SMTL ID : 6m32.1

Cryo-EM structure of FMO-RC complex from green sulfur bacteria

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-2-mer

Ligands

48 x BCL: BACTERIOCHLOROPHYLL A(Covalent)(Non-covalent)

BCL.1: 19 residues within 4Å: Chain A: V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, W.223 Chain C: S.127 Ligands: BCL.5, BCL.8, BCL.17 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.113, A:V.152, A:L.159, A:T.162, A:W.163, A:I.180, A:F.183, A:W.223 Metal complexes: A:H.111 BCL.2: 22 residues within 4Å: Chain A: A.12, S.14, Y.16, A.34, V.36, P.39, P.40, A.41, F.258, S.260, I.265, V.267, H.298, V.301, N.305, F.307, C.353 Ligands: BCL.3, BCL.4, BCL.5, BCL.6, BCL.8 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.12, A:A.34, A:V.36, A:F.258, A:I.265, A:V.301, A:F.307, A:F.307, A:F.307 Hydrogen bonds: A:Y.16, A:A.41 Metal complexes: A:H.298 BCL.3: 23 residues within 4Å: Chain A: Y.16, I.18, V.30, A.32, V.51, A.256, G.257, F.258, L.288, H.290, P.291, P.294, H.298, L.313, Y.345, W.348, V.349, V.352, C.353, F.360 Ligands: BCL.2, BCL.4, BCL.6 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.16, A:I.18, A:V.30, A:A.32, A:V.51, A:A.256, A:F.258, A:L.288, A:P.291, A:L.313, A:W.348, A:W.348, A:V.349, A:V.352 Hydrogen bonds: A:Y.345, A:Y.345 Metal complexes: A:H.290 BCL.4: 17 residues within 4Å: Chain A: V.55, F.71, D.234, R.238, E.241, L.242, F.243, P.244, L.248, V.254, A.256, F.273, L.288 Ligands: BCL.2, BCL.3, BCL.5, BCL.6 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:V.55, A:F.71, A:L.242, A:L.242, A:L.248, A:V.254, A:A.256, A:F.273 Hydrogen bonds: A:D.234 Salt bridges: A:R.238 Metal complexes: A:L.242 BCL.5: 23 residues within 4Å: Chain A: L.53, V.55, I.67, I.84, I.88, R.96, I.97, S.98, V.119, Q.144, H.146, I.148, W.184, H.227, S.235, A.252, V.254, F.273 Ligands: BCL.1, BCL.2, BCL.4, BCL.6, BCL.8 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:L.53, A:I.67, A:V.119, A:I.148, A:W.184, A:A.252, A:V.254, A:F.273 Hydrogen bonds: A:R.96 Metal complexes: A:H.146 BCL.6: 16 residues within 4Å: Chain A: A.41, I.186, P.188, A.189, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Ligands: BCL.2, BCL.3, BCL.4, BCL.5, BCL.8 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:P.188, A:P.188, A:I.293, A:P.294 Hydrogen bonds: A:Q.198 pi-Cation interactions: A:H.297 Metal complexes: A:H.297 BCL.7: 16 residues within 4Å: Chain A: L.122, F.123, Y.124, Y.125, R.126 Chain B: T.162, T.166, K.168, A.169, S.172, T.173, F.176, W.179, I.180, F.183 Ligands: BCL.10 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:T.162, B:T.166, B:A.169, B:T.173, B:F.176, B:F.176, B:I.180, B:F.183, A:Y.124 Hydrogen bonds: B:S.172 Salt bridges: B:K.168 Metal complexes: A:Y.124 BCL.8: 23 residues within 4Å: Chain A: L.44, S.73, V.75, N.80, K.81, L.82, I.84, V.106, F.115, F.183, W.184, I.186 Chain C: Y.125, V.130, V.134, P.137, I.138, Y.139, Q.141 Ligands: BCL.1, BCL.2, BCL.5, BCL.6 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain C, Hydrophobic interactions: A:L.44, A:V.75, A:N.80, A:L.82, A:L.82, A:V.106, A:F.115, A:F.115, A:F.183, A:I.186 Hydrogen bonds: A:S.73, C:Y.125, C:I.138, C:Y.139, C:Q.141 BCL.9: 23 residues within 4Å: Chain A: Y.125, V.130, V.134, P.137, I.138, Y.139, Q.141 Chain B: L.44, S.73, V.75, N.80, K.81, L.82, I.84, V.106, F.115, F.183, W.184, I.186 Ligands: BCL.10, BCL.11, BCL.14, BCL.15 