SMTL ID : 8hg3.1

Cryo-EM structure of the Lhcp complex from Ostreococcus tauri

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

24 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 24 residues within 4Å: Chain A: G.39, T.40, Y.41, P.42, G.45, E.46, 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 Ligands: CLA.2, Q6L.16, IWJ.19, Q6L.20, CLA.25 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.42, A:I.50, A:F.52, A:N.57, A:R.60, A:H.64, A:R.186, A:M.189, A:F.190, A:L.193 Hydrogen bonds: A:T.40 Salt bridges: A:R.186 pi-Cation interactions: A:R.186 Metal complexes: A:E.61 CLA.2: 16 residues within 4Å: Chain A: N.57, R.60, H.64, W.192, I.196 Chain C: I.49, L.193, F.197 Ligands: CLA.1, CHL.6, KC2.8, Q6L.16, Q6L.21, CLA.24, CLA.56, Q6L.60 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, Hydrophobic interactions: C:I.49, C:L.193, C:F.197, A:I.196 Salt bridges: A:R.60 Metal complexes: A:H.64 CLA.3: 17 residues within 4Å: Chain A: L.70, G.71, T.73, G.74, A.77, A.78, A.89, L.92, V.101, K.104, F.105, P.106 Ligands: CHL.5, CHL.14, Q6L.16, NEX.17, IWJ.18 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:L.70, A:T.73, A:A.78, A:V.101, A:F.105, A:F.105 pi-Stacking: A:F.105 CLA.9: 17 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, K.180, E.181, H.184 Ligands: CHL.7, CLA.11, Q6L.15 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:R.66, A:M.69, A:P.159, A:F.163, A:D.164, A:L.168, A:L.168, A:A.169, A:L.177, A:L.177, A:L.177, A:K.180, A:E.181, A:H.184 Hydrogen bonds: A:G.160 Metal complexes: A:E.181 CLA.10: 11 residues within 4Å: Chain A: I.34, P.36, E.37, E.176, I.179, K.180, K.183, H.184, L.187 Ligands: CLA.11, Q6L.20 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:K.183, A:K.183, A:L.187, A:L.187 Salt bridges: A:K.183 Metal complexes: A:E.37 CLA.11: 9 residues within 4Å: Chain A: T.73, W.76, L.177, K.180, H.184 Ligands: CLA.9, CLA.10, Q6L.15, IWJ.18 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:W.76 Salt bridges: A:K.180 Metal complexes: A:H.184 CLA.12: 19 residues within 4Å: Chain A: 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: CLA.13, Q6L.15, IWJ.19, Q6L.20, Q6L.23 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.190, A:F.190, A:F.197, A:Q.198, A:A.201, A:V.222, A:V.222 Hydrogen bonds: A:V.222, A:N.225 CLA.13: 9 residues within 4Å: Chain A: W.210, H.213, P.217, N.221, V.222, L.223 Ligands: CLA.12, IWJ.19, Q6L.20 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:P.217 Hydrogen bonds: A:N.221 Metal complexes: A:H.213 CLA.24: 26 residues within 4Å: Chain B: Y.35, F.38, G.39, T.40, Y.41, P.42, G.45, E.46, S.47, P.48, I.50, F.52, N.57, A.58, E.61, H.64, R.186, M.189, F.190, I.196 Ligands: CLA.2, CLA.25, CHL.29, Q6L.39, Q6L.42, CLA.47 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.38, B:P.42, B:F.52, B:F.52, B:N.57, B:E.61, B:H.64, B:R.186, B:M.189, B:F.190, B:F.190, B:I.196 Hydrogen bonds: B:T.40 Salt bridges: B:R.186 pi-Cation interactions: B:R.186 Metal complexes: B:E.61 CLA.25: 16 residues within 4Å: Chain A: F.38, I.49, F.190 Chain B: N.57, R.60, H.64, W.192, I.196 Ligands: CLA.1, Q6L.16, Q6L.20, Q6L.23, CLA.24, CHL.29, KC2.31, Q6L.39 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.196, A:F.190 Salt bridges: B:R.60 Metal complexes: B:H.64 CLA.26: 20 residues within 4Å: Chain B: W.67, L.70, G.71, T.73, G.74, A.77, A.78, T.82, I.84, L.92, V.101, K.104, F.105, P.106 Ligands: CHL.27, CHL.28, CHL.37, Q6L.39, NEX.40, IWJ.41 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:W.67, B:L.70, B:T.73, B:A.77, B:V.101, B:F.105, B:F.105, B:P.106 pi-Stacking: B:F.105 CLA.32: 18 residues