SMTL ID : 8hg5.1

Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

24 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 25 residues within 4Å: Chain A: F.38, G.39, T.40, Y.41, P.42, G.45, S.47, P.48, I.50, P.51, F.52, N.57, A.58, R.60, E.61, H.64, R.186, M.189, F.190, L.193, F.197 Ligands: CLA.2, Q6L.16, Q6L.41, CLA.46 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.50, A:F.52, A:F.52, A:N.57, A:R.60, A:R.186, A:R.186, A:M.189, A:F.190, A:L.193, A:F.197 Hydrogen bonds: A:T.40 Salt bridges: A:R.186 pi-Cation interactions: A:R.186 Metal complexes: A:E.61 CLA.2: 17 residues within 4Å: Chain A: H.64, I.196 Chain B: V.43, F.183, L.186, M.190 Ligands: CLA.1, CHL.6, KC2.8, Q6L.16, Q6L.19, IWJ.22, CLA.23, CLA.33, Q6L.39, IWJ.43, CLA.46 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.196, B:F.183, B:L.186 Salt bridges: A:R.60 Metal complexes: A:H.64 CLA.3: 19 residues within 4Å: Chain A: L.70, G.71, T.73, G.74, A.77, A.78, T.82, I.84, A.89, V.101, K.104, F.105, P.106 Ligands: CHL.4, CHL.5, CHL.14, Q6L.16, NEX.17, IWJ.18 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:L.70, A:T.73, A:A.78, A:V.101, A:F.105, A:F.105, A:F.105 Hydrogen bonds: A:T.82 CLA.9: 16 residues within 4Å: Chain A: R.66, M.69, N.158, P.159, G.160, F.163, D.164, L.168, A.169, L.177, K.178, E.181 Ligands: CHL.7, CLA.11, Q6L.15, IWJ.18 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:M.69, A:N.158, A:F.163, A:F.163, A:L.168, A:A.169, A:L.177, A:L.177 Hydrogen bonds: A:G.160 pi-Cation interactions: A:R.66 Metal complexes: A:E.181 CLA.10: 8 residues within 4Å: Chain A: D.33, P.36, E.37, K.180, K.183, H.184 Ligands: CLA.11, Q6L.41 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:P.36, A:E.37, A:K.183 Salt bridges: A:K.180, A:K.183 Metal complexes: A:E.37 CLA.11: 8 residues within 4Å: Chain A: L.177, K.180, H.184, L.187 Ligands: CLA.9, CLA.10, Q6L.15, IWJ.18 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.187 Hydrogen bonds: A:K.180 Salt bridges: A:K.180, A:K.180 Metal complexes: A:H.184 CLA.12: 21 residues within 4Å: Chain A: F.190, A.191, G.194, F.197, Q.198, A.201, T.202, N.209, W.210, S.212, H.213, S.220, N.221, V.222, N.225 Ligands: CLA.13, Q6L.15, Q6L.21, IWJ.22, Q6L.41, CLA.46 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.190, A:A.191, A:F.197, A:Q.198, A:A.201, A:V.222 Hydrogen bonds: A:V.222, A:N.225 CLA.13: 9 residues within 4Å: Chain A: W.210, H.213, V.214, P.217, V.218, N.221 Ligands: CLA.12, IWJ.22, Q6L.41 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.210, A:V.214, A:P.217, A:V.218 Hydrogen bonds: A:N.221 Metal complexes: A:H.213 CLA.23: 26 residues within 4Å: Chain B: Y.29, F.32, G.33, T.34, Y.35, P.36, G.39, S.41, P.42, I.44, P.45, F.46, G.47, N.51, A.52, R.54, E.55, H.58, R.179, M.182, F.183, L.186 Ligands: CLA.2, CLA.24, Q6L.37, Q6L.39 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:F.32, B:F.46, B:F.46, B:M.182, B:F.183, B:L.186 Hydrogen bonds: B:T.34, B:G.47, B:N.51, B:R.179 Salt bridges: B:R.179 pi-Cation interactions: B:R.179 Metal complexes: B:E.55 CLA.24: 11 residues within 4Å: Chain B: N.51, R.54, H.58, W.185, I.189 Chain C: I.49 Ligands: CLA.23, KC2.29, Q6L.39, Q6L.44, Q6L.60 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:I.189, C:I.49 Salt bridges: B:R.54 Metal complexes: B:H.58 CLA.25: 20 residues within 4Å: Chain B: L.64, G.65, T.67, G.68, A.71, A.72, T.76, A.83, L.86, V.95, K.98, F.99, P.100, L.106 Ligands: CHL.26, CHL.27, CHL.35, NEX.36, Q6L.39, IWJ.40 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.64, B:V.95, B:K.98, B:F.99, B:F.99 Hydrogen bonds: B:T.76 CLA.30: 18 residues within 4Å: Chain B: R.60, M.63, L.64, T.151, P.152, G.153, F.156, F.161, A.162, L.167, L.170, K.171, E.174, H.177 Ligands: CHL.28, CLA.32, Q6L.38, IWJ.40 