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.44, B:V.75, B:N.80, B:L.82, B:L.82, B:V.106, B:F.115, B:F.115, B:F.183, B:I.186 Hydrogen bonds: B:S.73, A:I.138, A:Y.139, A:Q.141 BCL.10: 19 residues within 4Å: Chain A: S.127 Chain B: V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, W.223 Ligands: BCL.7, BCL.9, BCL.14 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:F.113, B:V.152, B:L.159, B:T.162, B:W.163, B:I.180, B:F.183, B:W.223 Metal complexes: B:H.111 BCL.11: 22 residues within 4Å: Chain B: A.12, S.14, Y.16, A.34, V.36, P.39, P.40, A.41, F.258, S.260, I.265, V.267, H.298, V.301, N.305, F.307, C.353 Ligands: BCL.9, BCL.12, BCL.13, BCL.14, BCL.15 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:A.12, B:A.34, B:V.36, B:F.258, B:I.265, B:V.301, B:F.307, B:F.307, B:F.307 Hydrogen bonds: B:Y.16, B:A.41 Metal complexes: B:H.298 BCL.12: 23 residues within 4Å: Chain B: Y.16, I.18, V.30, A.32, V.51, A.256, G.257, F.258, L.288, H.290, P.291, P.294, H.298, L.313, Y.345, W.348, V.349, V.352, C.353, F.360 Ligands: BCL.11, BCL.13, BCL.15 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:Y.16, B:I.18, B:V.30, B:A.32, B:V.51, B:A.256, B:F.258, B:L.288, B:P.291, B:L.313, B:W.348, B:W.348, B:V.349, B:V.352 Hydrogen bonds: B:Y.345, B:Y.345 Metal complexes: B:H.290 BCL.13: 17 residues within 4Å: Chain B: V.55, F.71, D.234, R.238, E.241, L.242, F.243, P.244, L.248, V.254, A.256, F.273, L.288 Ligands: BCL.11, BCL.12, BCL.14, BCL.15 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:V.55, B:F.71, B:L.242, B:L.242, B:L.248, B:V.254, B:A.256, B:F.273 Hydrogen bonds: B:D.234 Salt bridges: B:R.238 Metal complexes: B:L.242 BCL.14: 23 residues within 4Å: Chain B: L.53, V.55, I.67, I.84, I.88, R.96, I.97, S.98, V.119, Q.144, H.146, I.148, W.184, H.227, S.235, A.252, V.254, F.273 Ligands: BCL.9, BCL.10, BCL.11, BCL.13, BCL.15 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.53, B:I.67, B:V.119, B:I.148, B:W.184, B:A.252, B:V.254, B:F.273 Hydrogen bonds: B:R.96 Metal complexes: B:H.146 BCL.15: 16 residues within 4Å: Chain B: A.41, I.186, P.188, A.189, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Ligands: BCL.9, BCL.11, BCL.12, BCL.13, BCL.14 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:P.188, B:P.188, B:I.293, B:P.294 Hydrogen bonds: B:Q.198 pi-Cation interactions: B:H.297 Metal complexes: B:H.297 BCL.16: 16 residues within 4Å: Chain B: L.122, F.123, Y.124, Y.125, R.126 Chain C: T.162, T.166, K.168, A.169, S.172, T.173, F.176, W.179, I.180, F.183 Ligands: BCL.19 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:T.166, C:A.169, C:T.173, C:F.176, C:F.176, C:F.183, B:Y.124 Hydrogen bonds: C:S.172 Salt bridges: C:K.168 Metal complexes: B:Y.124 BCL.17: 15 residues within 4Å: Chain A: T.162, T.166, K.168, A.169, S.172, F.176, W.179, I.180, F.183 Chain C: L.122, F.123, Y.124, Y.125, R.126 Ligands: BCL.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:T.162, A:T.166, A:A.169, A:F.176, A:F.176, A:I.180, A:F.183, C:Y.124 Hydrogen bonds: A:S.172 Salt bridges: A:K.168 Metal complexes: C:Y.124 BCL.18: 23 residues within 4Å: Chain B: Y.125, V.130, V.134, P.137, I.138, Y.139, Q.141 Chain C: L.44, S.73, V.75, N.80, K.81, L.82, I.84, V.106, F.115, F.183, W.184, I.186 Ligands: BCL.19, BCL.20, BCL.23, BCL.24 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.44, C:V.75, C:N.80, C:L.82, C:L.82, C:V.106, C:F.115, C:F.115, C:F.183, C:I.186 Hydrogen bonds: C:S.73, B:I.138, B:Y.139, B:Q.141 BCL.19: 19 residues within 4Å: Chain B: S.127 Chain C: V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, W.223 Ligands: BCL.16, BCL.18, BCL.23 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:F.113, C:V.152, C:L.159, C:T.162, C:W.163, C:I.180, C:F.183, C:W.223 Metal complexes: C:H.111 BCL.20: 22 residues within 4Å: Chain C: A.12, S.14, Y.16, A.34, V.36, P.39, P.40, A.41, F.258, S.260, I.265, V.267, H.298, V.301, N.305, F.307, C.353 Ligands: BCL.18, BCL.21, BCL.22, BCL.23, BCL.24 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:A.12, C:A.34, C:V.36, C:F.258, C:I.265, C:V.301, C:F.307, C:F.307, C:F.307 Hydrogen bonds: C:Y.16, C:A.41 Metal complexes: C:H.298 BCL.21: 23 residues within 4Å: Chain C: Y.16, I.18, V.30, A.32, V.51, A.256, G.257, F.258, L.288, H.290, P.291, P.294, H.298, L.313, Y.345, W.348, V.349, V.352, C.353, F.360 Ligands: BCL.20, BCL.22, BCL.24 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.16, C:I.18, C:V.30, C:A.32, C:V.51, C:A.256, C:F.258, C:L.288, C:P.291, C:L.313, C:W.348, C:W.348, C:V.349, C:V.352 Hydrogen bonds: C:Y.345, C:Y.345 Metal complexes: C:H.290 BCL.22: 17 residues within 4Å: Chain C: V.55, F.71, D.234, R.238, E.241, L.242, F.243, P.244, L.248, V.254, A.256, F.273, L.288 Ligands: BCL.20, BCL.21, BCL.23, BCL.24 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:V.55, C:F.71, C:L.242, C:L.242, C:L.248, C:V.254, C:A.256, C:F.273 Salt bridges: C:R.238 Metal complexes: C:L.242 BCL.23: 23 residues within 4Å: Chain C: L.53, V.55, I.67, I.84, I.88, R.96, I.97, S.98, V.119, Q.144, H.146, I.148, W.184, H.227, S.235, A.252, V.254, F.273 Ligands: BCL.18, BCL.19, BCL.20, BCL.22, BCL.24 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.53, C:I.67, C:V.119, C:I.148, C:W.184, C:A.252, C:V.254, C:F.273 Hydrogen bonds: C:R.96 Metal complexes: C:H.146 BCL.24: 16 residues within 4Å: Chain C: A.41, I.186, P.188, A.189, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Ligands: BCL.18, BCL.20, BCL.21, BCL.22, BCL.23 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:P.188, C:P.188, C:I.293, C:P.294 Hydrogen bonds: C:Q.198 pi-Cation interactions: C:H.297 Metal complexes: C:H.297 BCL.28: 11 residues within 4Å: Chain F: F.65, V.75, G.78, H.79, L.82, M.275, F.279, H.282 Ligands: BCL.34, BCL.37, F26.40 6 PLIP interactions: 6 interactions with chain F, Hydrophobic interactions: F:V.75, F:F.279, F:F.279, F:H.282 Hydrogen bonds: F:G.78 Metal complexes: F:H.79 BCL.29: 15 residues within 4Å: Chain F: I.269, H.270, S.280, V.281, T.284, Y.288, V.388, G.391, Y.394, W.411, K.414, G.415, L.497 Ligands: BCL.34, F39.41 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:V.281, F:V.281, F:V.388, F:W.411, F:W.411, F:W.411, F:W.411, F:K.414, F:L.497 Hydrogen bonds: F:H.270 Salt bridges: F:H.270 pi-Stacking: F:W.411 BCL.30: 19 residues within 4Å: Chain F: L.83, L.86, M.90, Y.94, I.117, R.120, M.121, W.146, F.149, H.150, V.153, L.216, F.217, W.220, V.223 Ligands: BCL.32, BCL.33, BCL.34, BCL.36 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:L.86, F:W.146, F:V.153, F:F.217, F:W.220, F:W.220, F:V.223 Salt bridges: F:R.120 Metal complexes: F:H.150 BCL.31: 15 residues within 4Å: Chain F: L.80, F.159, G.160, R.163, H.164, N.168, L.169, T.170, N.171, P.172, R.176, F.180, F.183, Y.212 Ligands: BCL.32 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:L.80, F:L.80, F:L.169, F:L.169, F:F.180, F:F.183 