SMTL ID : 7e0i.1

LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardti

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

18 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.1: 16 residues within 4Å: Chain A: A.46, K.47, W.48, L.49, G.50, P.51, Y.52, Y.69, W.71 Chain C: Q.148, G.153 Ligands: CLA.2, LHG.19, CHL.46, CHL.48, XAT.56 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:A.46, A:W.48, A:W.48, A:L.49, A:P.51, A:Y.52, A:Y.69, A:Y.69, A:W.71, A:W.71 Metal complexes: A:W.48 CHL.5: 10 residues within 4Å: Chain A: S.142, L.143, V.144, H.145, A.146, Q.147, N.148, T.152 Ligands: CLA.4, CHL.6 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:V.144, A:H.145, A:A.146, A:Q.147 Hydrogen bonds: A:Q.147, A:N.148 Metal complexes: A:V.144 CHL.6: 17 residues within 4Å: Chain A: W.96, G.126, L.135, V.144, A.146, I.149, T.152, V.155, Q.156, L.159, M.160 Ligands: CLA.4, CHL.5, CHL.7, CHL.9, LUT.16, NEX.18 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.96, A:L.135, A:L.135, A:V.144, A:A.146, A:I.149 CHL.7: 22 residues within 4Å: Chain A: W.122, F.123, K.124, A.125, G.126, A.127, F.130, L.153, Q.156, F.220 Chain B: F.259, A.262, Q.263, F.265, T.266, P.267 Ligands: CLA.3, CHL.6, CHL.9, LUT.16, XAT.17, CHL.20 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.122, A:F.123, A:F.130, A:L.153, A:F.220, B:F.259, B:F.259, B:F.259 Hydrogen bonds: A:G.126, A:Q.156 CHL.8: 16 residues within 4Å: Chain A: I.92, R.95, W.96, V.163, Y.166, R.167, G.170, G.171, P.172, A.173, G.174, P.179, P.182, F.186 Ligands: CLA.10, NEX.18 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.163, A:V.163, A:R.167, A:P.172, A:P.182, A:F.186 Hydrogen bonds: A:R.95, A:A.173, A:G.174 pi-Cation interactions: A:R.167 CHL.9: 21 residues within 4Å: Chain A: E.88, L.89, I.92, H.93, W.96, Q.156, V.157, M.160, G.161, E.164, R.167 Chain B: W.60, L.61, W.82, S.84 Ligands: CLA.3, CHL.6, CHL.7, CHL.20, CLA.21, LUT.35 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:L.89, A:I.92, A:W.96, A:W.96, A:V.157, B:W.60, B:L.61 Hydrogen bonds: A:H.93, A:Q.156, B:S.84 Salt bridges: A:R.167 pi-Cation interactions: A:R.167, A:R.167 Metal complexes: A:E.164 CHL.20: 17 residues within 4Å: Chain A: Q.156, G.161 Chain B: G.58, L.59, W.60, L.61, G.62, P.63, L.64, Y.80, W.82, F.226 Ligands: CHL.7, CHL.9, XAT.17, CLA.21, LHG.38 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:L.64, B:Y.80, B:Y.80, B:W.82, B:W.82 Metal complexes: B:W.60 CHL.24: 11 residues within 4Å: Chain B: P.152, G.153, L.154, V.155, H.156, A.157, Q.158, S.159, V.166 Ligands: CHL.25, LMG.39 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.155, B:V.155, B:H.156, B:A.157, B:Q.158, B:V.166 Hydrogen bonds: B:Q.158, B:S.159 Metal complexes: B:V.155 CHL.25: 17 residues within 4Å: Chain B: W.107, G.137, L.146, V.155, A.157, I.160, T.163, V.166, Q.167, L.170, M.171 Ligands: CLA.23, CHL.24, CHL.26, CHL.28, LUT.35, NEX.37 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:W.107, B:V.155, B:A.157, B:I.160, B:L.170 CHL.26: 21 residues within 4Å: Chain B: W.133, F.134, K.135, G.137, A.138, F.141, I.160, L.164, Q.167 Chain C: F.239, A.242, T.243, F.245, T.246, P.247 Ligands: CLA.22, CHL.25, CHL.28, LUT.35, XAT.36, CHL.40 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:W.133, B:F.141, B:L.164, C:F.239, C:F.239, C:A.242 Hydrogen bonds: B:G.137, B:A.138, B:Q.167 CHL.27: 20 residues within 4Å: Chain B: I.103, R.106, W.107, L.110, I.174, Y.177, R.178, G.181, G.182, P.183, A.184, G.185, K.190, L.191, P.193, F.197, F.198 Ligands: CLA.29, LUT.34, NEX.37 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:I.174, B:I.174, B:P.193, B:F.198 Hydrogen bonds: B:R.106, B:A.184 CHL.28: 21 residues within 4Å: Chain B: E.99, L.100, I.103, H.104, W.107, Q.167, V.168, M.171, G.172, E.175, R.178, V.179 Chain C: L.41, W.63, T.65 Ligands: CLA.22, CHL.25, CHL.26, CHL.40, CLA.41, LUT.55 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:L.100, B:I.103, B:W.107, B:V.168, B:V.179, C:L.41, C:T.65 Hydrogen bonds: B:H.104, B:Q.167, C:T.65 Salt bridges: B:R.178 pi-Cation interactions: B:R.178 Metal complexes: B:E.175 CHL.40: 18 residues within 4Å: Chain B: L.164, Q.167, G.172 Chain C: P.38, K.39, F.40, L.41, G.42, P.43, F.44, Y.61, W.63, F.206 Ligands: CHL.26, CHL.28, XAT.36, CLA.41, LHG.58 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:P.38, C:F.40, C:F.44, C:F.44, C:W.63, B:L.164 Metal complexes: C:F.40 CHL.44: 8 residues within 4Å: Chain C: N.134, L.135, I.136, H.137, Q.139, S.140, T.144 Ligands: CHL.45 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:T.144 Hydrogen bonds: C:Q.139, C:S.140 Metal complexes: C:I.136 CHL.45: 17 residues within 4Å: Chain C: W.88, G.118, I.121, L.127, I.136, A.138, I.141, F.147, Q.148, V.151, M.152 Ligands: CLA.43, CHL.44, CHL.46, CHL.48, LUT.55, NEX.57 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:W.88, C:I.121, C:L.127, C:L.127, C:I.136, C:A.138, C:I.141, C:Q.148, C:V.151 CHL.46: 22 residues within 4Å: Chain A: F.247, A.250, T.251, F.253, T.254 Chain C: W.114, F.115, K.116, A.117, G.118, A.119, F.122, I.141, L.145, F.212 Ligands: CHL.1, LHG.19, CLA.42, CHL.45, CHL.48, LUT.55, XAT.56 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C, Hydrophobic interactions: A:F.247, A:F.247, C:W.114, C:F.115, C:F.122, C:I.141, C:L.145, C:F.212 Hydrogen bonds: C:G.118, C:A.119 CHL.47: 19 residues within 4Å: Chain C: I.84, R.87, W.88, L.91, A.155, E.156, Y.158, R.159, G.162, G.163, P.164, L.165, G.166, P.171, L.172, P.174, F.178 Ligands: CLA.49, NEX.57 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:A.155, C:Y.158, C:P.164, C:P.174, C:F.178 Hydrogen bonds: C:R.87, C:L.165, C:G.166 pi-Stacking: C:F.178, C:F.178 pi-Cation interactions: C:R.159 CHL.48: 21 residues within 4Å: Chain A: W.48, W.71, T.73 Chain C: E.80, L.81, I.84, H.85, W.88, Q.148, M.152, G.153, E.156, R.159, F.209 Ligands: CHL.1, LUT.16, CLA.41, CLA.42, CHL.45, CHL.46, XAT.56 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:I.84, C:W.88, C:W.88, C:W.88, C:F.209, A:W.48, A:T.73 Hydrogen bonds: C:Q.148 Salt bridges: C:R.159 pi-Cation interactions: C:R.159 Metal complexes: C:E.156

