SMTL ID : 8yee.1

Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

CHL.1: 13 residues within 4Å: Chain A: V.9, K.10, Y.11, L.12, G.13, Y.31, W.33, F.176 Chain B: W.115, G.123 Ligands: CLA.2, LHG.18, CHL.27 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.9, A:Y.11, A:Y.11, A:L.12, A:W.33, A:W.33, B:W.115 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, A.113, I.114 Ligands: CHL.6 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: 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:L.121, A:L.121 Metal complexes: H2O.1 CHL.7: 14 residues within 4Å: Chain A: W.84, F.85, K.86, G.88, S.89, I.91, F.92, I.111, I.114, Q.118 Chain C: W.209 Ligands: CLA.3, CHL.6, 01.16 10 PLIP interactions: 1 interactions with chain C, 8 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.209, A:W.84, A:F.85, A:I.91, A:F.92, A:I.114 Hydrogen bonds: A:G.88, A:S.89, A:Q.118 Metal complexes: H2O.1 CHL.8: 19 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 Ligands: CLA.10, 01.15, NEX.17 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.128, A:Y.128, A:R.129, A:L.135, A:L.135, A:V.138, A:P.144, A:P.144, A:F.148, A:F.148, A:F.148 Hydrogen bonds: A:R.57, A:L.135 Metal complexes: H2O.1 CHL.9: 19 residues within 4Å: Chain A: E.50, L.51, I.54, H.55, W.58, Q.118, V.119, M.122, G.123, E.126, R.129, I.130 Chain C: W.33, T.35 Ligands: CLA.3, CHL.6, CHL.37, CLA.38, 01.52 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:L.51, A:I.54, A:W.58, A:W.58, A:E.126, A:I.130, C:T.35 Hydrogen bonds: A:Q.118 Salt bridges: A:R.129 Metal complexes: A:E.126 Water bridges: C:T.35 CHL.19: 13 residues within 4Å: Chain B: V.9, K.10, Y.11, L.12, G.13, P.14, Y.31, W.33, F.176 Chain C: W.115 Ligands: CLA.20, LHG.36, CHL.45 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.9, B:Y.11, B:Y.11, B:L.12, B:W.33, B:W.33, C:W.115 Metal complexes: B:Y.11 CHL.23: 13 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, C.117 Ligands: CLA.22, CHL.24 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: 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.24: 15 residues within 4Å: Chain B: W.58, G.88, L.97, V.106, A.108, I.114, C.117, Q.118, L.121 Ligands: CLA.22, CHL.23, CHL.25, CHL.27, 01.34, NEX.35 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.58, B:L.97, B:V.106, B:A.108, B:I.114, B:I.114, B:L.121, B:L.121 Metal complexes: H2O.3 CHL.25: 14 residues within 4Å: Chain A: W.209 Chain B: F.85, K.86, G.88, S.89, I.91, F.92, I.111, I.114, W.115, Q.118 Ligands: CLA.21, CHL.24, 01.34 10 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.85, B:I.91, B:F.92, B:I.114, B:W.115, A:W.209 Hydrogen bonds: B:G.88, B:S.89, B:Q.118 Metal complexes: H2O.3 CHL.26: 21 residues within 4Å: Chain B: I.54, R.57, W.58, L.61, 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.28, 01.33, NEX.35 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.128, B:Y.128, B:R.129, B:L.135, B:L.135, B:V.138, B:P.144, B:P.144, B:F.148, B:F.148, B:F.148 Hydrogen bonds: B:R.57, B:L.135 Metal complexes: H2O.3 CHL.27: 19 residues within 4Å: Chain A: W.33, T.35 Chain B: E.50, L.51, I.54, H.55, W.58, Q.118, V.119, M.122, G.123, E.126, R.129, I.130 Ligands: CHL.1, CLA.2, 01.16, CLA.21, CHL.24 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:L.51, B:I.54, B:W.58, B:W.58, B:I.130, A:T.35 Hydrogen bonds: B:Q.118 Salt bridges: B:R.129 Metal complexes: B:E.126 CHL.37: 13 residues within 4Å: Chain A: W.115, G.123 Chain C: V.9, K.10, Y.11, L.12, G.13, Y.31, W.33, F.176 Ligands: CHL.9, CLA.38, LHG.54 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.9, C:Y.11, C:Y.11, C:L.12, C:W.33, C:W.33, A:W.115 Metal complexes: C:Y.11 CHL.41: 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.40, CHL.42 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:V.106, 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.42: 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.40, CHL.41, CHL.43, CHL.45, 