Hydrogen bonds: F:T.170 Salt bridges: F:R.163 pi-Stacking: F:H.164 BCL.32: 17 residues within 4Å: Chain F: D.72, V.75, V.76, H.79, L.80, L.83, F.180, F.183, S.198, A.199, K.200, P.208, H.209, Y.212 Ligands: BCL.30, BCL.31, F26.40 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:V.75, F:V.76, F:L.83, F:F.180, F:F.183, F:A.199, F:Y.212 Salt bridges: F:H.79 pi-Stacking: F:F.180, F:Y.212 pi-Cation interactions: F:H.209 Metal complexes: F:H.209 BCL.33: 14 residues within 4Å: Chain F: R.120, T.238, I.239, S.241, E.242, M.245, S.246, F.249, F.306, Y.309, Y.310 Ligands: BCL.30, BCL.36, F39.41 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:R.120, F:E.242, F:F.306, F:F.306, F:F.306, F:Y.309, F:Y.310 pi-Cation interactions: F:R.120 Metal complexes: F:E.242 BCL.34: 13 residues within 4Å: Chain F: Y.202, A.205, L.206, G.207, H.209, M.213, P.265, H.282, I.286 Ligands: BCL.28, BCL.29, BCL.30, F26.40 8 PLIP interactions: 8 interactions with chain F, Hydrophobic interactions: F:Y.202, F:L.206, F:L.206, F:P.265, F:I.286 Hydrogen bonds: F:H.209 Salt bridges: F:H.282 Metal complexes: F:H.282 BCL.35: 16 residues within 4Å: Chain F: Y.93, F.113, T.116, L.371, F.374, N.375, I.378, C.379, F.679, G.683, F.686, M.687, V.689, F.690 Ligands: BCL.36, BCL.37 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:F.113, F:T.116, F:L.371, F:F.374, F:F.679, F:F.679, F:V.689, F:F.690 Hydrogen bonds: F:Y.93 BCL.36: 15 residues within 4Å: Chain F: L.86, I.89, M.90, I.286, N.290, L.293, N.375, H.376, C.379, Y.383 Ligands: BCL.30, BCL.33, BCL.35, F26.40, F39.41 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:L.86, F:L.86, F:I.89, F:I.286, F:L.293, F:Y.383 Metal complexes: F:H.376 BCL.37: 16 residues within 4Å: Chain F: Y.62, Q.63, I.64, F.65, D.66, K.276, F.279, L.382, Y.383, A.386, Y.389, H.390, Q.393, M.548 Ligands: BCL.28, BCL.35 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:F.279, F:Y.383, F:A.386, F:Y.389 Hydrogen bonds: F:Q.63, F:I.64, F:F.65 Salt bridges: F:K.276 pi-Cation interactions: F:K.276 BCL.38: 12 residues within 4Å: Chain F: L.431, A.434, T.435, S.438, P.467, L.468, F.471, F.475, W.483, A.486, H.487, T.490 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:L.431, F:A.434, F:L.468, F:F.471, F:W.483, F:T.490 Hydrogen bonds: F:L.468 Salt bridges: F:H.487 pi-Stacking: F:W.483 Metal complexes: F:H.487 BCL.39: 12 residues within 4Å: Chain F: W.112, F.113, L.320, Y.321, G.322, H.612, I.616, I.619, M.687, F.690 Chain G: I.453, F.454 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain G, Hydrophobic interactions: F:I.619, F:F.690, G:I.453, G:F.454 Hydrogen bonds: F:W.112, F:F.113, F:Y.321 Salt bridges: F:H.612 pi-Cation interactions: F:H.612 BCL.51: 11 residues within 4Å: Chain G: F.65, V.75, G.78, H.79, L.82, M.275, F.279, H.282 Ligands: BCL.57, BCL.60, F26.63 6 PLIP interactions: 6 interactions with chain G, Hydrophobic interactions: G:V.75, G:F.279, G:F.279, G:H.282 Hydrogen bonds: G:G.78 Metal complexes: G:H.79 BCL.52: 15 residues within 4Å: Chain G: I.269, H.270, S.280, V.281, T.284, Y.288, V.388, G.391, Y.394, W.411, K.414, G.415, L.497 Ligands: BCL.57, F39.64 13 PLIP interactions: 13 interactions with chain G, Hydrophobic interactions: G:V.281, G:V.281, G:T.284, G:V.388, G:W.411, G:W.411, G:W.411, G:W.411, G:K.414, G:L.497 Hydrogen bonds: G:H.270 Salt bridges: G:H.270 pi-Stacking: G:W.411 BCL.53: 19 residues within 