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.64, B:F.156, B:F.161, B:A.162, B:L.170 Hydrogen bonds: B:G.153 pi-Cation interactions: B:R.60 Metal complexes: B:E.174 CLA.31: 12 residues within 4Å: Chain B: A.24, D.27, L.28, P.30, E.31, E.169, I.172, K.173, K.176, H.177, L.180 Ligands: CLA.32 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:P.30, B:K.176, B:K.176, B:L.180 Hydrogen bonds: B:H.177 Salt bridges: B:K.173, B:K.176 pi-Cation interactions: B:K.176 Metal complexes: B:E.31 CLA.32: 9 residues within 4Å: Chain B: W.70, L.170, K.173, H.177, L.180 Ligands: CLA.30, CLA.31, Q6L.38, IWJ.40 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:W.70, B:K.173, B:L.180 Salt bridges: B:K.173, B:K.173 Metal complexes: B:H.177 CLA.33: 19 residues within 4Å: Chain B: F.183, A.184, G.187, M.190, Q.191, A.194, T.195, N.202, H.206, A.213, N.214, V.215, N.218 Ligands: CLA.2, Q6L.19, CLA.34, Q6L.37, Q6L.38, IWJ.43 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.183, B:Q.191, B:A.194, B:V.215 Hydrogen bonds: B:V.215, B:N.218 CLA.34: 9 residues within 4Å: Chain B: W.203, H.206, V.207, P.210, N.214, L.216 Ligands: CLA.33, Q6L.37, IWJ.43 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:V.207, B:P.210 Metal complexes: B:H.206 CLA.45: 22 residues within 4Å: Chain C: G.39, T.40, Y.41, P.42, S.47, I.50, P.51, F.52, N.57, A.58, R.60, E.61, H.64, R.186, M.189, F.190, L.193, I.196 Ligands: IWJ.20, CLA.46, Q6L.60, Q6L.63 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:F.52, C:A.58, C:R.60, C:E.61, C:E.61, C:H.64, C:R.186, C:R.186, C:M.189, C:F.190, C:I.196 Hydrogen bonds: C:T.40, C:N.57 Salt bridges: C:R.186 pi-Cation interactions: C:R.186 Metal complexes: C:E.61 CLA.46: 19 residues within 4Å: Chain A: I.49, F.190, L.193, F.197 Chain C: N.57, R.60, H.64, W.192 Ligands: CLA.1, CLA.2, CLA.12, Q6L.16, IWJ.20, Q6L.21, IWJ.22, CLA.45, CHL.50, KC2.52, Q6L.60 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C, Hydrophobic interactions: A:I.49, A:F.190, A:L.193, A:F.197, C:R.60 Salt bridges: C:R.60, C:H.64 Metal complexes: C:H.64 CLA.47: 18 residues within 4Å: Chain C: L.70, G.71, T.73, G.74, A.77, T.82, I.84, A.89, V.101, K.104, F.105, P.106 Ligands: CHL.48, CHL.49, CHL.58, Q6L.60, NEX.61, IWJ.62 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.70, C:T.73, C:A.77, C:V.101, C:F.105, C:F.105 CLA.53: 19 residues within 4Å: Chain C: R.66, M.69, L.70, N.158, P.159, G.160, F.163, D.164, L.168, A.169, L.174, L.177, K.178, E.181, H.184 Ligands: CHL.51, CLA.55, Q6L.59, IWJ.62 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.70, C:F.163, C:L.168, C:L.177, C:E.181 Hydrogen bonds: C:G.160 Salt bridges: C:K.178 pi-Cation interactions: C:R.66 Metal complexes: C:E.181, C:E.181 CLA.54: 8 residues within 4Å: Chain C: P.36, E.37, K.180, K.183, H.184, L.187 Ligands: CLA.55, Q6L.63 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:E.37, C:K.183, C:K.183, C:L.187, C:L.187 Salt bridges: C:K.180, C:K.183 Metal complexes: C:E.37 CLA.55: 7 residues within 4Å: Chain C: L.177, K.180, H.184, L.187 Ligands: CLA.53, CLA.54, Q6L.59 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.177, C:L.187 Hydrogen bonds: C:K.180 Salt bridges: C:K.180, C:K.180 Metal complexes: C:H.184 CLA.56: 19 residues within 4Å: Chain C: F.190, A.191, G.194, F.197, Q.198, A.201, T.202, N.209, W.210, H.213, S.220, N.221, V.222, N.225 Ligands: IWJ.20, Q6L.44, CLA.57, Q6L.59, Q6L.63 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:F.190, C:F.190, C:A.191, C:F.197, C:Q.198, C:A.201, C:V.222, C:V.222 Hydrogen bonds: C:N.225 Salt bridges: C:H.213 CLA.57: 8 residues within 4Å: Chain C: W.210, H.213, P.217, N.221, L.223 Ligands: IWJ.20, CLA.56, Q6L.63 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:W.210, C:P.217 Metal complexes: C:H.213