within 4Å: Chain B: R.66, M.69, L.70, N.158, P.159, G.160, F.163, D.164, L.168, L.174, L.177, K.178, E.181, H.184 Ligands: CHL.30, CLA.34, Q6L.38, IWJ.41 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:R.66, B:L.70, B:F.163, B:L.168, B:L.177, B:K.178, B:H.184 Hydrogen bonds: B:N.158, B:G.160 Metal complexes: B:E.181, B:E.181 CLA.33: 10 residues within 4Å: Chain B: D.33, P.36, E.37, E.176, K.180, K.183, H.184, L.187 Ligands: CLA.34, Q6L.42 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:E.37, B:K.183, B:K.183, B:K.183, B:L.187 Salt bridges: B:K.180, B:K.183 Metal complexes: B:E.37 CLA.34: 8 residues within 4Å: Chain B: L.166, L.177, K.180, H.184 Ligands: CLA.32, CLA.33, Q6L.38, IWJ.41 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:L.166 Hydrogen bonds: B:K.180 Salt bridges: B:K.180, B:K.180 Metal complexes: B:H.184 CLA.35: 20 residues within 4Å: Chain B: 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.22, CLA.36, Q6L.38, Q6L.42, Q6L.45, CLA.47 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:F.190, B:F.190, B:F.190, B:A.191, B:F.197, B:Q.198, B:A.201, B:H.213, B:N.221, B:V.222, B:V.222 Hydrogen bonds: B:N.225 CLA.36: 9 residues within 4Å: Chain B: W.210, H.213, P.217, N.221, V.222, L.223 Ligands: IWJ.22, CLA.35, Q6L.42 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:P.217 Metal complexes: B:H.213 CLA.46: 23 residues within 4Å: Chain C: Y.35, F.38, G.39, T.40, Y.41, P.42, G.45, E.46, S.47, P.48, I.50, P.51, F.52, N.57, A.58, E.61, H.64, R.186, M.189, F.190 Ligands: CLA.47, Q6L.60, Q6L.62 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:F.38, C:F.52, C:F.52, C:H.64, C:M.189, C:F.190 Hydrogen bonds: C:T.40, C:T.40, C:N.57, C:R.186 Salt bridges: C:R.186 pi-Cation interactions: C:R.186 Metal complexes: C:E.61 CLA.47: 16 residues within 4Å: Chain B: I.49, F.190 Chain C: N.57, R.60, H.64, W.192, I.196 Ligands: CLA.24, CLA.35, Q6L.39, Q6L.42, CHL.43, Q6L.45, CLA.46, KC2.52, Q6L.60 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:I.196, B:F.190, B:F.190 Salt bridges: C:R.60 Metal complexes: C:H.64 CLA.48: 18 residues within 4Å: Chain C: W.67, L.70, T.73, G.74, A.77, A.78, T.82, A.89, L.92, V.101, K.104, F.105, P.106 Ligands: CHL.49, CHL.50, CHL.58, Q6L.60, IWJ.61 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:W.67, C:L.70, C:T.73, C:A.77, C:A.78, C:V.101 pi-Stacking: C:F.105 CLA.53: 15 residues within 4Å: Chain C: R.66, M.69, N.158, P.159, G.160, D.164, A.169, L.174, L.177, K.178, E.181, H.184 Ligands: CHL.51, CLA.55, Q6L.59 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:R.66, C:R.66, C:L.177, C:E.181 Hydrogen bonds: C:N.158 Metal complexes: C:E.181 CLA.54: 9 residues within 4Å: Chain C: I.34, P.36, E.37, E.176, K.180, K.183, H.184 Ligands: CLA.55, Q6L.62 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:P.36, C:K.183, C:K.183, C:K.183 Salt bridges: C:K.180, C:K.183 Metal complexes: C:E.37, C:E.37 CLA.55: 5 residues within 4Å: Chain C: K.180, H.184 Ligands: CLA.53, CLA.54, Q6L.59 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:K.180 Hydrogen bonds: C:K.180 Salt bridges: C:K.180 Metal complexes: C:H.184 CLA.56: 21 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, F.230 Ligands: CLA.2, Q6L.21, IWJ.44, CLA.57, Q6L.59, Q6L.62 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:F.190, C:F.197, C:Q.198, C:A.201, C:W.210, C:H.213, C:V.222, C:V.222, C:V.222, C:F.230 Hydrogen bonds: C:V.222, C:N.225 CLA.57: 6 residues within 4Å: Chain C: H.213, P.217, N.221 Ligands: IWJ.44, CLA.56, Q6L.62 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:P.217, C:P.217 Metal complexes: C:H.213

