.33, CLA.34, CLA.64, CLA.73, CLA.96, BCR.110, CLA.113 Ligand excluded by PLIP BCR.115: 12 residues within 4Å: Chain G: M.27, L.30, F.31 Chain I: A.90, C.93, L.94, Y.97, F.125 Ligands: CLA.33, CLA.67, CLA.96, CLA.113 Ligand excluded by PLIP BCR.116: 8 residues within 4Å: Chain B: L.59 Chain J: L.12, V.13, A.15, A.19, A.22 Ligands: CLA.67, CLA.70 Ligand excluded by PLIP

2 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.50: 19 residues within 4Å: Chain A: W.49, N.50, H.52, A.53, L.54, F.403, R.575, W.592, S.723, I.725, Q.726, A.729, V.732, L.736 Chain E: G.51 Ligands: CLA.6, CLA.11, CLA.30, CLA.41 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.52, A:F.403, A:V.732, A:L.736, A:L.736 Hydrogen bonds: A:N.50, A:R.575, A:S.723 Salt bridges: A:R.575, A:R.575 LHG.51: 11 residues within 4Å: Chain A: H.332, K.333, G.334, P.335, F.336, T.337, H.341 Ligands: CLA.24, CLA.31, CLA.42, BCR.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.336, A:T.337, A:H.341

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.65: 8 residues within 4Å: Chain A: C.578, G.580, C.587, I.724, R.728 Chain B: C.566, G.568, C.575 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, Metal complexes: A:C.578, B:C.566 SF4.106: 13 residues within 4Å: Chain C: C.21, P.22, T.23, V.25, L.26, C.48, V.49, G.50, C.51, K.52, R.53, C.54, V.67 0 PLIP interactions: SF4.107: 10 residues within 4Å: Chain C: C.11, I.12, G.13, C.14, T.15, Q.16, C.17, C.58, P.59, I.65 0 PLIP interactions:

1 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.104: 17 residues within 4Å: Chain B: Y.23, A.26, Y.562, A.563, W.580, F.583, Q.711, L.714, S.721, V.722 Ligands: CLA.67, CLA.69, CLA.70, CLA.84, CLA.86, CLA.97, PQN.98 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.23, B:A.26, B:F.583, B:Q.711, B:L.714 Hydrogen bonds: B:R.400, B:Y.562, B:S.708

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coruh, O. et al., Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Commun Biol (2021)

Release Date

2021-03-17

Peptides

Photosystem I P700 chlorophyll a apoprotein A1: A
Photosystem I P700 chlorophyll a apoprotein A2: B
Photosystem I iron-sulfur center: C
Photosystem I reaction center subunit II: D
Photosystem I reaction center subunit IV: E
Photosystem I reaction center subunit III: F
Photosystem I reaction center subunit VIII: G
Photosystem I reaction center subunit IX: H
Photosystem I reaction center subunit XI: I
Photosystem I reaction center subunit XII: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
I

H
J

I
L

J
M

Membrane

We predict this structure to be a membrane protein.
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Photosystem I P700 chlorophyll a apoprotein A1

Photosystem I P700 chlorophyll a apoprotein A2

Photosystem I iron-sulfur center

Photosystem I reaction center subunit II

Photosystem I reaction center subunit IV

Photosystem I reaction center subunit III

Photosystem I reaction center subunit VIII

Photosystem I reaction center subunit IX

Photosystem I reaction center subunit XI

Photosystem I reaction center subunit XII

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