SMTL ID : 8y15.1

Cryo-EM structure of Light-harvesting complex from Spinacia oleracea

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

CHL.1: 17 residues within 4Å: Chain A: V.9, K.10, Y.11, L.12, G.13, P.14, Y.31, W.33, W.209 Chain C: W.115, Q.118, V.119 Ligands: CLA.2, LHG.18, XAT.39, CHL.46, CHL.48 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.9, A:Y.11, A:L.12, A:Y.31, A:W.33, A:W.33, A:W.209, C:V.119 Metal complexes: A:Y.11 CHL.5: 11 residues within 4Å: Chain A: P.103, S.104, L.105, V.106, H.107, A.108, Q.109, S.110, I.114 Ligands: CLA.4, CHL.6 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:H.107, A:A.108, A:Q.109, A:I.114 Hydrogen bonds: A:V.106, A:Q.109, A:S.110 Metal complexes: A:V.106 CHL.6: 15 residues within 4Å: Chain A: W.58, G.88, L.97, V.106, A.108, I.114, C.117, Q.118, L.121 Ligands: CLA.4, CHL.5, CHL.7, CHL.9, 01.16, NEX.17 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.58, A:L.97, A:V.106, A:A.108, A:I.114, A:I.114, A:Q.118, A:L.121 Metal complexes: H2O.1 CHL.7: 18 residues within 4Å: Chain A: W.84, F.85, K.86, G.88, S.89, I.91, F.92, I.111, Q.118 Chain B: W.209, A.212, T.213, F.215, V.216 Ligands: CHL.6, 01.16, XAT.19, CHL.20 12 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.84, A:F.85, A:I.91, A:F.92, A:I.111, B:W.209, B:W.209 Hydrogen bonds: A:G.88, A:S.89, A:Q.118 Water bridges: A:A.87 Metal complexes: H2O.1 CHL.8: 20 residues within 4Å: Chain A: I.54, R.57, W.58, V.125, Y.128, R.129, G.133, P.134, L.135, G.136, E.137, V.138, P.141, P.144, S.147, F.148, P.150 Ligands: CLA.10, 01.15, NEX.17 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.125, A:Y.128, A:R.129, A:L.135, A:V.138, A:P.144, A:P.144, A:F.148, A:F.148, A:F.148, A:F.148, A:P.150 Hydrogen bonds: A:R.57, A:L.135, A:G.136 Metal complexes: H2O.2 CHL.9: 21 residues within 4Å: Chain A: E.50, L.51, I.54, H.55, W.58, Q.118, M.122, G.123, E.126, R.129, I.130, F.179, F.182, I.186 Chain B: W.33, T.35 Ligands: CLA.3, CHL.6, CHL.20, CLA.21, 01.35 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.54, A:W.58, A:W.58, A:M.122, A:E.126, A:I.130, A:F.179, A:F.182, A:I.186 Hydrogen bonds: A:Q.118 Salt bridges: A:R.129 Metal complexes: A:E.126 Water bridges: B:T.35 CHL.20: 17 residues within 4Å: Chain A: Q.118, V.119 Chain B: V.9, K.10, Y.11, L.12, G.13, P.14, F.15, Y.31, W.33, W.209 Ligands: CHL.7, CHL.9, XAT.19, CLA.21, LHG.37 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.9, B:Y.11, B:L.12, B:F.15, B:W.33, B:W.33, B:W.209, A:V.119 Metal complexes: B:Y.11 CHL.24: 12 residues within 4Å: Chain B: P.103, S.104, L.105, V.106, H.107, A.108, Q.109, S.110, A.113, I.114 Ligands: CLA.23, CHL.25 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:H.107, B:A.108, B:Q.109, B:I.114 Hydrogen bonds: B:V.106, B:Q.109, B:S.110 Metal complexes: B:V.106 CHL.25: 16 residues within 4Å: Chain B: W.58, G.88, L.97, V.106, A.108, I.111, I.114, C.117, Q.118, L.121 Ligands: CLA.23, CHL.24, CHL.26, CHL.28, 01.35, NEX.36 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.58, B:L.97, B:V.106, B:A.108, B:I.111, B:I.114, B:I.114, B:Q.118, B:L.121 Metal complexes: H2O.2 CHL.26: 18 residues within 4Å: Chain B: W.84, F.85, K.86, G.88, S.89, I.91, F.92, I.111, Q.118 Chain C: W.209, A.212, T.213, F.215, V.216 Ligands: CHL.25, 01.35, XAT.38, CHL.40 12 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.84, B:F.85, B:I.91, B:F.92, B:I.111, C:W.209, C:W.209 Hydrogen bonds: B:G.88, B:S.89, B:Q.118 Water bridges: B:A.87 Metal complexes: H2O.3 CHL.27: 20 residues within 4Å: Chain B: I.54, R.57, W.58, V.125, Y.128, R.129, G.133, P.134, L.135, G.136, E.137, V.138, P.141, P.144, S.147, F.148, P.150 Ligands: CLA.29, 01.34, NEX.36 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:V.125, B:Y.128, B:L.135, B:V.138, B:P.144, B:P.144, B:F.148, B:F.148, B:F.148, B:P.150 Hydrogen bonds: B:R.57, B:L.135, B:G.136 Metal complexes: H2O.3 CHL.28: 21 residues within 4Å: Chain B: E.50, L.51, I.54, H.55, W.58, Q.118, M.122, G.123, E.126, R.129, I.130, F.179, F.182, I.186 Chain C: W.33, T.35 Ligands: CLA.22, CHL.25, CHL.40, CLA.41, 01.55 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:I.54, B:W.58, B:W.58, B:E.126, B:I.130, B:F.179, B:F.182, B:I.186 Hydrogen bonds: B:Q.118 Salt bridges: B:R.129 Metal complexes: B:E.126 Water bridges: C:T.35 CHL.40: 18 residues within 4Å: Chain B: W.115, Q.118, V.119 Chain C: V.9, K.10, Y.11, L.12, G.13, P.14, F.15, Y.31, W.33, W.209 Ligands: CHL.26, CHL.28, XAT.38, CLA.41, LHG.57 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.9, C:Y.11, C:L.12, C:F.15, C:W.33, C:W.33, C:W.209, B:V.119 Metal complexes: C:Y.11 CHL.44: 12 residues within 4Å: Chain C: P.103, S.104, L.105, V.106, H.107, A.108, Q.109, S.110, A.113, I.114 Ligands: CLA.43, CHL.45 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:H.107, C:A.108, C:Q.109, C:I.114 Hydrogen bonds: C:V.106, C:Q.109, C:S.110 Metal complexes: C:V.106 CHL.45: 15 residues within 4Å: Chain C: W.58, G.88, L.97, V.106, A.108, I.114, C.117, Q.118, L.121 Ligands: CLA.43, CHL.44, CHL.46, CHL.48, 01.55, NEX.56 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.58, C:L.97, C:V.106, C:A.108, C:I.114, C:I.114, C:Q.118, C:L.121 Metal complexes: H2O.4 CHL.46: 18 residues within 4Å: Chain A: W.209, A.212, T.213, F.215, V.216 Chain C: W.84, F.85, K.86, G.88, S.89, I.91, F.92, I.111, Q.118 Ligands: CHL.1, XAT.39, CHL.45, 01.55 12 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.84, C:F.85, C:I.91, C:F.92, C:I.111, A:W.209, A:W.209 Hydrogen bonds: C:G.88, C:S.89, C:Q.118 Water bridges: C:A.87 Metal complexes: H2O.5 CHL.47: 20 residues within 4Å: Chain C: 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, P.150 Ligands: CLA.49, 01.54, NEX.56 13 PLIP interactions: 12 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:V.125, C:Y.128, C:L.135, C:V.138, C:P.144, C:F.148, C:F.148, C:F.148, C:P.150 Hydrogen bonds: C:R.57, C:L.135, C:G.136 Metal complexes: H2O.5 CHL.48: 20 residues within 4Å: Chain A: W.33, T.35 Chain C: E.50, L.51, I.54, H.55, W.58, Q.118, M.122, G.123, E.126, R.129, I.130, F.179, F.182, I.186 Ligands: CHL.1, 01.16, CLA.42, CHL.45 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain C, Water bridges: A:T.35 Hydrophobic interactions: C:I.54, C:W.58, C:W.58, C:E.126, C:I.130, C:F.179, C:F.182, C:I.186 Hydrogen bonds: C:Q.118 Salt bridges: C:R.129 Metal complexes: C:E.126