01.52, NEX.53 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:L.121, C:L.121 Metal complexes: H2O.4 CHL.43: 15 residues within 4Å: Chain B: W.209 Chain C: W.84, F.85, K.86, G.88, S.89, I.91, F.92, I.111, I.114, W.115, Q.118 Ligands: CLA.39, CHL.42, 01.52 12 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.84, C:F.85, C:I.91, C:F.92, C:I.111, C:I.114, C:W.115, B:W.209 Hydrogen bonds: C:G.88, C:S.89, C:Q.118 Metal complexes: H2O.4 CHL.44: 20 residues within 4Å: Chain C: 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.46, 01.51, NEX.53 16 PLIP interactions: 15 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:Y.128, 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, C:F.148 Hydrogen bonds: C:R.57, C:L.135, C:G.136 pi-Cation interactions: C:R.129 Metal complexes: H2O.4 CHL.45: 18 residues within 4Å: Chain B: 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 Ligands: CHL.19, CLA.20, 01.34, CLA.39, CHL.42 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:L.51, C:I.54, C:W.58, C:W.58, C:E.126, C:I.130, B:T.35 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: 26 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, L.51, E.52, H.55, R.172, M.175, F.176, F.179 Ligands: CHL.1, CLA.3, CLA.13, 01.16, CLA.21, CHL.27 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:L.51, 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: 13 residues within 4Å: Chain A: L.51, H.55, F.179 Chain C: A.36, L.38 Ligands: CLA.2, CHL.7, CHL.9, 01.16, CLA.21, CLA.38, CLA.39, 01.52 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.51, A:F.179 Metal complexes: A:H.55 CLA.4: 20 residues within 4Å: Chain A: L.61, G.62, L.64, G.65, F.68, P.69, F.79, E.81, A.82, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106 Ligands: CHL.6, CLA.10, 01.16, NEX.17 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.61, A:L.64, A:P.69, A:A.87, A:L.97, A:Y.99, A:Y.99, A:L.100, A:L.105, A:V.106 Hydrogen bonds: A:Q.90, A:L.100 pi-Stacking: A:Y.99 Metal complexes: H2O.1 CLA.10: 21 residues within 4Å: Chain A: 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, K.164, K.166, E.167 Ligands: CLA.4, CHL.8, CLA.12, 01.15, NEX.17 16 PLIP interactions: 16 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:F.148, A:A.154, A:F.160, A:L.163, A:K.164, A:E.167, A:E.167 Hydrogen bonds: A:G.145 pi-Cation interactions: A:R.57 Metal complexes: A:E.167 CLA.11: 10 residues within 4Å: Chain A: W.3, L.64, V.67, E.162, 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:L.64, A:V.67, A:K.169, A:L.173 Hydrogen bonds: A:N.170 Salt bridges: 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, 01.15 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:L.64, A:L.64, A:L.163, 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, D.198, H.199, N.206, N.207, A.208 Ligands: CLA.2, CLA.14, 01.15, LHG.18 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.176, A:F.176, A:F.179, A:V.183, A:Q.184, A:L.196, A:A.208 Hydrogen bonds: A:A.208 CLA.14: 7 residues within 4Å: Chain A: L.196, H.199, L.200, P.203, N.207 Chain B: L.112 Ligands: CLA.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.112, A:L.196, A:P.203 Metal complexes: A:H.199 CLA.20: 23 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, R.172, M.175, F.176, F.179 Ligands: CHL.19, CLA.21, CLA.31, 01.34, CHL.45 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:Y.31, B:W.33, B:W.33, B:W.33, B:L.38, B:F.45, B:N.48, B:R.49, B:R.172, B:R.172, B:M.175, B:F.176, B:F.176, B:F.179, B:F.179, 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.21: 13 residues within 4Å: Chain A: A.36, L.38 Chain B: L.51, H.55, F.179 Ligands: CLA.2, CLA.3, 01.16, CLA.20, CHL.25, CHL.27, 01.34, CLA.39 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.51, B:F.179 Metal complexes: B:H.55 CLA.22: 22 residues within 4Å: Chain B: W.58, L.61, G.62, L.64, G.65, F.68, P.69, F.79, E.81, A.82, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106 