SMTL ID : 8iwz.1

Cryo-EM structure of unprotonated LHCII in detergent solution at low pH value

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 x CHL: CHLOROPHYLL B(Covalent)(Non-covalent)

CHL.1: 15 residues within 4Å: Chain A: V.9, K.10, Y.11, L.12, G.13, P.14, F.15, Y.31, W.33 Chain B: W.115 Ligands: CLA.2, LHG.18, XAT.19, CHL.26, CHL.28 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:V.9, A:L.12, A:F.15, A:Y.31, A:W.33, A:W.33 Metal complexes: A:Y.11 CHL.5: 10 residues within 4Å: Chain A: P.103, S.104, L.105, V.106, H.107, Q.109, S.110, A.113, I.114 Ligands: CHL.6 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:V.106, A:Q.109, A:I.114 Hydrogen bonds: A:Q.109, A:S.110 pi-Cation interactions: A:H.107 Metal complexes: A:H.107 CHL.6: 9 residues within 4Å: Chain A: W.58, G.88, I.114, Q.118, L.121 Ligands: CLA.4, CHL.5, CHL.7, NEX.17 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:W.58, A:I.114, A:Q.118, A:L.121 CHL.7: 19 residues within 4Å: Chain A: W.84, F.85, K.86, G.88, S.89, F.182, I.186 Chain C: A.212, T.213, F.215, V.216, P.217 Ligands: CLA.3, CHL.6, CHL.9, LUT.16, XAT.39, CHL.40, LHG.57 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:W.84, A:F.85, A:F.182, A:I.186, A:I.186 Hydrogen bonds: A:G.88, A:S.89 CHL.8: 20 residues within 4Å: Chain A: R.57, W.58, L.61, V.125, Y.128, R.129, G.132, G.133, P.134, L.135, G.136, V.138, P.141, L.142, P.144, S.147, F.148 Ligands: CLA.10, LUT.15, NEX.17 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:L.61, A:V.125, A:V.125, A:Y.128, A:Y.128, A:L.135, A:V.138, A:P.144 Hydrogen bonds: A:R.57, A:L.135 CHL.9: 17 residues within 4Å: Chain A: E.50, L.51, I.54, H.55, W.58, M.122, E.126, R.129, I.130, F.179 Chain C: W.33, T.35 Ligands: CLA.3, CHL.7, CHL.40, CLA.41, LUT.55 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:I.54, A:E.126, A:I.130, A:F.179, C:T.35 Salt bridges: A:R.129 Metal complexes: A:E.126 CHL.20: 13 residues within 4Å: Chain B: V.9, K.10, Y.11, L.12, G.13, P.14, Y.31, W.33 Ligands: CLA.21, LHG.37, XAT.38, CHL.46, CHL.48 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:V.9, B:Y.11, B:Y.11, B:Y.31, B:W.33, B:W.33 CHL.24: 10 residues within 4Å: Chain B: P.103, L.105, V.106, H.107, Q.109, S.110, A.113, I.114, C.117 Ligands: CHL.25 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:V.106, B:H.107, B:A.113, B:I.114 Hydrogen bonds: B:S.110 pi-Cation interactions: B:H.107 Metal complexes: B:H.107 CHL.25: 11 residues within 4Å: Chain B: G.88, A.108, I.114, C.117, Q.118, L.121, M.122 Ligands: CLA.23, CHL.24, CHL.26, NEX.36 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:A.108, B:I.114, B:I.114, B:Q.118, B:L.121 CHL.26: 15 residues within 4Å: Chain A: V.216, P.217 Chain B: F.85, K.86, S.89, F.92, Q.118, I.186 Ligands: CHL.1, LHG.18, XAT.19, CLA.22, CHL.25, CHL.28, LUT.35 