24 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.2: 23 residues within 4Å: Chain A: L.61, P.66, G.67, D.68, Y.69, G.70, W.71, D.72, L.76, S.77, F.83, Y.86, R.87, L.89, E.90, H.93, R.210, M.213 Ligands: CHL.1, CLA.3, LUT.16, LHG.19, CLA.42 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Y.69, A:W.71, A:L.76, A:Y.86, A:Y.86, A:L.89, A:R.210, A:M.213 Hydrogen bonds: A:Y.69, A:G.70, A:W.71, A:L.76, A:S.77 Salt bridges: A:R.210 Metal complexes: A:E.90 CLA.3: 13 residues within 4Å: Chain A: Y.86, L.89, H.93, F.220 Chain B: A.85, L.87 Ligands: CLA.2, CHL.7, CHL.9, LUT.16, CLA.21, LUT.35, CLA.42 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:Y.86, A:L.89, A:F.220 Hydrogen bonds: A:Y.86 Metal complexes: A:H.93 CLA.4: 18 residues within 4Å: Chain A: W.96, L.99, L.102, G.103, T.106, P.107, F.117, E.119, Q.128, L.135, D.136, Y.137, L.138, V.144 Ligands: CHL.5, CHL.6, LUT.16, NEX.18 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:W.96, A:L.99, A:L.99, A:L.102, A:F.117, A:L.135, A:Y.137, A:L.138 Hydrogen bonds: A:Q.128 pi-Stacking: A:Y.137 CLA.10: 14 residues within 4Å: Chain A: R.95, M.98, Y.181, P.182, G.183, F.186, L.191, F.198, L.201, K.202, E.205 Ligands: CHL.8, CLA.12, LUT.15 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:R.95, A:F.186, A:F.198, A:K.202, A:E.205 Hydrogen bonds: A:G.183 Metal complexes: A:E.205 CLA.11: 9 residues within 4Å: Chain A: E.39, F.40, K.204, K.207, N.208, L.211 Ligands: CLA.12, LHG.19, XAT.56 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.40, A:K.207, A:L.211 Hydrogen bonds: A:N.208 Salt bridges: A:K.207 pi-Cation interactions: A:K.207, A:K.207 CLA.12: 7 residues within 4Å: Chain A: L.102, L.201, K.204, N.208 Ligands: CLA.10, CLA.11, LUT.15 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.102, A:L.201, A:K.204, A:K.204 CLA.13: 16 residues within 4Å: Chain A: F.214, F.217, G.218, V.221, Q.222, T.226, N.233, L.234, H.237, N.244, N.245, A.246 Ligands: CLA.14, LUT.15, LHG.19, XAT.56 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.217, A:Q.222, A:L.234, A:H.237, A:A.246 Hydrogen bonds: A:N.245, A:A.246 pi-Stacking: A:H.237 CLA.14: 8 residues within 4Å: Chain A: L.234, H.237, P.241, N.245, F.247 Chain C: I.142 Ligands: CLA.13, XAT.56 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:L.234, A:P.241, C:I.142 Metal complexes: A:H.237 CLA.21: 24 residues within 4Å: Chain B: L.72, P.77, G.78, D.79, Y.80, G.81, W.82, D.83, L.87, S.88, F.94, Y.97, R.98, L.100, E.101, H.104, R.222, M.225 Ligands: CLA.3, CHL.9, CHL.20, CLA.22, LUT.35, LHG.38 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:Y.80, B:W.82, B:W.82, B:W.82, B:L.87, B:F.94, B:Y.97, B:R.98, B:L.100, B:E.101, B:H.104, B:M.225 Hydrogen bonds: B:Y.80, B:W.82 Salt bridges: B:R.222 Metal complexes: B:E.101 CLA.22: 13 residues within 4Å: Chain B: L.100, H.104, F.229, F.232 Chain C: T.65, A.66, L.68 Ligands: CLA.21, CHL.26, CHL.28, LUT.35, CLA.41, LUT.55 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:L.100, B:F.229, B:F.232, B:F.232 Metal complexes: B:H.104 Hydrogen bonds: C:T.65 CLA.23: 17 residues within 4Å: Chain B: W.107, L.110, L.113, G.114, T.117, P.118, L.121, I.128, A.136, Q.139, L.146, D.147, Y.148, V.155 Ligands: CHL.25, LUT.35, NEX.37 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:W.107, B:L.110, B:L.113, B:P.118, B:L.121, B:Y.148, B:V.155 CLA.29: 17 residues within 4Å: Chain B: R.106, M.109, L.110, L.113, H.192, P.193, G.194, F.198, L.203, A.204, F.210, L.213, K.214, E.217 Ligands: CHL.27, CLA.31, LUT.34 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:R.106, B:M.109, B:L.110, B:L.113, B:F.198, B:A.204, B:F.210, B:L.213 