Ligands: CHL.23, CHL.24, CLA.28, 01.34, NEX.35 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.58, B:L.61, B:L.64, B:P.69, B:A.87, B:L.97, B:Y.99, B:L.100, B:L.105, B:V.106 Hydrogen bonds: B:Q.90, B:L.100 pi-Stacking: B:Y.99 Metal complexes: H2O.2 CLA.28: 21 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, K.164, K.166, E.167 Ligands: CLA.22, CHL.26, CLA.30, 01.33, NEX.35 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:R.57, B:R.57, B:L.61, B:L.64, B:F.148, B:A.154, B:F.160, B:L.163, B:K.164, B:K.166, B:E.167, B:E.167 Hydrogen bonds: B:G.145 pi-Cation interactions: B:R.57 Metal complexes: B:E.167 CLA.29: 10 residues within 4Å: Chain B: W.3, L.64, V.67, E.162, K.166, K.169, N.170, L.173 Ligands: CLA.30, LHG.36 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:W.3, B:L.64, B:V.67, B:K.169, B:L.173 Hydrogen bonds: B:N.170 Salt bridges: B:K.169 CLA.30: 8 residues within 4Å: Chain B: L.64, L.163, K.166, N.170, L.173 Ligands: CLA.28, CLA.29, 01.33 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.64, B:L.64, B:L.163, B:L.173 Salt bridges: B:K.166, B:K.166 CLA.31: 16 residues within 4Å: Chain B: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, L.196, D.198, H.199, N.207, A.208 Ligands: CLA.20, CLA.32, 01.33, LHG.36 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:F.176, B:F.176, B:F.179, B:V.183, B:Q.184, B:L.196, B:A.208 Hydrogen bonds: B:A.208 CLA.32: 7 residues within 4Å: Chain B: L.196, H.199, L.200, P.203, N.207 Chain C: L.112 Ligands: CLA.31 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:L.196, B:P.203, C:L.112 Metal complexes: B:H.199 CLA.38: 26 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.37, CLA.39, CLA.49, 01.52 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:L.51, C:R.172, C:R.172, C:M.175, C:F.176, C:F.176, C:F.179, 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.39: 12 residues within 4Å: Chain B: A.36, L.38 Chain C: L.51, H.55, F.179 Ligands: CLA.3, CLA.21, 01.34, CLA.38, CHL.43, CHL.45, 01.52 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.51, C:F.179 Metal complexes: C:H.55 CLA.40: 23 residues within 4Å: Chain C: W.58, L.61, G.62, L.64, G.65, F.68, P.69, F.79, E.81, A.82, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106 Ligands: CHL.41, CHL.42, CLA.46, CLA.48, 01.52, NEX.53 13 PLIP interactions: 12 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.58, C:L.61, C:L.64, C:P.69, C:A.87, C:L.97, C:Y.99, C:L.100, C:L.105 Hydrogen bonds: C:Q.90, C:L.100 pi-Stacking: C:Y.99 Metal complexes: H2O.4 CLA.46: 20 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, K.164, E.167 Ligands: CLA.40, CHL.44, CLA.48, 01.51, NEX.53 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:R.57, C:R.57, C:M.60, C:L.61, C:L.61, C:L.64, C:F.148, C:A.154, C:F.160, C:L.163, C:K.164, C:E.167, C:E.167 Hydrogen bonds: C:G.145 pi-Cation interactions: C:R.57 Metal complexes: C:E.167 CLA.47: 10 residues within 4Å: Chain C: W.3, L.64, V.67, E.162, K.166, K.169, N.170, L.173 Ligands: CLA.48, LHG.54 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:W.3, C:L.64, C:V.67, C:K.169, C:L.173 Hydrogen bonds: C:N.170 Salt bridges: C:K.169 CLA.48: 9 residues within 4Å: Chain C: L.64, L.163, K.166, N.170, L.173 Ligands: CLA.40, CLA.46, CLA.47, 01.51 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.64, C:L.64, C:L.163, C:L.173 Salt bridges: C:K.166, C:K.166 CLA.49: 16 residues within 4Å: Chain C: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, L.196, D.198, H.199, N.207, A.208 Ligands: CLA.38, CLA.50, 01.51, LHG.54 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:F.176, C:F.176, C:F.179, C:V.183, C:Q.184, C:L.196, C:A.208 Hydrogen bonds: C:A.208 CLA.50: 6 residues within 4Å: Chain C: L.196, H.199, L.200, P.203, N.207 Ligands: CLA.49 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.196, C:P.203 Metal complexes: C:H.199