15 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.4: 10 residues within 4Å: Chain A: A.110, P.111, L.112, P.114, Y.119, N.124, I.128 Ligands: CLA.3, CHL.5, CHL.14 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:P.114, A:Y.119, A:I.128 Metal complexes: A:L.112 CHL.5: 14 residues within 4Å: Chain A: A.89, G.90, C.93, V.101, V.125, I.128, E.129, L.132, V.133 Ligands: CLA.3, CHL.4, CHL.6, Q6L.16, NEX.17 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.125, A:V.125, A:E.129, A:V.133 CHL.6: 19 residues within 4Å: Chain A: W.86, F.87, G.90, T.91, C.93, F.122, L.126, E.129 Chain B: V.215, L.216, A.219, A.220, F.223 Ligands: CLA.2, CHL.5, Q6L.19, IWJ.22, Q6L.37, IWJ.43 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.86, A:L.126, B:L.216, B:L.216, B:A.219 Hydrogen bonds: A:G.90, A:T.91 CHL.7: 20 residues within 4Å: Chain A: R.66, W.67, L.70, A.136, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, V.154, D.156, V.157, N.158, P.159, F.163 Ligands: CLA.9, NEX.17, IWJ.18 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:Y.139, A:Y.139, A:P.147, A:F.148, A:F.148, A:L.152, A:V.154, A:F.163 Hydrogen bonds: A:R.66 pi-Cation interactions: A:R.140 CHL.14: 9 residues within 4Å: Chain A: A.77, F.105, P.106, G.107, V.109 Ligands: CLA.3, CHL.4, NEX.17, IWJ.18 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.105 Metal complexes: A:P.106 CHL.26: 12 residues within 4Å: Chain B: A.104, P.105, L.106, P.108, G.112, Y.113, P.114, V.119, I.122 Ligands: CLA.25, CHL.27, CHL.35 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:A.104, B:L.106, B:L.106, B:P.108, B:P.114, B:P.114, B:V.119, B:I.122 Metal complexes: B:L.106 CHL.27: 14 residues within 4Å: Chain B: A.83, G.84, C.87, V.95, L.106, V.119, E.123, V.127 Ligands: CLA.25, CHL.26, NEX.36, Q6L.39, IWJ.40, CHL.42 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:V.95, B:V.119, B:V.119, B:E.123, B:V.127 Metal complexes: B:E.123 CHL.28: 17 residues within 4Å: Chain B: R.60, W.61, A.130, Y.133, R.134, N.140, P.141, F.142, L.145, T.146, D.149, V.150, P.152, F.156 Ligands: CLA.30, NEX.36, IWJ.40 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:Y.133, B:F.142, B:L.145, B:P.152, B:F.156 Hydrogen bonds: B:R.60, B:F.142 pi-Cation interactions: B:R.134 CHL.35: 11 residues within 4Å: Chain B: A.71, N.74, F.99, P.100, G.101, A.102, V.103 Ligands: CLA.25, CHL.26, NEX.36, IWJ.40 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.99, B:F.99, B:V.103 Hydrogen bonds: B:V.103 Metal complexes: B:P.100 CHL.42: 19 residues within 4Å: Chain B: W.80, F.81, T.82, G.84, T.85, C.87, T.88, F.116, E.123 Chain C: V.222, L.223, A.226, A.227, F.230 Ligands: IWJ.20, CHL.27, Q6L.39, Q6L.44, Q6L.63 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:W.80, B:F.81, B:F.116, C:L.223, C:A.226 Hydrogen bonds: B:T.85, C:A.227 CHL.48: 12 residues within 4Å: Chain C: A.110, P.111, L.112, A.113, P.114, Y.119, P.120, N.124, V.125 Ligands: CLA.47, CHL.49, CHL.58 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.110, C:L.112, C:L.112, C:P.114, C:P.114, C:Y.119, C:Y.119, C:Y.119, C:P.120, C:P.120, C:V.125 Hydrogen bonds: C:S.121 Metal complexes: C:L.112 CHL.49: 12 residues within 4Å: Chain C: A.89, C.93, V.101, V.125, I.128, E.129, L.132 Ligands: CLA.47, CHL.48, CHL.50, Q6L.60, NEX.61 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:V.101, C:V.125 CHL.50: 20 residues within 4Å: Chain A: V.222, L.223, A.226, A.227, F.230 Chain C: W.86, F.87, T.88, G.90, T.91, C.93, F.122, L.126 Ligands: IWJ.20, Q6L.21, IWJ.22, Q6L.41, CLA.46, CHL.49, Q6L.60 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C, Hydrophobic interactions: A:L.223, A:L.223, A:L.223, A:A.226, C:W.86, C:F.122, C:L.126 Hydrogen bonds: C:G.90, C:T.91 CHL.51: 17 residues within 4Å: Chain C: R.66, W.67, A.136, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, D.156, V.157, P.159, F.163 Ligands: CLA.53, NEX.61, IWJ.62 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:A.136, C:Y.139, C:Y.139, C:P.147, C:F.148, C:L.152, C:P.159, C:P.159, C:F.163 Hydrogen bonds: C:R.66 pi-Cation interactions: C:R.140 CHL.58: 10 residues within 4Å: Chain C: A.77, N.80, F.105, P.106, G.107, A.108 Ligands: CLA.47, CHL.48, NEX.61, IWJ.62 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:P.106 Metal complexes: C:P.106