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.85, B:F.92, B:I.186, B:I.186 Hydrogen bonds: B:S.89 CHL.27: 20 residues within 4Å: Chain B: I.54, R.57, W.58, V.125, Y.128, R.129, G.132, G.133, P.134, L.135, G.136, E.137, V.138, P.141, P.144, S.147, F.148 Ligands: CLA.29, LUT.34, NEX.36 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:V.125, B:V.125, B:V.125, B:Y.128, B:R.129, B:L.135, B:L.135, B:V.138, B:P.144, B:P.144, B:F.148 Hydrogen bonds: B:R.57, B:L.135, B:G.136 Salt bridges: B:R.129 pi-Stacking: B:F.148 CHL.28: 20 residues within 4Å: Chain A: L.12, W.33, T.35 Chain B: E.50, L.51, I.54, H.55, W.58, M.122, E.126, R.129, I.130, F.179, I.186 Ligands: CHL.1, CLA.2, LUT.16, XAT.19, CLA.22, CHL.26 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B, Hydrophobic interactions: A:L.12, A:T.35, B:I.54, B:I.130, B:F.179, B:I.186 Hydrogen bonds: B:E.50 Salt bridges: B:R.129 Metal complexes: B:E.126, B:E.126 CHL.40: 13 residues within 4Å: Chain A: W.115 Chain C: V.9, K.10, Y.11, L.12, G.13, Y.31, W.33 Ligands: CHL.7, CHL.9, XAT.39, CLA.41, LHG.57 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:V.9, C:Y.31, C:W.33 Metal complexes: C:Y.11 CHL.44: 9 residues within 4Å: Chain C: P.103, S.104, L.105, V.106, H.107, Q.109, S.110, I.114 Ligands: CHL.45 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:V.106, C:V.106, C:H.107, C:I.114 Hydrogen bonds: C:Q.109, C:S.110 pi-Cation interactions: C:H.107 Metal complexes: C:H.107 CHL.45: 13 residues within 4Å: Chain C: W.58, L.97, V.106, A.108, I.114, C.117, Q.118, L.121, M.122 Ligands: CLA.43, CHL.44, CHL.46, NEX.56 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:W.58, C:L.97, C:A.108, C:I.114, C:L.121 Hydrogen bonds: C:Q.118 CHL.46: 22 residues within 4Å: Chain B: A.212, T.213, F.215, V.216, P.217 Chain C: W.84, F.85, K.86, A.87, G.88, S.89, I.91, F.92, I.111, F.182, I.186 Ligands: CHL.20, XAT.38, CLA.42, CHL.45, CHL.48, LUT.55 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:W.84, C:W.84, C:F.85, C:I.91, C:I.111, C:F.182, C:I.186, C:I.186 Hydrogen bonds: C:G.88, C:S.89 CHL.47: 19 residues within 4Å: Chain C: R.57, W.58, L.61, V.125, Y.128, R.129, G.132, G.133, P.134, L.135, G.136, V.138, P.141, P.144, S.147, F.148 Ligands: CLA.49, LUT.54, NEX.56 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.61, C:V.125, C:V.125, C:Y.128, C:R.129, C:L.135, C:L.135, C:V.138, C:P.144, C:P.144, C:F.148, C:F.148 Hydrogen bonds: C:R.57, C:L.135 pi-Stacking: C:F.148 CHL.48: 16 residues within 4Å: Chain B: W.33, T.35 Chain C: E.50, I.54, H.55, W.58, M.122, E.126, R.129, I.130, F.179 Ligands: CHL.20, LUT.35, XAT.38, CLA.42, CHL.46 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C, Hydrophobic interactions: B:T.35, C:I.54, C:E.126, C:I.130, C:F.179 Hydrogen bonds: C:E.50, C:H.55 Salt bridges: C:R.129 Metal complexes: C:E.126