Hydrogen bonds: B:G.194 Salt bridges: B:H.192 pi-Cation interactions: B:H.192, B:H.192 Metal complexes: B:E.217 CLA.30: 9 residues within 4Å: Chain B: F.52, V.215, K.216, K.219, N.220, L.223 Ligands: XAT.17, CLA.31, LHG.38 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:K.219, B:L.223 Hydrogen bonds: B:N.220 Salt bridges: B:K.216, B:K.219 CLA.31: 6 residues within 4Å: Chain B: K.216, N.220, L.223 Ligands: CLA.29, CLA.30, LUT.34 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.223 Salt bridges: B:K.216, B:K.216 CLA.32: 23 residues within 4Å: Chain A: V.150, L.153, A.154, V.157 Chain B: F.226, S.227, F.229, G.230, V.233, Q.234, V.237, T.238, N.245, L.246, H.249, S.256, N.257, A.258, Y.261 Ligands: XAT.17, CLA.33, LUT.34, LHG.38 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:F.229, B:F.229, B:Q.234, B:V.237, B:L.246, B:H.249, A:V.150, A:L.153, A:L.153, A:V.157 Hydrogen bonds: B:T.238, B:A.258 Salt bridges: B:H.249 CLA.33: 8 residues within 4Å: Chain A: V.150, L.153 Chain B: H.249, P.253, F.254, N.257 Ligands: XAT.17, CLA.32 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:P.253, B:F.254, A:V.150 Metal complexes: B:H.249 CLA.41: 25 residues within 4Å: Chain C: L.53, G.59, D.60, Y.61, G.62, W.63, D.64, L.68, S.69, F.75, Y.78, R.79, L.81, E.82, R.202, M.205, F.206, F.209 Ligands: CLA.22, CHL.28, CHL.40, CLA.42, CHL.48, LUT.55, LHG.58 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Y.61, C:W.63, C:W.63, C:L.68, C:Y.78, C:R.79, C:L.81, C:R.202, C:R.202, C:M.205, C:F.209 Hydrogen bonds: C:Y.61, C:G.62, C:W.63 Salt bridges: C:R.202 Metal complexes: C:E.82 CLA.42: 15 residues within 4Å: Chain A: T.73, A.74, L.76 Chain C: Y.78, L.81, H.85, F.209, F.212 Ligands: CLA.2, CLA.3, LUT.16, CLA.41, CHL.46, CHL.48, LUT.55 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.81, C:L.81, C:F.209, C:F.212 Hydrogen bonds: C:Y.78 Metal complexes: C:H.85 CLA.43: 16 residues within 4Å: Chain C: W.88, L.91, L.94, G.95, T.98, P.99, L.102, F.109, Q.120, L.127, N.128, Y.129, I.136 Ligands: CHL.45, LUT.55, NEX.57 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:W.88, C:L.91, C:L.94, C:P.99, C:L.102, C:L.127 CLA.49: 17 residues within 4Å: Chain C: R.87, M.90, L.91, H.173, P.174, G.175, F.178, D.179, L.183, F.190, L.193, K.194, K.196, E.197 Ligands: CHL.47, CLA.51, LUT.54 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:R.87, C:M.90, C:L.91, C:L.91, C:L.183, C:F.190, C:L.193, C:K.194, C:K.196, C:E.197 Hydrogen bonds: C:G.175 Salt bridges: C:H.173 Metal complexes: C:E.197 CLA.50: 9 residues within 4Å: Chain C: I.30, W.32, K.196, K.199, N.200, L.203 Ligands: XAT.36, CLA.51, LHG.58 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:I.30, C:W.32, C:K.199, C:L.203 Hydrogen bonds: C:N.200 Salt bridges: C:K.199 CLA.51: 8 residues within 4Å: Chain C: L.94, L.193, K.196, N.200, L.203 Ligands: CLA.49, CLA.50, LUT.54 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:L.94, C:K.196, C:L.203 Salt bridges: C:K.196 CLA.52: 23 residues within 4Å: Chain B: L.161, L.164, A.165, V.168 Chain C: F.206, S.207, F.209, G.210, V.213, Q.214, V.217, T.218, N.225, L.226, H.229, V.236, N.237, A.238, Y.241 Ligands: XAT.36, CLA.53, LUT.54, LHG.58 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.206, C:F.209, C:Q.214, C:V.217, C:L.226, C:H.229, B:L.161, B:L.164, B:A.165, B:V.168 Hydrogen bonds: C:A.238 CLA.53: 8 residues within 4Å: Chain B: L.161 Chain C: H.229, L.230, P.233, N.237, F.239 Ligands: XAT.36, CLA.52 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:L.230, C:P.233, B:L.161 Hydrogen bonds: C:N.237 Metal complexes: C:H.229