3 x KC2: Chlorophyll c2(Non-covalent)

KC2.8: 12 residues within 4Å: Chain A: R.60, I.63, H.64, W.67, V.133, G.134, E.137, R.140, T.141, I.143 Ligands: CLA.2, Q6L.19 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.63, A:W.67, A:E.137, A:E.137, A:T.141, A:I.143 Hydrogen bonds: A:T.141 Salt bridges: A:K.56, A:R.140 pi-Cation interactions: A:R.140, A:R.140 Metal complexes: A:E.137 KC2.29: 15 residues within 4Å: Chain B: K.50, E.53, R.54, I.57, H.58, W.61, V.127, G.128, E.131, C.132, R.134, T.135 Ligands: CLA.24, Q6L.39, Q6L.44 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:I.57, B:W.61, B:V.127, B:E.131, B:E.131 Salt bridges: B:K.50, B:R.54, B:R.134 pi-Cation interactions: B:R.134 Metal complexes: B:E.131 KC2.52: 11 residues within 4Å: Chain C: K.56, E.59, R.60, I.63, W.67, V.133, E.137, R.140, T.141 Ligands: Q6L.21, CLA.46 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:I.63, C:W.67, C:W.67, C:W.67, C:V.133, C:E.137, C:T.141 Hydrogen bonds: C:T.141 Salt bridges: C:K.56, C:R.140 pi-Cation interactions: C:R.140 Metal complexes: C:E.137

12 x Q6L: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol(Non-covalent)