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

CLA.2: 22 residues within 4Å: Chain A: 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, E.52, R.172, M.175, F.176, F.179 Ligands: CHL.1, CLA.3, 01.16, CLA.42 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.31, A:W.33, A:W.33, A:L.38, A:F.45, A:N.48, A:R.49, A:E.52, A:R.172, A:R.172, A:M.175, A:F.176, A:F.176, A:F.179, A:F.179 Hydrogen bonds: A:Y.31, A:W.33 Salt bridges: A:R.172 pi-Cation interactions: A:R.172 Metal complexes: A:E.52 CLA.3: 10 residues within 4Å: Chain A: L.51, H.55, F.179 Chain B: A.36, L.38 Ligands: CLA.2, CHL.9, 01.16, CLA.21, 01.35 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.179 Metal complexes: A:H.55 CLA.4: 18 residues within 4Å: Chain A: L.61, G.62, L.64, G.65, F.68, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, V.106 Ligands: CHL.5, CHL.6, CLA.10, 01.16, NEX.17 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.61, A:L.64, A:A.87, A:L.97, A:Y.99, A:Y.99, A:L.100 Hydrogen bonds: A:Q.90, A:L.100 pi-Stacking: A:Y.99 Metal complexes: H2O.1 CLA.10: 18 residues within 4Å: Chain A: R.57, M.60, L.61, Y.143, P.144, G.145, F.148, D.149, L.153, F.160, L.163, K.164, E.167 Ligands: CLA.4, CHL.8, CLA.12, 01.15, NEX.17 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:R.57, A:R.57, A:L.61, A:L.61, A:F.148, A:F.160, A:L.163, A:E.167, A:E.167 Hydrogen bonds: A:G.145 pi-Cation interactions: A:R.57 Metal complexes: A:E.167 CLA.11: 9 residues within 4Å: Chain A: W.3, V.67, L.71, K.166, K.169, N.170, L.173 Ligands: CLA.12, LHG.18 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:W.3, A:V.67, A:K.169, A:L.173 Hydrogen bonds: A:N.170 Salt bridges: A:K.169 pi-Cation interactions: A:K.169 CLA.12: 6 residues within 4Å: Chain A: K.166, N.170, L.173 Ligands: CLA.10, CLA.11, 01.15 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.173 Salt bridges: A:K.166, A:K.166 CLA.13: 17 residues within 4Å: Chain A: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, L.196, H.199, N.206, N.207, A.208, F.211 Ligands: CLA.14, 01.15, LHG.18, XAT.39 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.176, A:F.176, A:F.179, A:V.183, A:Q.184, A:A.208 Hydrogen bonds: A:A.208 CLA.14: 8 residues within 4Å: Chain A: L.196, H.199, L.200, P.203, N.207, W.209 Ligands: CLA.13, XAT.39 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.196, A:P.203, 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, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CLA.3, CHL.9, CHL.20, CLA.22, 01.35 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:Y.31, B:W.33, B:W.33, B:L.38, B:F.45, B:N.48, B:R.49, B:E.52, B:R.172, B:R.172, B:M.175, B:F.176, B:F.179 Hydrogen bonds: B:Y.31, B:W.33 Salt bridges: B:R.172 pi-Cation interactions: B:R.172 Metal complexes: B:E.52 CLA.22: 10 residues within 4Å: Chain B: L.51, H.55, F.179 Chain C: A.36, L.38 Ligands: CLA.21, CHL.28, 01.35, CLA.41, 01.55 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.51, B:L.51, B:F.179 Metal complexes: B:H.55 CLA.23: 18 residues within 4Å: Chain B: L.61, G.62, L.64, G.65, F.68, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, V.106 Ligands: CHL.24, CHL.25, CLA.29, 01.35, NEX.36 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.61, B:L.64, B:A.87, B:L.97, B:Y.99, B:Y.99, B:L.100 Hydrogen bonds: B:Q.90, B:L.100 pi-Stacking: B:Y.99 Metal complexes: H2O.3 CLA.29: 18 residues within 4Å: Chain B: R.57, M.60, L.61, Y.143, P.144, G.145, F.148, D.149, L.153, F.160, L.163, K.164, E.167 Ligands: CLA.23, CHL.27, CLA.31, 01.34, NEX.36 