SMTL ID : 8j0d.1

FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds to the PSII core in the diatom Thalassiosira pseudonana

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

39 x CLA: CHLOROPHYLL A(Non-covalent)(Covalent)(Non-functional Binders)

CLA.1: 11 residues within 4Å: Chain A: R.6, A.7, L.8, P.9, F.10, V.25, F.27 Ligands: CLA.2, CLA.8, LHG.17, LHG.18 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.8, A:P.9, A:F.10, A:F.27 Salt bridges: A:R.6 CLA.2: 20 residues within 4Å: Chain A: L.17, G.23, D.24, V.25, G.26, F.27, D.28, G.31, F.32, V.54, L.57, R.58, E.61, R.175, M.178 Ligands: CLA.1, CLA.3, DD6.14, LHG.18, CLA.34 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.25, A:F.27, A:F.32, A:F.32, A:L.57, A:L.57 Hydrogen bonds: A:V.25, A:G.26, A:F.27, A:R.175 Salt bridges: A:R.58 pi-Cation interactions: A:R.175, A:R.175 CLA.3: 11 residues within 4Å: Chain A: F.37, H.64 Ligands: CLA.2, CLA.6, CLA.11, CLA.12, DD6.14, DGD.20, A86.24, CLA.28, LMT.37 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.37 Metal complexes: A:H.64 CLA.4: 11 residues within 4Å: Chain A: L.70, A.71, G.74, W.77, T.83, F.84, Y.96, Y.98, A.104, I.108 Ligands: DD6.14 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.77, A:F.84, A:I.108, A:I.108 Hydrogen bonds: A:T.83, A:F.84 CLA.5: 11 residues within 4Å: Chain A: L.70, L.111, Y.114, Q.115, I.116, G.118, G.119, M.120, W.122 Ligands: CLA.6, DD6.14 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:L.70, A:Y.114, A:Q.115, A:Q.115, A:W.122, A:W.122, A:W.122 CLA.6: 13 residues within 4Å: Chain A: W.56, A.60, T.63, H.64, M.120, E.124, R.127, V.128 Ligands: CLA.3, CLA.5, CLA.11, CLA.12, A86.22 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:W.56, A:T.63, A:V.128 Salt bridges: A:R.127 Metal complexes: A:E.124 CLA.7: 17 residues within 4Å: Chain A: R.66, Q.69, L.70, I.139, S.140, D.142, G.144, L.145, A.146, Y.147, Y.158, Y.163, K.166, Q.167, E.170 Ligands: KC1.9, A86.13 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:R.66, A:R.66, A:L.70, A:L.145, A:L.145, A:Y.163, A:K.166, A:Q.167 Hydrogen bonds: A:L.145 pi-Cation interactions: A:R.66 Metal complexes: A:E.170 CLA.8: 8 residues within 4Å: Chain A: E.165, L.168, Q.169, K.172, H.173 Ligands: CLA.1, KC1.9, LHG.17 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:K.172 Salt bridges: A:K.172 CLA.10: 10 residues within 4Å: Chain A: G.183, F.186, Q.187, N.190, S.191, Q.198 Ligands: A86.13, LMG.16, LHG.18, CLA.19 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:F.186, A:Q.187 Hydrogen bonds: A:N.190, A:Q.198 CLA.11: 10 residues within 4Å: Chain A: Y.125 Chain D: L.11, F.14, M.148, L.151 Ligands: CLA.3, CLA.6, CLA.12, A86.60, A86.62 3 PLIP interactions: 3 interactions with chain D, Hydrophobic interactions: D:L.11, D:F.14, D:L.151 CLA.12: 11 residues within 4Å: Chain A: F.37, F.40, N.41, N.42, P.43 Chain B: S.103 Ligands: CLA.3, CLA.6, CLA.11, CLA.34, A86.62 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.40, A:P.43 CLA.19: 12 residues within 4Å: Chain A: F.182, F.186, N.190 Chain B: L.46, A.50, T.53, Y.54, F.161, L.162 Ligands: CLA.10, LHG.18, CLA.28 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.46, B:A.50, B:Y.54, B:Y.54, B:L.162, A:F.182, A:F.186 Hydrogen bonds: A:N.190 CLA.25: 10 residues within 4Å: Chain B: L.7, P.8, P.9, K.117, T.120, A.121, Q.124, H.125, L.128 Ligands: CLA.32 