Q6L.15: 20 residues within 4Å: Chain A: M.69, V.72, T.73, F.163, D.164, L.166, L.168, H.184, L.187, S.188, A.191, C.195, Q.198, P.206, I.207, W.210 Ligands: CLA.9, CLA.11, CLA.12, IWJ.18 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.69, A:D.164, A:L.187, A:L.187, A:L.187, A:A.191, A:W.210 Hydrogen bonds: A:L.166, A:L.166, A:Q.198, A:P.206 Q6L.16: 18 residues within 4Å: Chain A: F.38, S.47, P.48, I.49, H.64, W.67, A.68, G.71, W.86, A.89, M.189, W.192, L.193 Ligands: CLA.1, CLA.2, CLA.3, CHL.5, CLA.46 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.38, A:I.49, A:I.49, A:W.67, A:W.192, A:L.193 Hydrogen bonds: A:I.49 Q6L.19: 16 residues within 4Å: Chain A: W.86, F.87, I.196, A.199, L.200 Chain B: F.32, A.219, G.222, F.223, Y.226 Ligands: CLA.2, CHL.6, KC2.8, IWJ.22, CLA.33, IWJ.43 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.86, A:F.87, A:F.87, A:I.196, A:I.196, A:A.199, A:L.200, B:F.32, B:F.32, B:F.223, B:Y.226, B:Y.226 Q6L.21: 16 residues within 4Å: Chain A: F.38, A.226, G.229, F.230, Y.233 Chain C: W.86, F.87, W.192, I.196, A.199, L.200 Ligands: CLA.12, IWJ.22, CLA.46, CHL.50, KC2.52 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.87, C:F.87, C:W.192, C:I.196, C:A.199, C:L.200, A:A.226, A:F.230, A:F.230, A:Y.233, A:Y.233 Q6L.37: 20 residues within 4Å: Chain A: P.95, F.122, W.123, L.126, I.130 Chain B: Y.29, E.31, F.32, K.176, R.179, L.180, F.183, I.211, N.214, L.216 Ligands: CHL.6, CLA.23, CLA.33, CLA.34, IWJ.43 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.31, B:K.176, B:R.179, B:L.180, B:F.183, B:F.183, B:I.211, B:L.216, A:F.122, A:F.122, A:L.126, A:I.130 Hydrogen bonds: B:I.211 Q6L.38: 22 residues within 4Å: Chain B: M.63, V.66, T.67, W.70, F.156, D.157, P.158, L.159, G.160, H.177, L.180, A.181, A.184, C.188, Q.191, P.199, I.200, W.203 Ligands: CLA.30, CLA.32, CLA.33, IWJ.40 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:M.63, B:W.70, B:D.157, B:L.159, B:L.180, B:L.180, B:A.181, B:A.184, B:P.199, B:I.200 Hydrogen bonds: B:D.157, B:L.159, B:G.160, B:F.161, B:Q.191 Q6L.39: 22 residues within 4Å: Chain B: S.41, P.42, V.43, I.44, H.58, W.61, A.62, G.65, G.68, A.69, W.80, A.83, M.182, W.185, L.186 Ligands: CLA.2, CLA.23, CLA.24, CLA.25, CHL.27, KC2.29, CHL.42 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.43, B:I.44, B:W.61, B:W.61, B:A.62, B:W.80, B:W.80, B:W.185, B:W.185, B:L.186 Hydrogen bonds: B:S.41, B:V.43, B:I.44 Q6L.41: 21 residues within 4Å: Chain A: Y.35, E.37, F.38, K.183, R.186, L.187, F.190, P.217, V.218, N.221, L.223 Chain C: P.95, F.122, W.123, L.126 Ligands: CLA.1, CLA.10, CLA.12, CLA.13, IWJ.22, CHL.50 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:P.95, C:F.122, C:F.122, C:F.122, C:L.126, A:Y.35, A:E.37, A:R.186, A:L.187, A:F.190, A:V.218, A:L.223 Hydrogen bonds: A:V.218 Q6L.44: 15 residues within 4Å: Chain B: W.80, F.81, I.189, A.192, L.193 Chain C: F.38, I.49, A.226, F.230, Y.233 Ligands: IWJ.20, CLA.24, KC2.29, CHL.42, CLA.56 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.38, C:A.226, C:F.230, C:Y.233, C:Y.233, B:F.81, B:F.81, B:I.189, B:I.189, B:A.192, B:L.193 Q6L.59: 17 residues within 4Å: Chain C: V.72, T.73, F.163, D.164, P.165, L.166, H.184, S.188, A.191, Q.198, P.206, N.209, W.210 Ligands: CLA.53, CLA.55, CLA.56, IWJ.62 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.72, C:T.73, C:L.166, C:A.191, C:P.206 Hydrogen bonds: C:F.163, C:Q.198, C:P.206, C:W.210 Q6L.60: 19 residues within 4Å: Chain C: S.47, P.48, I.49, I.50, H.64, W.67, A.68, G.71, W.86, A.89, M.189, W.192, L.193 Ligands: CLA.24, CLA.45, CLA.46, CLA.47, CHL.49, CHL.50 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.49, C:I.50, C:W.67, C:W.67, C:A.68, C:W.192, C:W.192, C:L.193 Hydrogen bonds: C:I.49, C:I.50 Q6L.63: 20 residues within 4Å: Chain B: T.88, P.89, F.116, W.117, L.120 Chain C: Y.35, E.37, G.39, K.183, L.187, F.190, V.218, N.221, L.223 Ligands: IWJ.20, CHL.42, CLA.45, CLA.54, CLA.56, CLA.57 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.37, C:E.37, C:K.183, C:L.187, C:F.190, C:F.190, C:L.223, B:F.116, B:F.116, B:W.117 Hydrogen bonds: C:Y.35, C:F.38, C:G.39