4Å: Chain G: L.83, L.86, M.90, Y.94, I.117, R.120, M.121, W.146, F.149, H.150, V.153, L.216, F.217, W.220, V.223 Ligands: BCL.55, BCL.56, BCL.57, BCL.59 10 PLIP interactions: 10 interactions with chain G, Hydrophobic interactions: G:L.86, G:W.146, G:V.153, G:F.217, G:W.220, G:W.220, G:V.223 Hydrogen bonds: G:Y.94 Salt bridges: G:R.120 Metal complexes: G:H.150 BCL.54: 15 residues within 4Å: Chain G: L.80, F.159, G.160, R.163, H.164, N.168, L.169, T.170, N.171, P.172, R.176, F.180, F.183, Y.212 Ligands: BCL.55 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:L.80, G:L.80, G:L.169, G:L.169, G:F.180, G:F.183 Hydrogen bonds: G:T.170 Salt bridges: G:R.163 pi-Stacking: G:H.164 BCL.55: 17 residues within 4Å: Chain G: D.72, V.75, V.76, H.79, L.80, L.83, F.180, F.183, S.198, A.199, K.200, P.208, H.209, Y.212 Ligands: BCL.53, BCL.54, F26.63 13 PLIP interactions: 13 interactions with chain G, Hydrophobic interactions: G:V.75, G:V.76, G:L.83, G:F.180, G:F.183, G:A.199, G:Y.212 Hydrogen bonds: G:H.79 Salt bridges: G:H.79 pi-Stacking: G:F.180, G:Y.212 pi-Cation interactions: G:H.209 Metal complexes: G:H.209 BCL.56: 14 residues within 4Å: Chain G: R.120, T.238, I.239, S.241, E.242, M.245, S.246, F.249, F.306, Y.309, Y.310 Ligands: BCL.53, BCL.59, F39.64 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:R.120, G:E.242, G:F.306, G:F.306, G:F.306, G:Y.309, G:Y.310 pi-Cation interactions: G:R.120 Metal complexes: G:E.242 BCL.57: 13 residues within 4Å: Chain G: Y.202, A.205, L.206, G.207, H.209, M.213, P.265, H.282, I.286 Ligands: BCL.51, BCL.52, BCL.53, F26.63 8 PLIP interactions: 8 interactions with chain G, Hydrophobic interactions: G:Y.202, G:L.206, G:L.206, G:P.265, G:I.286 Hydrogen bonds: G:H.209 Salt bridges: G:H.282 Metal complexes: G:H.282 BCL.58: 16 residues within 4Å: Chain G: Y.93, F.113, T.116, L.371, F.374, N.375, I.378, C.379, F.679, G.683, F.686, M.687, V.689, F.690 Ligands: BCL.59, BCL.60 8 PLIP interactions: 8 interactions with chain G, Hydrophobic interactions: G:F.113, G:T.116, G:L.371, G:F.374, G:F.679, G:F.679, G:V.689, G:F.690 BCL.59: 15 residues within 4Å: Chain G: L.86, I.89, M.90, I.286, N.290, L.293, N.375, H.376, C.379, Y.383 Ligands: BCL.53, BCL.56, BCL.58, F26.63, F39.64 7 PLIP interactions: 7 interactions with chain G, Hydrophobic interactions: G:L.86, G:L.86, G:I.89, G:I.286, G:L.293, G:Y.383 Metal complexes: G:H.376 BCL.60: 16 residues within 4Å: Chain G: Y.62, Q.63, I.64, F.65, D.66, K.276, F.279, L.382, Y.383, A.386, Y.389, H.390, Q.393, M.548 Ligands: BCL.51, BCL.58 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:F.279, G:Y.383, G:A.386, G:Y.389 Hydrogen bonds: G:Q.63, G:I.64, G:F.65 Salt bridges: G:K.276 pi-Cation interactions: G:K.276 BCL.61: 12 residues within 4Å: Chain G: L.431, A.434, T.435, S.438, P.467, L.468, F.471, F.475, W.483, A.486, H.487, T.490 10 PLIP interactions: 10 interactions with chain G, Hydrophobic interactions: G:L.431, G:A.434, G:L.468, G:F.471, G:W.483, G:T.490 Hydrogen bonds: G:L.468 Salt bridges: G:H.487 pi-Stacking: G:W.483 Metal complexes: G:H.487 BCL.62: 12 residues within 4Å: Chain F: I.453, F.454 Chain G: W.112, F.113, L.320, Y.321, G.322, H.612, I.616, I.619, M.687, F.690 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain F, Hydrophobic interactions: G:I.619, G:F.690, F:F.454 Hydrogen bonds: G:W.112, G:F.113, G:Y.321 Salt bridges: G:H.612 pi-Cation interactions: G:H.612