6 x 01: Lutein

01.15: 19 residues within 4Å: Chain A: M.60, L.64, F.148, D.149, P.150, L.151, L.153, N.170, L.173, S.177, F.181, Q.184, P.192, N.195, L.196 Ligands: CHL.8, CLA.10, CLA.12, CLA.13 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.60, A:L.64, A:L.151, A:L.153, A:L.173, A:F.181, A:L.196 Hydrogen bonds: A:D.149, A:L.151, A:G.152, A:Q.184, A:P.192, A:L.196 01.16: 23 residues within 4Å: Chain A: W.33, D.34, T.35, A.36, L.38, 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.21, CHL.27 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.33, A:W.33, A:W.33, A:A.36, A:L.38, A:W.58, A:A.59, A:M.175, A:F.179 Hydrogen bonds: A:D.34, A:T.35, A:A.36, A:W.84 01.33: 19 residues within 4Å: Chain B: M.60, L.64, F.148, D.149, P.150, L.151, L.153, N.170, L.173, S.177, F.181, Q.184, P.192, N.195, L.196 Ligands: CHL.26, CLA.28, CLA.30, CLA.31 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:M.60, B:L.64, B:L.151, B:L.153, B:L.173, B:F.181, B:L.196 Hydrogen bonds: B:D.149, B:L.151, B:G.152, B:Q.184, B:P.192, B:L.196 01.34: 22 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, F.179 Ligands: CLA.20, CLA.21, CLA.22, CHL.24, CHL.25, CLA.39, CHL.45 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.33, B:W.33, B:W.33, B:A.36, B:W.58, B:A.59, B:M.175, B:F.179 Hydrogen bonds: B:D.34, B:T.35, B:A.36, B:G.37, B:W.84 01.51: 20 residues within 4Å: Chain C: M.60, A.63, L.64, F.148, D.149, P.150, L.151, L.153, N.170, L.173, S.177, F.181, Q.184, P.192, N.195, L.196 Ligands: CHL.44, CLA.46, CLA.48, CLA.49 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:M.60, C:A.63, C:L.64, C:L.151, C:L.153, C:L.173, C:F.181, C:L.196 Hydrogen bonds: C:D.149, C:L.151, C:G.152, C:Q.184, C:P.192, C:L.196 01.52: 23 residues within 4Å: Chain C: W.33, D.34, T.35, A.36, L.38, 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.38, CLA.39, CLA.40, CHL.42, CHL.43 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.33, C:W.33, C:A.36, C:L.38, C:W.58, C:A.59, C:M.175, C:M.178, C:F.179 Hydrogen bonds: C:D.34, C:T.35, C:A.36, C:G.37, 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: 11 residues within 4Å: Chain A: W.58, Y.99, L.121, A.124, V.125, Y.128, P.134 Ligands: CLA.4, CHL.6, CHL.8, CLA.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.58, A:L.121, A:A.124, A:V.125, A:Y.128, A:P.134 Hydrogen bonds: A:Y.99 NEX.35: 10 residues within 4Å: Chain B: W.58, Y.99, A.124, V.125, Y.128, P.134 Ligands: CLA.22, CHL.24, CHL.26, CLA.28 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.58, B:A.124, B:V.125, B:Y.128, B:P.134 Hydrogen bonds: B:Y.99 NEX.53: 11 residues within 4Å: Chain C: W.58, Y.99, L.121, A.124, V.125, Y.128, P.134 Ligands: CLA.40, CHL.42, CHL.44, CLA.46 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.58, C:L.121, C:A.124, C:V.125, C:Y.128, C:P.134 Hydrogen bonds: C:Y.99

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

LHG.18: 11 residues within 4Å: Chain A: W.3, V.9, Y.31, K.169, R.172, L.173, F.176 Chain B: W.115 Ligands: CHL.1, CLA.11, CLA.13 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.172, A:L.173, A:F.176, A:F.176, B:W.115 Salt bridges: A:K.169, A:K.169 LHG.36: 10 residues within 4Å: Chain B: V.9, Y.31, K.169, R.172, L.173, F.176 Chain C: W.115 Ligands: CHL.19, CLA.29, CLA.31 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.115, B:R.172, B:L.173, B:F.176, B:F.176 Salt bridges: B:K.169, B:K.169 LHG.54: 10 residues within 4Å: Chain A: W.115 Chain C: V.9, Y.31, K.169, R.172, L.173, F.176 Ligands: CHL.37, CLA.47, CLA.49 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:R.172, C:L.173, C:F.176, C:F.176, A:W.115 Salt bridges: C:K.169, C:K.169

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