24 x CLA: CHLOROPHYLL A(Non-covalent)(Covalent)

CLA.2: 24 residues within 4Å: Chain A: L.23, G.29, D.30, Y.31, G.32, W.33, D.34, L.38, S.39, F.45, N.48, R.49, L.51, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CHL.1, CLA.3, LUT.16, CLA.22, CHL.28 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:Y.31, A:W.33, A:W.33, A:W.33, A:D.34, A:N.48, A:R.172, A:F.176, A:F.176, A:F.179 Hydrogen bonds: A:Y.31, A:G.32, A:W.33, A:L.38 pi-Cation interactions: A:R.172 Metal complexes: A:E.52 CLA.3: 11 residues within 4Å: Chain A: L.51, H.55 Chain C: A.36, F.179 Ligands: CLA.2, CHL.7, CHL.9, LUT.16, CLA.41, LUT.55, LHG.57 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C, Metal complexes: A:H.55 Hydrophobic interactions: C:A.36, C:F.179, C:F.179 CLA.4: 16 residues within 4Å: Chain A: L.61, G.62, G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105 Ligands: CHL.6, LUT.16, NEX.17 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:L.61, A:L.61, A:P.69, A:A.87, A:L.97, A:Y.99 Hydrogen bonds: A:L.100 CLA.10: 15 residues within 4Å: Chain A: R.57, M.60, L.61, L.64, Y.143, P.144, F.148, D.149, L.153, A.154, L.163, E.167 Ligands: CHL.8, CLA.12, LUT.15 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:R.57, A:R.57, A:M.60, A:L.61, A:L.61, A:L.64, A:A.154, A:L.163 Hydrogen bonds: A:G.145 Metal complexes: A:E.167 CLA.11: 10 residues within 4Å: Chain A: W.3, L.64, V.67, K.166, K.169, N.170, L.173 Ligands: CLA.12, LHG.18, XAT.19 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:W.3, A:L.64, A:V.67, A:K.169, A:K.169, A:L.173 Hydrogen bonds: A:K.169 Salt bridges: A:K.166, A:K.169 CLA.12: 8 residues within 4Å: Chain A: L.64, L.163, K.166, N.170, L.173 Ligands: CLA.10, CLA.11, LUT.15 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.64, A:L.64, A:L.163, A:K.166, A:L.173 CLA.13: 15 residues within 4Å: Chain A: F.176, G.180, V.183, Q.184, V.187, T.188, N.195, H.199, N.206, N.207, A.208 Ligands: CLA.14, LUT.15, LHG.18, XAT.19 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.176, A:F.176, A:Q.184, A:V.187 Hydrogen bonds: A:Q.184, A:T.188, A:A.208 CLA.14: 7 residues within 4Å: Chain A: H.199, P.203, W.209 Chain B: L.112, W.115 Ligands: CLA.13, XAT.19 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:P.203 Metal complexes: A:H.199 CLA.21: 24 residues within 4Å: Chain B: L.23, P.28, G.29, D.30, Y.31, G.32, W.33, D.34, L.38, S.39, F.45, N.48, R.49, L.51, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CHL.20, CLA.22, LUT.35, CLA.42 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:W.33, B:L.38, B:N.48, B:R.172, B:F.179, B:F.179 Hydrogen bonds: B:Y.31, B:G.32, B:W.33 CLA.22: 12 residues within 4Å: Chain A: A.36, L.38 Chain B: L.51, H.55 Ligands: CLA.2, LUT.16, LHG.18, CLA.21, CHL.26, CHL.28, LUT.35, CLA.42 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:L.51 Metal complexes: B:H.55 CLA.23: 15 residues within 4Å: Chain B: W.58, L.61, G.65, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106 Ligands: CHL.25, LUT.35, NEX.36 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:W.58, B:L.97, B:L.100, B:L.100, B:L.105, B:L.105, B:V.106 Hydrogen bonds: B:Q.90, B:L.100 CLA.29: 17 residues within 4Å: Chain B: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, E.167 Ligands: CHL.27, CLA.31, LUT.34 