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

SF4.25: 13 residues within 4Å: Chain E: I.135, C.140, V.141, G.142, C.143, G.144, C.146, C.172, C.191, P.192, S.193, A.195, L.196 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.140, E:C.143, E:C.146, E:C.191 SF4.26: 10 residues within 4Å: Chain E: Y.133, C.150, V.154, I.174, C.179, I.180, S.181, C.182, S.183, C.185 5 PLIP interactions: 5 interactions with chain E, pi-Cation interactions: E:Y.133 Metal complexes: E:C.150, E:C.179, E:C.182, E:C.185 SF4.45: 11 residues within 4Å: Chain F: C.527, G.529, P.530, C.536, E.633, I.670 Chain G: C.527, G.529, C.536, E.633, I.670 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G, Metal complexes: F:C.527, F:C.536, G:C.527, G:C.536

2 x GS0: Bacteriochlorophyll A isomer(Non-covalent)

GS0.27: 18 residues within 4Å: Chain F: V.488, G.492, K.553, S.556, W.560, F.600, L.617, H.621, W.624, Y.681, T.685, L.688, V.689, F.692 Chain G: F.600 Ligands: G2O.46, G2O.48, GS0.50 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:V.488, F:K.553, F:W.560, F:W.560, F:W.624, F:W.624, F:L.688, F:F.692, F:F.692 Hydrogen bonds: F:Y.681 pi-Stacking: F:F.600, F:W.624, F:W.624 Metal complexes: F:H.621 GS0.50: 18 residues within 4Å: Chain F: F.600 Chain G: V.488, G.492, K.553, S.556, W.560, F.600, L.617, H.621, W.624, Y.681, T.685, L.688, V.689, F.692 Ligands: GS0.27, G2O.46, G2O.48 14 PLIP interactions: 14 interactions with chain G, Hydrophobic interactions: G:V.488, G:K.553, G:W.560, G:W.560, G:W.624, G:W.624, G:L.688, G:F.692, G:F.692 Hydrogen bonds: G:T.685 pi-Stacking: G:F.600, G:W.624, G:W.624 Metal complexes: G:H.621

2 x F26: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene(Non-covalent)

F26.40: 10 residues within 4Å: Chain F: H.79, L.82, L.83, L.86, Y.202, H.282 Ligands: BCL.28, BCL.32, BCL.34, BCL.36 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.82, F:L.82, F:L.83, F:L.86, F:Y.202 F26.63: 10 residues within 4Å: Chain G: H.79, L.82, L.83, L.86, Y.202, H.282 Ligands: BCL.51, BCL.55, BCL.57, BCL.59 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:L.82, G:L.82, G:L.83, G:L.86, G:Y.202

2 x F39: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate(Non-covalent)

F39.41: 16 residues within 4Å: Chain F: F.236, Q.237, Y.288, C.295, I.296, V.299, A.300, Q.303, S.305, F.306, H.376, F.505 Ligands: BCL.29, BCL.33, BCL.36, LHG.42 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:Y.288, F:Y.288, F:I.296, F:V.299, F:A.300, F:F.306, F:F.505 Hydrogen bonds: F:Q.237, F:S.305, F:S.305 F39.64: 16 residues within 4Å: Chain G: F.236, Q.237, Y.288, C.295, I.296, V.299, A.300, Q.303, S.305, F.306, H.376, F.505 Ligands: BCL.52, BCL.56, BCL.59, LHG.65 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:Y.288, G:Y.288, G:I.296, G:V.299, G:A.300, G:F.306, G:F.505 Hydrogen bonds: G:Q.237, G:S.305, G:S.305