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:P.8, B:P.9, B:Q.124, B:L.128 CLA.26: 14 residues within 4Å: Chain B: G.5, F.12, F.13, L.18, Y.30, R.31, E.34, H.37, R.127, M.130, L.131 Ligands: A86.21, DD6.23, KC2.27 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:F.13, B:F.13, B:L.18, B:Y.30, B:E.34, B:H.37, B:L.131 Salt bridges: B:R.31 pi-Cation interactions: B:R.127, B:R.127 Metal complexes: B:E.34 CLA.28: 20 residues within 4Å: Chain B: L.43, A.44, G.47, A.50, P.51, Y.54, R.55, F.56, Y.58, T.67, I.70, W.85, M.88 Ligands: CLA.3, CLA.19, A86.22, DD6.23, CLA.34, LMT.37, LHG.38 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.43, B:A.44, B:A.50, B:Y.54, B:F.56, B:F.56, B:W.85 Hydrogen bonds: B:F.56 Salt bridges: B:R.55 CLA.29: 15 residues within 4Å: Chain B: L.60, I.61, P.81, G.83, G.84, Q.87, M.88, I.89, A.90, F.91 Chain C: N.78 Ligands: A86.22, KC2.48, CLA.51, LHG.56 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:I.89, B:A.90, B:F.91 CLA.30: 16 residues within 4Å: Chain B: L.32, A.33, K.36, H.37, I.89, V.92, G.93, E.96, T.97 Chain C: F.97, T.100, R.101 Ligands: A86.22, KC2.27, LHG.38, CLA.51 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:K.36, B:V.92 Salt bridges: B:K.36, C:R.101 pi-Cation interactions: B:K.36, B:K.36 CLA.31: 14 residues within 4Å: Chain A: I.30 Chain B: R.39, M.42, L.43, V.107, L.108, L.110, R.118, Q.119, E.122, H.125 Ligands: A86.24, CLA.32, CLA.34 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B, Hydrophobic interactions: A:I.30, B:R.39, B:R.39, B:M.42, B:L.43, B:R.118, B:Q.119, B:H.125 Salt bridges: B:R.118 pi-Cation interactions: B:R.39, B:R.39 Metal complexes: B:E.122 CLA.32: 9 residues within 4Å: Chain A: P.29, I.30 Chain B: A.121, H.125, L.128 Ligands: LMG.15, A86.24, CLA.25, CLA.31 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:A.121, B:L.128, A:P.29, A:I.30 Salt bridges: B:K.117, B:R.118 pi-Cation interactions: B:H.125, B:H.125 Metal complexes: B:H.125 CLA.33: 9 residues within 4Å: Chain B: L.131, A.132, L.134, E.135, R.138, D.150 Ligands: A86.21, A86.24, CLA.36 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:L.134, B:E.135 Salt bridges: B:R.138 pi-Cation interactions: B:R.138 Metal complexes: B:E.135 CLA.34: 11 residues within 4Å: Chain B: F.91, F.101, T.102, S.103, G.106 Ligands: CLA.2, CLA.12, A86.22, A86.24, CLA.28, CLA.31 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.91, B:F.91, B:F.101, B:F.101 Hydrogen bonds: B:S.103 Metal complexes: B:F.101 CLA.35: 4 residues within 4Å: Chain B: R.138, S.141, Q.142, A.145 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:R.138 CLA.36: 7 residues within 4Å: Chain B: L.152, T.157, G.158, L.159, P.160, F.161 Ligands: CLA.33 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:P.160, B:F.161 CLA.46: 9 residues within 4Å: Chain C: A.8, P.9, N.134, A.137, I.138, N.141, Q.142 Ligands: A86.39, KC1.53 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:P.9 Hydrogen bonds: C:N.141 CLA.47: 17 residues within 4Å: Chain C: G.5, A.6, L.10, G.11, F.12, W.13, F.18, L.19, L.30, R.31, E.34, R.144, M.147, M.148 Ligands: A86.39, A86.41, KC2.48 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.10, C:F.18, C:L.19, C:L.30, C:E.34, C:E.34, C:R.144 Hydrogen bonds: C:W.13 Salt bridges: C:R.31, C:R.144 pi-Cation interactions: C:R.144, C:R.144 Metal complexes: C:E.34 CLA.49: 11 residues within 4Å: Chain C: L.43, A.44, G.47, I.50, T.51, H.56, L.57, F.67, V.70 