3 x NEX: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL(Non-covalent)

NEX.17: 10 residues within 4Å: Chain A: W.67, L.70, L.132, A.135, P.147 Ligands: CLA.3, CHL.5, CHL.7, CHL.14, IWJ.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.67, A:L.70, A:L.132, A:L.132, A:A.135 NEX.36: 12 residues within 4Å: Chain B: W.61, L.126, S.129, A.130, Y.133, P.141, F.142 Ligands: CLA.25, CHL.27, CHL.28, CHL.35, IWJ.40 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.61, B:L.126, B:L.126, B:Y.133, B:P.141, B:F.142 NEX.61: 9 residues within 4Å: Chain C: L.132, A.135, A.136, P.147 Ligands: CLA.47, CHL.49, CHL.51, CHL.58, IWJ.62 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.132, C:L.132, C:A.135, C:P.147

6 x IWJ: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one(Non-covalent)

IWJ.18: 15 residues within 4Å: Chain A: T.73, W.76, A.77, N.80, F.148, R.162, F.163, P.165 Ligands: CLA.3, CHL.7, CLA.9, CLA.11, CHL.14, Q6L.15, NEX.17 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.73, A:W.76, A:W.76, A:F.148, A:F.148, A:R.162, A:F.163 Hydrogen bonds: A:W.76, A:N.80 IWJ.20: 17 residues within 4Å: Chain A: Y.233 Chain C: F.197, L.200, A.201, V.222, F.230, F.232 Ligands: IWJ.22, CHL.42, IWJ.43, Q6L.44, CLA.45, CLA.46, CHL.50, CLA.56, CLA.57, Q6L.63 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Y.233, C:L.200, C:L.200, C:L.200, C:A.201, C:V.222, C:F.230, C:F.230 IWJ.22: 18 residues within 4Å: Chain A: F.197, L.200, A.201, V.222, F.230, F.232 Chain B: Y.226 Ligands: CLA.2, CHL.6, CLA.12, CLA.13, Q6L.19, IWJ.20, Q6L.21, Q6L.41, IWJ.43, CLA.46, CHL.50 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.197, A:L.200, A:L.200, A:L.200, A:A.201, A:F.230, A:F.230, A:F.230, A:F.232, A:F.232 IWJ.40: 13 residues within 4Å: Chain B: W.70, N.74, R.155, F.156, P.158 Ligands: CLA.25, CHL.27, CHL.28, CLA.30, CLA.32, CHL.35, NEX.36, Q6L.38 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.70, B:W.70 Hydrogen bonds: B:W.70, B:N.74 IWJ.43: 16 residues within 4Å: Chain B: M.190, L.193, A.194, V.215, F.223, F.225 Chain C: F.197, Y.233 Ligands: CLA.2, CHL.6, Q6L.19, IWJ.20, IWJ.22, CLA.33, CLA.34, Q6L.37 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:F.197, C:Y.233, B:L.193, B:L.193, B:L.193, B:A.194, B:F.223, B:F.225, B:F.225 IWJ.62: 13 residues within 4Å: Chain C: T.73, W.76, N.80, F.148, R.162, F.163, P.165 Ligands: CLA.47, CHL.51, CLA.53, CHL.58, Q6L.59, NEX.61 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.162, C:F.163 Hydrogen bonds: C:W.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishii, A. et al., The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers. Elife (2023)

Release Date

2023-04-26

Peptides

Chlorophyll a-b binding protein, chloroplastic: AC
Chlorophyll a-b binding protein, chloroplastic: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

C
R

B
Q

Membrane

We predict this structure to be a membrane protein.
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Chlorophyll a-b binding protein, chloroplastic

Chlorophyll a-b binding protein, chloroplastic

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