15 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.4: 9 residues within 4Å: Chain A: A.110, P.111, L.112, A.113, P.114, Y.119, P.120 Ligands: CHL.5, CHL.14 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.112, A:A.113, A:P.114 Metal complexes: A:L.112 CHL.5: 14 residues within 4Å: Chain A: A.89, C.93, V.101, L.112, P.120, V.125, I.128, E.129, L.132 Ligands: CLA.3, CHL.4, CHL.6, Q6L.16, NEX.17 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.101, A:L.112, A:P.120, A:V.125, A:V.125, A:L.132 Metal complexes: A:E.129 CHL.6: 21 residues within 4Å: Chain A: W.86, F.87, T.88, G.90, T.91, C.93, F.122, V.125, E.129 Chain C: L.223, A.226, A.227, F.230 Ligands: CLA.2, CHL.5, KC2.8, Q6L.16, IWJ.19, Q6L.21, IWJ.44, Q6L.62 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.86, A:F.122, A:F.122, A:V.125, C:L.223 CHL.7: 19 residues within 4Å: Chain A: I.63, R.66, W.67, A.136, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, V.154, D.156, V.157, P.159, F.163 Ligands: CLA.9, NEX.17, IWJ.18 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:A.136, A:Y.139, A:P.147, A:F.148, A:F.148, A:L.152, A:V.154, A:P.159, A:F.163 CHL.14: 11 residues within 4Å: Chain A: A.77, G.81, F.105, P.106, G.107, A.108, V.109 Ligands: CLA.3, CHL.4, NEX.17, IWJ.18 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:F.105, A:F.105, A:V.109 Metal complexes: A:P.106 CHL.27: 12 residues within 4Å: Chain B: A.110, P.111, L.112, A.113, P.114, Y.119, N.124, V.125, I.128 Ligands: CLA.26, CHL.28, CHL.37 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.110, B:L.112, B:A.113, B:P.114, B:Y.119, B:Y.119, B:Y.119, B:V.125, B:I.128 Metal complexes: B:L.112 CHL.28: 13 residues within 4Å: Chain B: G.90, C.93, V.101, V.125, I.128, E.129, V.133 Ligands: CLA.26, CHL.27, CHL.29, KC2.31, Q6L.39, NEX.40 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:V.101, B:V.125, B:E.129, B:V.133 CHL.29: 19 residues within 4Å: Chain A: L.223, A.226, A.227 Chain B: W.86, F.87, T.88, G.90, T.91, C.93, F.122, E.129 Ligands: IWJ.19, Q6L.20, IWJ.22, Q6L.23, CLA.24, CLA.25, CHL.28, Q6L.39 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:L.223, A:A.226, B:W.86, B:F.87, B:F.122 Hydrogen bonds: A:A.227, B:G.90, B:T.91 CHL.30: 19 residues within 4Å: Chain B: I.63, R.66, W.67, A.136, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, V.154, D.156, V.157, P.159, F.163 Ligands: CLA.32, NEX.40, IWJ.41 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:Y.139, B:Y.139, B:Y.139, B:F.148, B:F.148, B:V.154, B:P.159, B:F.163 Hydrogen bonds: B:R.66 pi-Stacking: B:F.163 pi-Cation interactions: B:R.140 CHL.37: 10 residues within 4Å: Chain B: A.77, G.81, F.105, P.106, G.107, A.108 Ligands: CLA.26, CHL.27, NEX.40, IWJ.41 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.105, B:F.105, B:P.106, B:A.108 Metal complexes: B:P.106 CHL.43: 19 residues within 4Å: Chain B: V.222, L.223, A.226, A.227, F.230 Chain C: W.86, F.87, T.88, G.90, T.91, C.93, E.129 Ligands: IWJ.22, Q6L.42, IWJ.44, Q6L.45, CLA.47, CHL.50, Q6L.60 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:L.223, C:W.86, C:F.87 CHL.49: 6 residues within 4Å: Chain C: L.112, Y.119, P.120, I.128 Ligands: CLA.48, CHL.50 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.112, C:Y.119, C:P.120, C:I.128 Metal complexes: C:L.112 CHL.50: 10 residues within 4Å: Chain C: A.89, C.93, V.101, V.125, I.128, E.129 Ligands: CHL.43, CLA.48, CHL.49, Q6L.60 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:V.101, C:V.125 CHL.51: 15 residues within 4Å: Chain C: I.63, R.66, W.67, L.70, A.136, Y.139, R.140, S.146, P.147, F.148, V.154, P.159, F.163 Ligands: CLA.53, IWJ.61 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:Y.139, C:P.147, C:F.148, C:F.148, C:V.154, C:P.159, C:F.163, C:F.163 Hydrogen bonds: C:R.66 pi-Stacking: C:F.163 pi-Cation interactions: C:R.140 CHL.58: 7 residues within 4Å: Chain C: A.77, N.80, F.105, P.106, G.107 Ligands: CLA.48, IWJ.61 1 PLIP interactions: 1 interactions with chain C, Metal complexes: C:P.106