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:R.57, B:R.57, B:M.60, B:L.61, B:L.61, B:F.148, B:F.160, B:L.163, B:E.167, B:E.167 Hydrogen bonds: B:G.145 pi-Cation interactions: B:R.57 Metal complexes: B:E.167 CLA.30: 9 residues within 4Å: Chain B: W.3, V.67, L.71, K.166, K.169, N.170, L.173 Ligands: CLA.31, LHG.37 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:W.3, B:V.67, B:L.71, B:K.169, B:L.173 Hydrogen bonds: B:N.170 Salt bridges: B:K.169 pi-Cation interactions: B:K.169 CLA.31: 6 residues within 4Å: Chain B: K.166, N.170, L.173 Ligands: CLA.29, CLA.30, 01.34 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.173 Salt bridges: B:K.166, B:K.166 CLA.32: 18 residues within 4Å: Chain A: W.115 Chain B: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, L.196, H.199, N.206, N.207, A.208, F.211 Ligands: XAT.19, CLA.33, 01.34, LHG.37 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:F.176, B:F.176, B:F.179, B:V.183, B:Q.184, B:A.208, A:W.115 Hydrogen bonds: B:A.208 CLA.33: 8 residues within 4Å: Chain B: L.196, H.199, L.200, P.203, N.207, W.209 Ligands: XAT.19, CLA.32 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.196, B:P.203, B:P.203 Metal complexes: B:H.199 CLA.41: 24 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, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CLA.22, CHL.28, CHL.40, CLA.42, 01.55 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:Y.31, C:W.33, C:W.33, C:L.38, C:F.45, C:N.48, C:R.49, C:E.52, C:E.52, C:R.172, C:R.172, C:M.175, C:F.176, C:F.176, C:F.179, C:F.179 Hydrogen bonds: C:Y.31, C:W.33 Salt bridges: C:R.172 pi-Cation interactions: C:R.172 Metal complexes: C:E.52 CLA.42: 10 residues within 4Å: Chain A: A.36, L.38 Chain C: L.51, H.55, F.179 Ligands: CLA.2, 01.16, CLA.41, CHL.48, 01.55 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:L.51, C:L.51, C:F.179 Metal complexes: C:H.55 CLA.43: 18 residues within 4Å: Chain C: L.61, G.62, L.64, G.65, F.68, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, V.106 Ligands: CHL.44, CHL.45, CLA.49, 01.55, NEX.56 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:L.61, C:L.64, C:A.87, C:L.97, C:Y.99, C:Y.99, C:L.100 Hydrogen bonds: C:Q.90, C:L.100 pi-Stacking: C:Y.99 Metal complexes: H2O.4 CLA.49: 17 residues within 4Å: Chain C: R.57, M.60, L.61, Y.143, P.144, G.145, F.148, L.153, F.160, L.163, K.164, E.167 Ligands: CLA.43, CHL.47, CLA.51, 01.54, NEX.56 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:R.57, C:R.57, C:M.60, C:L.61, C:L.61, C:F.148, C:F.160, C:L.163, C:E.167, C:E.167 Hydrogen bonds: C:G.145 pi-Cation interactions: C:R.57 Metal complexes: C:E.167 CLA.50: 9 residues within 4Å: Chain C: W.3, V.67, L.71, K.166, K.169, N.170, L.173 Ligands: CLA.51, LHG.57 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:W.3, C:V.67, C:L.71, C:K.169, C:L.173 Hydrogen bonds: C:N.170 Salt bridges: C:K.169 pi-Cation interactions: C:K.169 CLA.51: 6 residues within 4Å: Chain C: K.166, N.170, L.173 Ligands: CLA.49, CLA.50, 01.54 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.173 Salt bridges: C:K.166, C:K.166 CLA.52: 17 residues within 4Å: Chain C: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, L.196, H.199, N.206, N.207, A.208, F.211 Ligands: XAT.38, CLA.53, 01.54, LHG.57 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:F.176, C:F.176, C:F.179, C:V.183, C:Q.184, C:A.208 Hydrogen bonds: C:A.208 CLA.53: 8 residues within 4Å: Chain C: L.196, H.199, L.200, P.203, N.207, W.209 Ligands: XAT.38, CLA.52 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:L.196, C:P.203, C:P.203 Metal complexes: C:H.199