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:R.57, B:R.57, B:L.61, B:L.61, B:L.64, B:F.148, B:A.154, B:F.160, B:L.163 Hydrogen bonds: B:G.145 CLA.30: 10 residues within 4Å: Chain B: W.3, L.64, V.67, K.166, K.169, N.170, L.173 Ligands: CLA.31, LHG.37, XAT.38 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:W.3, B:L.64, B:V.67, B:L.173 Salt bridges: B:K.169 pi-Cation interactions: B:K.169 CLA.31: 8 residues within 4Å: Chain B: L.64, L.163, K.166, N.170, L.173 Ligands: CLA.29, CLA.30, LUT.34 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.64, B:L.163, B:K.166, B:L.173 Salt bridges: B:K.166, B:K.166 CLA.32: 15 residues within 4Å: Chain B: F.176, F.179, G.180, V.183, Q.184, V.187, T.188, N.195, H.199, A.208, F.211 Ligands: CLA.33, LUT.34, LHG.37, XAT.38 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:F.176, B:F.176, B:F.176, B:F.179, B:F.179, B:V.187 Hydrogen bonds: B:Q.184, B:A.208 CLA.33: 9 residues within 4Å: Chain B: L.196, H.199, L.200, P.203, N.207, W.209 Chain C: L.112 Ligands: CLA.32, XAT.38 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:L.196, B:L.200, B:P.203, C:L.112 Metal complexes: B:H.199 CLA.41: 25 residues within 4Å: Chain C: L.23, P.28, G.29, D.30, Y.31, G.32, W.33, D.34, L.38, S.39, F.45, N.48, R.49, L.51, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CLA.3, CHL.9, CHL.40, CLA.42, LUT.55 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Y.31, C:W.33, C:N.48, C:R.172, C:F.176, C:F.176, C:F.179, C:F.179 Hydrogen bonds: C:D.30, C:Y.31, C:G.32, C:W.33, C:L.38 Metal complexes: C:E.52 CLA.42: 11 residues within 4Å: Chain B: A.36 Chain C: L.51, H.55 Ligands: CLA.21, CLA.22, LUT.35, LHG.37, CLA.41, CHL.46, CHL.48, LUT.55 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:L.51 Metal complexes: C:H.55 CLA.43: 15 residues within 4Å: Chain C: G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106 Ligands: CHL.45, LUT.55, NEX.56 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:F.68, C:P.69, C:A.87, C:L.97, C:Y.99, C:L.100, C:V.106 Hydrogen bonds: C:Q.90, C:L.100 CLA.49: 17 residues within 4Å: Chain C: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, E.167 Ligands: CHL.47, CLA.51, LUT.54 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:R.57, C:R.57, C:L.61, C:L.64, C:F.148, C:A.154, C:F.160 Hydrogen bonds: C:G.145 Metal complexes: C:E.167 CLA.50: 10 residues within 4Å: Chain C: W.3, L.64, V.67, F.68, K.166, K.169, N.170 Ligands: XAT.39, CLA.51, LHG.57 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:W.3, C:L.64, C:V.67, C:F.68, C:K.169 Hydrogen bonds: C:N.170 Salt bridges: C:K.166, C:K.169 pi-Cation interactions: C:K.169 CLA.51: 9 residues within 4Å: Chain C: L.64, F.68, L.163, K.166, N.170, L.173 Ligands: CLA.49, CLA.50, LUT.54 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.64, C:F.68, C:L.163, C:K.166, C:L.173 CLA.52: 17 residues within 4Å: Chain C: F.176, S.177, F.179, G.180, V.183, Q.184, V.187, T.188, N.195, H.199, N.206, N.207, A.208 Ligands: XAT.39, CLA.53, LUT.54, LHG.57 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:F.176, C:F.176, C:F.176, C:F.179, C:V.187 Hydrogen bonds: C:A.208 CLA.53: 8 residues within 4Å: Chain A: L.112, W.115 Chain C: H.199, L.200, P.203, W.209 Ligands: XAT.39, CLA.52 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:L.200, C:P.203, A:L.112, A:W.115 Metal complexes: C:H.199