3 x KC2: Chlorophyll c2(Non-covalent)

KC2.8: 13 residues within 4Å: Chain A: K.56, E.59, R.60, I.63, H.64, W.67, V.133, E.137, R.140, T.141 Ligands: CLA.2, CHL.6, Q6L.21 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:I.63, A:W.67, A:W.67, A:V.133, A:T.141 Hydrogen bonds: A:H.64 Salt bridges: A:K.56, A:R.140 pi-Cation interactions: A:R.140 Metal complexes: A:E.137 KC2.31: 13 residues within 4Å: Chain B: E.59, R.60, I.63, H.64, W.67, V.133, E.137, R.140, T.141, I.143 Ligands: Q6L.23, CLA.25, CHL.28 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:I.63, B:W.67, B:V.133, B:E.137, B:E.137, B:T.141, B:I.143 Hydrogen bonds: B:H.64, B:H.64 Salt bridges: B:K.56, B:R.140 Metal complexes: B:E.137 KC2.52: 14 residues within 4Å: Chain C: K.56, E.59, R.60, I.63, H.64, W.67, V.133, G.134, E.137, R.140, T.141, I.143 Ligands: Q6L.45, CLA.47 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:I.63, C:W.67, C:V.133, C:E.137, C:E.137, C:T.141, C:I.143 Salt bridges: C:K.56, C:R.140 pi-Cation interactions: C:R.140, 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: T.73, W.76, F.163, D.164, P.165, L.166, G.167, L.168, H.184, L.187, S.188, A.191, 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:W.76, A:L.166, A:L.168, A:L.187, A:A.191, A:P.206 Hydrogen bonds: A:D.164, A:D.164, A:L.166, A:G.167, A:W.210 Q6L.16: 21 residues within 4Å: Chain A: F.38, S.47, I.49, I.50, H.64, W.67, A.68, G.71, G.74, A.75, W.86, A.89, M.189, W.192, L.193 Ligands: CLA.1, CLA.2, CLA.3, CHL.5, CHL.6, CLA.25 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.38, A:I.50, A:W.67, A:A.68, A:W.86, A:W.86, A:M.189, A:L.193 Hydrogen bonds: A:S.47 Q6L.20: 20 residues within 4Å: Chain A: Y.35, E.37, F.38, K.183, R.186, L.187, F.190, V.218, N.221, L.223 Chain B: P.95, F.122, L.126 Ligands: CLA.1, CLA.10, CLA.12, CLA.13, IWJ.19, CLA.25, CHL.29 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.122, B:F.122, B:F.122, B:L.126, A:E.37, A:L.187, A:F.190, A:L.223 Hydrogen bonds: A:F.38 Q6L.21: 16 residues within 4Å: Chain A: W.86, F.87, W.192, I.196, A.199, L.200, Q.203 Chain C: F.38, A.226, F.230, Y.233 Ligands: CLA.2, CHL.6, KC2.8, IWJ.44, CLA.56 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.86, A:F.87, A:F.87, A:W.192, A:I.196, A:A.199, A:L.200, A:Q.203, C:F.38, C:F.230 Q6L.23: 16 residues within 4Å: Chain A: F.38, A.226, G.229, Y.233 Chain B: W.86, F.87, W.192, I.196, A.199, L.200 Ligands: CLA.12, IWJ.19, IWJ.22, CLA.25, CHL.29, KC2.31 