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

LHG.42: 6 residues within 4Å: Chain F: V.299, W.473, M.474, S.493 Ligands: F39.41, LMG.43 No protein-ligand interaction detected (PLIP) LHG.65: 6 residues within 4Å: Chain G: V.299, W.473, M.474, S.493 Ligands: F39.64, LMG.66 No protein-ligand interaction detected (PLIP)

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

LMG.43: 12 residues within 4Å: Chain F: C.295, F.298, M.474, F.475, A.476, A.486, I.489, T.490, G.554, V.558, Y.561 Ligands: LHG.42 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.298, F:V.558 Hydrogen bonds: F:A.476, F:Y.561, F:Y.561 LMG.66: 12 residues within 4Å: Chain G: C.295, F.298, M.474, F.475, A.476, A.486, I.489, T.490, G.554, V.558, Y.561 Ligands: LHG.65 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.298, G:V.558 Hydrogen bonds: G:A.476, G:Y.561

2 x CA: CALCIUM ION(Non-covalent)

CA.44: 5 residues within 4Å: Chain F: D.563, E.603, F.692, N.695, G.696 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.563, F:E.603, F:F.692, F:G.696 CA.67: 5 residues within 4Å: Chain G: D.563, E.603, F.692, N.695, G.696 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.563, G:E.603, G:F.692, G:G.696

4 x G2O: Chlorophyll A ester(Covalent)(Non-covalent)

G2O.46: 16 residues within 4Å: Chain F: M.618, H.621, L.622, F.625 Chain G: Y.440, V.444, I.448, L.549, W.550, K.553, M.570, F.597, Y.681 Ligands: GS0.27, G2O.47, GS0.50 10 PLIP interactions: 5 interactions with chain F, 5 interactions with chain G, Hydrophobic interactions: F:L.622, F:F.625, F:F.625, F:F.625, G:Y.440, G:V.444, G:I.448, G:K.553, G:F.597 pi-Stacking: F:F.625 G2O.47: 18 residues within 4Å: Chain F: F.625, F.628, A.629, D.634, S.637, R.638, G.641, Q.645 Chain G: M.429, C.432, F.433, M.436, F.495, I.498, R.502, F.546, W.550 Ligands: G2O.46 11 PLIP interactions: 6 interactions with chain G, 5 interactions with chain F, Hydrophobic interactions: G:F.433, G:F.546, F:F.625, F:F.625, F:F.628, F:A.629, F:D.634 Hydrogen bonds: G:R.502, G:R.502 pi-Stacking: G:W.550, G:W.550 G2O.48: 16 residues within 4Å: Chain F: Y.440, V.444, I.448, L.549, W.550, K.553, M.570, F.597, Y.681 Chain G: M.618, H.621, L.622, F.625 Ligands: GS0.27, G2O.49, GS0.50 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain F, Hydrophobic interactions: G:L.622, G:F.625, G:F.625, G:F.625, F:Y.440, F:V.444, F:I.448, F:K.553, F:F.597 pi-Stacking: G:F.625 G2O.49: 18 residues within 4Å: Chain F: M.429, C.432, F.433, M.436, F.495, I.498, R.502, F.546, W.550 Chain G: F.625, F.628, A.629, D.634, S.637, R.638, G.641, Q.645 Ligands: G2O.48 11 PLIP interactions: 5 interactions with chain G, 6 interactions with chain F, Hydrophobic interactions: G:F.625, G:F.625, G:F.628, G:A.629, G:D.634, F:F.433, F:F.546 Hydrogen bonds: F:R.502, F:R.502 pi-Stacking: F:W.550, F:W.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J.H. et al., Architecture of the photosynthetic complex from a green sulfur bacterium. Science (2020)

Release Date

2020-11-25

Peptides

Bacteriochlorophyll a protein: ABC
P840 reaction center 17 kDa protein: D
Photosystem P840 reaction center iron-sulfur protein: E
Photosystem P840 reaction center, large subunit: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
D

E
B

F
A

G
a

Membrane

We predict this structure to be a membrane protein.
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Bacteriochlorophyll a protein

P840 reaction center 17 kDa protein

Photosystem P840 reaction center iron-sulfur protein

Photosystem P840 reaction center, large subunit

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