6 x 01: Lutein

01.15: 16 residues within 4Å: Chain A: M.60, L.64, F.148, D.149, P.150, L.151, L.153, N.170, S.177, F.181, Q.184, P.192 Ligands: CHL.8, CLA.10, CLA.12, CLA.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.60, A:L.64, A:L.151, A:L.153, A:F.181 Hydrogen bonds: A:D.149, A:L.151, A:Q.184, A:P.192 01.16: 22 residues within 4Å: Chain A: 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.2, CLA.3, CLA.4, CHL.6, CHL.7, CLA.42, CHL.48 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.33, A:W.33, A:W.33, A:A.36, A:A.59, A:W.84, A:M.175, A:F.179 Hydrogen bonds: A:D.34, A:T.35, A:A.36, A:W.84 Water bridges: A:T.35 01.34: 16 residues within 4Å: Chain B: M.60, L.64, F.148, D.149, P.150, L.151, L.153, N.170, S.177, F.181, Q.184, P.192 Ligands: CHL.27, CLA.29, CLA.31, CLA.32 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:M.60, B:L.64, B:L.151, B:L.153, B:F.181 Hydrogen bonds: B:D.149, B:L.151, B:Q.184, B:P.192 01.35: 21 residues within 4Å: Chain B: 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 Ligands: CLA.3, CHL.9, CLA.21, CLA.22, CLA.23, CHL.25, CHL.26 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.33, B:W.33, B:A.36, B:A.59, B:W.84, B:M.175 Hydrogen bonds: B:D.34, B:T.35, B:A.36, B:W.84 01.54: 16 residues within 4Å: Chain C: M.60, L.64, F.148, D.149, P.150, L.151, L.153, N.170, S.177, F.181, Q.184, P.192 Ligands: CHL.47, CLA.49, CLA.51, CLA.52 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:M.60, C:L.64, C:L.151, C:L.153, C:F.181 Hydrogen bonds: C:D.149, C:L.151, C:Q.184, C:P.192, C:L.196 01.55: 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 Ligands: CLA.22, CHL.28, CLA.41, CLA.42, CLA.43, CHL.45, CHL.46 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.33, C:W.33, C:W.33, C:A.36, C:A.59, C:W.84, C:M.175 Hydrogen bonds: C:D.34, C:T.35, C:A.36, C:W.84

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: Y.99, A.124, V.125, Y.128, P.134 Ligands: CLA.4, CHL.6, CHL.8, CLA.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.124, A:Y.128, A:P.134 Hydrogen bonds: A:Y.99 NEX.36: 9 residues within 4Å: Chain B: Y.99, A.124, V.125, Y.128, P.134 Ligands: CLA.23, CHL.25, CHL.27, CLA.29 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.124, B:Y.128, B:P.134 Hydrogen bonds: B:Y.99 NEX.56: 10 residues within 4Å: Chain C: W.58, Y.99, A.124, V.125, Y.128, P.134 Ligands: CLA.43, CHL.45, CHL.47, CLA.49 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.58, C:A.124, C:Y.128, C:P.134 Hydrogen bonds: C:Y.99

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

LHG.18: 9 residues within 4Å: Chain A: Y.31, K.169, R.172, L.173, F.176 Ligands: CHL.1, CLA.11, CLA.13, XAT.39 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.172, A:L.173, A:F.176 Salt bridges: A:K.169, A:K.169 LHG.37: 9 residues within 4Å: Chain B: Y.31, K.169, R.172, L.173, F.176 Ligands: XAT.19, CHL.20, CLA.30, CLA.32 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.172, B:L.173, B:F.176, B:F.176 Salt bridges: B:K.169, B:K.169 LHG.57: 9 residues within 4Å: Chain C: Y.31, K.169, R.172, L.173, F.176 Ligands: XAT.38, CHL.40, CLA.50, CLA.52 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.172, C:L.173, C:F.176, C:F.176 Salt bridges: C:K.169, C:K.169

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: 11 residues within 4Å: Chain A: W.115 Chain B: A.208, W.209, F.211, A.212, F.215 Ligands: CHL.7, CHL.20, CLA.32, CLA.33, LHG.37 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.208, B:W.209, B:W.209, B:W.209, B:A.212, B:F.215 XAT.38: 11 residues within 4Å: Chain B: W.115 Chain C: A.208, W.209, F.211, A.212, F.215 Ligands: CHL.26, CHL.40, CLA.52, CLA.53, LHG.57 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.208, C:W.209, C:W.209, C:W.209, C:A.212, C:F.215 XAT.39: 11 residues within 4Å: Chain A: A.208, W.209, F.211, A.212, F.215 Chain C: W.115 Ligands: CHL.1, CLA.13, CLA.14, LHG.18, CHL.46 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.208, A:W.209, A:W.209, A:W.209, A:A.212, A:F.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seki, S. et al., Structure-based validation of recombinant light-harvesting complex II. Pnas Nexus (2024)

Release Date

2024-11-20

Peptides

Chlorophyll a-b binding protein, chloroplastic: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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