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.87, B:F.87, B:I.196, B:I.196, B:A.199, B:L.200 Q6L.38: 20 residues within 4Å: Chain B: M.69, V.72, T.73, F.163, D.164, P.165, L.166, G.167, H.184, L.187, S.188, A.191, C.195, Q.198, P.206, W.210 Ligands: CLA.32, CLA.34, CLA.35, IWJ.41 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.191, B:W.210 Hydrogen bonds: B:D.164, B:L.166, B:G.167, B:L.168, B:Q.198, B:P.206 Q6L.39: 20 residues within 4Å: Chain B: S.47, P.48, I.49, I.50, H.64, W.67, A.68, G.71, G.74, W.86, A.89, M.189, W.192, L.193 Ligands: CLA.24, CLA.25, CLA.26, CHL.28, CHL.29, CLA.47 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.49, B:I.50, B:A.68, B:W.86, B:W.86, B:M.189, B:L.193 Hydrogen bonds: B:I.49 Q6L.42: 20 residues within 4Å: Chain B: Y.35, E.37, F.38, K.183, R.186, L.187, F.190, V.218, N.221, L.223 Chain C: P.95, F.122, L.126 Ligands: IWJ.22, CLA.24, CLA.33, CLA.35, CLA.36, CHL.43, CLA.47 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain B Hydrophobic interactions: C:P.95, C:F.122, C:F.122, C:L.126, B:Y.35, B:E.37, B:F.38, B:K.183, B:R.186, B:F.190, B:F.190, B:V.218, B:L.223, B:L.223 Hydrogen bonds: B:F.38, B:F.38, B:V.218, B:N.221 Q6L.45: 16 residues within 4Å: Chain B: F.38, A.226, G.229, F.230, Y.233 Chain C: W.86, W.192, I.196, A.199, L.200, Q.203 Ligands: IWJ.22, CLA.35, CHL.43, CLA.47, KC2.52 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.38, B:F.230, B:Y.233, C:W.86, C:W.192, C:I.196, C:I.196, C:A.199, C:L.200, C:Q.203 Q6L.59: 19 residues within 4Å: Chain C: M.69, V.72, T.73, W.76, F.163, D.164, P.165, L.166, G.167, H.184, L.187, A.191, Q.198, P.206, W.210 Ligands: CLA.53, CLA.55, CLA.56, IWJ.61 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:M.69, C:V.72, C:W.76, C:W.210 Hydrogen bonds: C:D.164, C:L.166, C:G.167, C:Q.198, C:P.206, C:W.210 Q6L.60: 21 residues within 4Å: Chain C: S.47, P.48, I.49, I.50, H.64, W.67, A.68, G.71, G.74, A.75, W.86, A.89, M.189, W.192, L.193 Ligands: CLA.2, CHL.43, CLA.46, CLA.47, CLA.48, CHL.50 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.49, C:I.49, C:I.50, C:W.67, C:A.68, C:M.189, C:W.192, C:W.192, C:L.193 Hydrogen bonds: C:I.49, C:I.50 Q6L.62: 17 residues within 4Å: Chain A: P.95, F.122, L.126 Chain C: Y.35, E.37, F.38, K.183, L.187, F.190, N.221, L.223 Ligands: CHL.6, IWJ.44, CLA.46, CLA.54, CLA.56, CLA.57 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:F.122, A:F.122, C:F.38, C:L.187, C:F.190, C:L.223 Hydrogen bonds: C:E.37, C:E.37, C:F.38