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

LUT.15: 18 residues within 4Å: Chain A: M.60, A.63, L.64, F.148, D.149, P.150, N.170, A.174, S.177, F.181, Q.184, P.192, N.195, L.196 Ligands: CHL.8, CLA.10, CLA.12, CLA.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.60, A:A.63, A:L.64, A:A.174, A:F.181, A:F.181, A:L.196 Hydrogen bonds: A:Q.184, A:P.192 LUT.16: 20 residues within 4Å: Chain A: W.33, D.34, T.35, A.36, G.37, L.38, H.55, A.59, G.62, W.84, A.87, M.175, M.178, F.179 Ligands: CLA.2, CLA.3, CLA.4, CHL.7, CLA.22, CHL.28 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.33, A:A.36, A:A.59, A:W.84, A:M.175, A:F.179 Hydrogen bonds: A:D.34, A:A.36, A:G.37 LUT.34: 16 residues within 4Å: Chain B: M.60, A.63, L.64, F.148, D.149, P.150, A.174, S.177, F.181, Q.184, P.192, N.195 Ligands: CHL.27, CLA.29, CLA.31, CLA.32 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:M.60, B:A.63, B:L.64, B:A.174, B:F.181, B:F.181, B:P.192 Hydrogen bonds: B:Q.184 LUT.35: 16 residues within 4Å: Chain B: W.33, D.34, T.35, A.36, H.55, G.62, W.84, M.175, M.178, F.179 Ligands: CLA.21, CLA.22, CLA.23, CHL.26, CLA.42, CHL.48 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.33, B:W.84, B:F.179 Hydrogen bonds: B:D.34, B:T.35, B:A.36, B:A.36, B:W.84 LUT.54: 17 residues within 4Å: Chain C: M.60, A.63, L.64, F.148, D.149, P.150, A.174, S.177, F.181, Q.184, P.192, N.195, L.196 Ligands: CHL.47, CLA.49, CLA.51, CLA.52 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:M.60, C:A.63, C:L.64, C:A.174, C:F.181, C:F.181, C:P.192 Hydrogen bonds: C:L.151, C:Q.184 LUT.55: 21 residues within 4Å: Chain C: W.33, D.34, T.35, A.36, H.55, W.58, A.59, G.62, G.65, C.66, W.84, A.87, M.175, M.178, F.179 Ligands: CLA.3, CHL.9, CLA.41, CLA.42, CLA.43, CHL.46 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.33, C:W.33, C:W.33, C:A.59, C:W.84, C:F.179 Hydrogen bonds: C:T.35, C:A.36, C:A.36

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: 9 residues within 4Å: Chain A: W.58, Y.99, L.121, V.125, Y.128, P.134 Ligands: CLA.4, CHL.6, CHL.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.58, A:L.121, A:L.121, A:P.134 Hydrogen bonds: A:Y.99 NEX.36: 9 residues within 4Å: Chain B: W.58, Y.99, A.124, V.125, Y.128, P.134 Ligands: CLA.23, CHL.25, CHL.27 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.58, B:A.124, B:P.134 Hydrogen bonds: B:Y.99, B:Y.99 NEX.56: 10 residues within 4Å: Chain C: W.58, Y.99, L.121, A.124, V.125, Y.128, P.134 Ligands: CLA.43, CHL.45, CHL.47 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.58, C:A.124, C:Y.128, C:P.134, C:P.134 Hydrogen bonds: C:Y.99, C:Y.99

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

LHG.18: 11 residues within 4Å: Chain A: W.3, Y.31, K.169, R.172, F.176 Ligands: CHL.1, CLA.11, CLA.13, XAT.19, CLA.22, CHL.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.172, A:F.176, A:F.176 LHG.37: 11 residues within 4Å: Chain B: W.3, Y.31, K.169, R.172, L.173, F.176 Ligands: CHL.20, CLA.30, CLA.32, XAT.38, CLA.42 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.172, B:L.173, B:F.176, B:F.176, B:F.176, B:F.176 Hydrogen bonds: B:Y.31, B:R.172 Salt bridges: B:K.169 LHG.57: 12 residues within 4Å: Chain C: W.3, Y.31, K.169, R.172, L.173, F.176 Ligands: CLA.3, CHL.7, XAT.39, CHL.40, CLA.50, CLA.52 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.176, C:F.176, C:F.176 Salt bridges: C:K.169, C:K.169, C:R.172

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.19: 12 residues within 4Å: Chain A: A.208, W.209, A.212 Chain B: W.115, V.119 Ligands: CHL.1, CLA.11, CLA.13, CLA.14, LHG.18, CHL.26, CHL.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.209, A:A.212, B:V.119 XAT.38: 10 residues within 4Å: Chain B: W.209, A.212 Chain C: W.115 Ligands: CHL.20, CLA.30, CLA.32, CLA.33, LHG.37, CHL.46, CHL.48 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.209, B:A.212 XAT.39: 11 residues within 4Å: Chain A: W.115, V.119 Chain C: A.208, W.209, A.212 Ligands: CHL.7, CHL.40, CLA.50, CLA.52, CLA.53, LHG.57 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.119, C:W.209, C:A.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruan, M. et al., Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation. Nat.Plants (2023)

Release Date

2023-09-06

Peptides

Chlorophyll a-b binding protein, chloroplastic: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
G

C
Y

Membrane

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

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