6 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)

LUT.15: 21 residues within 4Å: Chain A: M.98, L.99, A.101, L.102, F.186, D.187, L.189, G.190, L.191, N.208, L.211, A.212, S.215, F.219, Q.222, P.230, I.231, L.234 Ligands: CLA.10, CLA.12, CLA.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:M.98, A:L.99, A:A.101, A:L.102, A:L.102, A:L.191, A:A.212, A:F.219, A:I.231, A:L.234 Hydrogen bonds: A:G.190, A:L.191, A:Q.222, A:P.230, A:L.234 LUT.16: 22 residues within 4Å: Chain A: W.71, D.72, T.73, A.74, H.93, W.96, A.97, G.100, G.103, C.104, W.122, A.125, M.213, M.216, F.217 Ligands: CLA.2, CLA.3, CLA.4, CHL.6, CHL.7, CLA.42, CHL.48 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.71, A:W.96, A:A.97, A:M.213, A:F.217 Hydrogen bonds: A:A.74, A:W.122 LUT.34: 22 residues within 4Å: Chain B: M.109, A.112, L.113, F.198, D.199, P.200, L.201, G.202, L.203, N.220, L.223, A.224, S.227, F.231, Q.234, P.242, N.245, L.246 Ligands: CHL.27, CLA.29, CLA.31, CLA.32 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:M.109, B:A.112, B:L.113, B:L.201, B:L.203, B:L.223, B:L.223, B:A.224, B:F.231 Hydrogen bonds: B:L.201, B:G.202, B:Q.234, B:P.242 LUT.35: 23 residues within 4Å: Chain B: W.82, D.83, S.84, A.85, L.87, H.104, W.107, A.108, G.111, G.114, C.115, W.133, A.136, M.225, M.228, F.229 Ligands: CLA.3, CHL.9, CLA.21, CLA.22, CLA.23, CHL.25, CHL.26 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.82, B:W.82, B:A.85, B:L.87, B:W.107, B:A.108, B:W.133, B:W.133, B:M.225, B:F.229 Hydrogen bonds: B:S.84, B:S.84, B:A.85 LUT.54: 21 residues within 4Å: Chain C: M.90, L.91, A.93, L.94, I.97, F.178, D.179, P.180, L.181, L.183, N.200, L.203, A.204, S.207, F.211, Q.214, P.222, L.226 Ligands: CLA.49, CLA.51, CLA.52 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:M.90, C:L.91, C:A.93, C:I.97, C:L.181, C:L.183, C:L.203, C:L.203, C:A.204, C:F.211, C:F.211 Hydrogen bonds: C:Q.214 LUT.55: 22 residues within 4Å: Chain C: W.63, D.64, A.66, H.85, W.88, A.89, L.91, G.92, G.95, W.114, A.117, M.205, M.208, F.209, F.212 Ligands: CLA.22, CHL.28, CLA.41, CLA.42, CLA.43, CHL.45, CHL.46 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.63, C:W.63, C:A.66, C:W.88, C:A.89, C:W.114, C:W.114, C:M.205, C:F.209, C:F.212 Hydrogen bonds: C:A.66, C:W.114