2 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: 12 residues within 4Å: Chain A: W.67, L.70, F.105, L.132, A.135, A.136, P.147, F.148 Ligands: CLA.3, CHL.5, CHL.7, CHL.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.67, A:L.70, A:A.135, A:F.148 NEX.40: 11 residues within 4Å: Chain B: W.67, F.105, L.132, A.135, Y.139, P.147, F.148 Ligands: CLA.26, CHL.28, CHL.30, CHL.37 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.67, B:L.132, B:L.132, B:A.135, B:P.147, B:F.148

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: 12 residues within 4Å: Chain A: T.73, W.76, A.77, N.80, F.148, R.162, F.163 Ligands: CLA.3, CHL.7, CLA.11, CHL.14, Q6L.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.73, A:W.76, A:A.77, A:F.148, A:R.162, A:F.163 Hydrogen bonds: A:N.80 IWJ.19: 17 residues within 4Å: Chain A: F.197, L.200, A.201, V.222, L.223, F.230, F.232 Chain C: Y.233 Ligands: CLA.1, CHL.6, CLA.12, CLA.13, Q6L.20, IWJ.22, Q6L.23, CHL.29, IWJ.44 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.197, A:L.200, A:L.200, A:A.201, A:V.222, A:L.223, A:F.230, A:F.230, A:F.232 IWJ.22: 15 residues within 4Å: Chain A: Y.233 Chain B: L.200, A.201, V.222, F.230, F.232 Ligands: IWJ.19, Q6L.23, CHL.29, CLA.35, CLA.36, Q6L.42, CHL.43, IWJ.44, Q6L.45 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.200, B:L.200, B:A.201, B:V.222, B:V.222, B:F.230, B:F.230 IWJ.41: 14 residues within 4Å: Chain B: L.70, T.73, W.76, A.77, N.80, F.148, R.162, F.163 Ligands: CLA.26, CHL.30, CLA.32, CLA.34, CHL.37, Q6L.38 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.73, B:A.77, B:F.148, B:R.162, B:F.163 Hydrogen bonds: B:W.76, B:R.162 IWJ.44: 14 residues within 4Å: Chain B: Y.233 Chain C: L.200, A.201, V.222, F.230, F.232 Ligands: CHL.6, IWJ.19, Q6L.21, IWJ.22, CHL.43, CLA.56, CLA.57, Q6L.62 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.200, C:L.200, C:A.201, C:V.222, C:F.230, C:F.230, C:F.230, C:F.232 IWJ.61: 11 residues within 4Å: Chain C: T.73, W.76, A.77, N.80, R.162, F.163, P.165 Ligands: CLA.48, CHL.51, CHL.58, Q6L.59 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:T.73, C:W.76, C:W.76, C:A.77, C:F.163, C:F.163, C:P.165 Hydrogen bonds: C:N.80

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

C
U

Membrane

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

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