3 x XAT: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)

XAT.17: 13 residues within 4Å: Chain A: L.153, V.157 Chain B: A.258, F.259, Y.261, A.262, F.265 Ligands: CHL.7, CHL.20, CLA.30, CLA.32, CLA.33, LHG.38 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.153, A:V.157, B:A.258, B:F.259, B:A.262 Hydrogen bonds: B:F.265 XAT.36: 13 residues within 4Å: Chain B: L.164, V.168 Chain C: A.238, F.239, Y.241, A.242, F.245 Ligands: CHL.26, CHL.40, CLA.50, CLA.52, CLA.53, LHG.58 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.238, C:F.239, C:A.242, B:L.164, B:V.168 Hydrogen bonds: C:F.245 XAT.56: 14 residues within 4Å: Chain A: A.246, F.247, F.249, A.250, F.253 Chain C: L.145, V.149 Ligands: CHL.1, CLA.11, CLA.13, CLA.14, LHG.19, CHL.46, CHL.48 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.246, A:F.247, A:A.250, C:V.149

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.18: 9 residues within 4Å: Chain A: W.96, Y.137, L.159, V.163, Y.166, P.172 Ligands: CLA.4, CHL.6, CHL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.96, A:L.159, A:L.159 NEX.37: 10 residues within 4Å: Chain B: W.107, Y.148, L.170, A.173, I.174, Y.177, P.183 Ligands: CLA.23, CHL.25, CHL.27 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.107, B:L.170, B:A.173, B:I.174, B:P.183 NEX.57: 7 residues within 4Å: Chain C: Y.129, V.151, Y.158, P.164 Ligands: CLA.43, CHL.45, CHL.47 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.164, C:P.164 Hydrogen bonds: C:Y.129

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

LHG.19: 13 residues within 4Å: Chain A: E.39, F.40, Y.69, K.207, R.210, L.211, F.214 Ligands: CHL.1, CLA.2, CLA.11, CLA.13, CHL.46, XAT.56 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.210, A:L.211, A:F.214, A:F.214, A:F.214 Hydrogen bonds: A:E.39, A:Y.69 Salt bridges: A:K.207, A:K.207 LHG.38: 10 residues within 4Å: Chain B: Y.80, K.219, R.222, L.223, F.226 Ligands: XAT.17, CHL.20, CLA.21, CLA.30, CLA.32 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.222, B:L.223, B:L.223, B:F.226, B:F.226 Salt bridges: B:K.219, B:K.219 LHG.58: 10 residues within 4Å: Chain C: Y.61, K.199, R.202, L.203, F.206 Ligands: XAT.36, CHL.40, CLA.41, CLA.50, CLA.52 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:R.202, C:L.203, C:F.206, C:F.206 Hydrogen bonds: C:Y.61 Salt bridges: C:K.199, C:K.199

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

LMG.39: 4 residues within 4Å: Chain B: N.151, G.153, L.154 Ligands: CHL.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., Structural basis of LhcbM5-mediated state transitions in green algae. Nat.Plants (2021)

Release Date

2021-06-30

Peptides

Chlorophyll a-b binding protein, chloroplastic: A
Chlorophyll a-b binding protein, chloroplastic: B
Chlorophyll a-b binding protein, chloroplastic: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
V

C
W

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

Chlorophyll a-b binding protein, chloroplastic

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