Ligands: A86.40, A86.41 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.43, C:A.44, C:I.50, C:L.57 Hydrogen bonds: C:H.56, C:L.57 Salt bridges: C:H.56 CLA.50: 6 residues within 4Å: Chain C: A.87, Q.90, T.91, F.94 Ligands: A86.40, LMG.57 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:A.87, C:Q.90, C:T.91 CLA.51: 21 residues within 4Å: Chain B: A.90, G.93, C.94, Y.98 Chain C: Y.32, V.33, K.36, H.37, I.40, L.92, I.95, G.96, E.99 Ligands: CLA.29, CLA.30, LHG.38, A86.40, A86.41, A86.44, KC2.48, LHG.56 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:K.36, C:I.40, C:L.92, C:I.95 Salt bridges: C:K.36 pi-Cation interactions: C:K.36, C:K.36 CLA.52: 18 residues within 4Å: Chain C: R.39, Q.42, F.112, G.114, D.115, F.116, R.117, F.122, G.123, W.124, K.126, K.135, I.138, E.139, Q.142 Ligands: A86.40, A86.42, A86.43 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:R.39, C:R.39, C:Q.42, C:F.116, C:W.124, C:W.124, C:K.135, C:K.135, C:E.139, C:Q.142 Hydrogen bonds: C:D.115, C:F.116, C:F.122, C:G.123, C:W.124 Salt bridges: C:R.117, C:K.135 pi-Cation interactions: C:R.39 Metal complexes: C:E.139 CLA.54: 9 residues within 4Å: Chain C: M.148, L.151, G.152, M.155, H.156, V.159 Ligands: A86.39, A86.43, CLA.55 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.151, C:M.155 pi-Stacking: C:H.156 CLA.55: 2 residues within 4Å: Ligands: A86.45, CLA.54 0 PLIP interactions: CLA.65: 12 residues within 4Å: Chain A: Y.125, Q.126, Q.129 Chain D: Q.8, P.9, P.10, A.137, I.138, N.141, N.142 Ligands: A86.60, KC1.72 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: D:P.9, D:P.10, D:I.138, A:Y.125, A:Q.126 Hydrogen bonds: D:Q.8, D:N.142 CLA.66: 17 residues within 4Å: Chain D: F.1, L.5, G.6, G.12, F.13, F.14, M.19, L.20, L.31, R.32, V.34, E.35, R.144, M.147 Ligands: A86.60, A86.62, KC2.67 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.20, D:L.31, D:L.31, D:V.34, D:E.35, D:E.35, D:R.144 Hydrogen bonds: D:F.14, D:D.15, D:R.144 Salt bridges: D:R.32 pi-Cation interactions: D:R.144, D:R.144 Metal complexes: D:E.35 CLA.68: 12 residues within 4Å: Chain D: L.44, A.45, L.47, G.48, I.51, T.52, H.57, L.58, I.72, G.73 Ligands: A86.61, A86.62 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:L.44, D:A.45, D:L.47, D:T.52, D:L.58 Hydrogen bonds: D:L.58 Salt bridges: D:H.57 CLA.69: 8 residues within 4Å: Chain D: L.64, P.83, D.85, G.86, Q.89, I.90, F.93 Ligands: A86.61 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:F.93 CLA.70: 12 residues within 4Å: Chain D: R.30, Y.33, V.34, K.37, H.38, I.41, V.94, G.95, E.98 Ligands: A86.59, A86.61, KC2.67 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:K.37, D:I.41, D:V.94 Hydrogen bonds: D:Y.33 Salt bridges: D:K.37 pi-Cation interactions: D:K.37, D:K.37, D:K.37 Metal complexes: D:E.98 CLA.71: 12 residues within 4Å: Chain D: R.40, Q.43, L.44, F.111, G.113, D.114, F.115, R.116, W.124, I.138, E.139 Ligands: A86.63 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:R.40, D:Q.43, D:L.44, D:L.44, D:W.124, D:W.124, D:I.138, D:E.139 Hydrogen bonds: D:D.114, D:F.115, D:R.116 Salt bridges: D:R.116 pi-Cation interactions: D:R.40, D:R.40 CLA.73: 10 residues within 4Å: Chain A: Y.114 Chain D: M.148, G.152, V.155, H.156, L.159, L.163, P.164 Ligands: A86.60, A86.63 4 PLIP interactions: 4 interactions with chain D, Hydrophobic interactions: D:V.155, D:L.159, D:L.163 Metal complexes: D:H.156 CLA.74: 7 residues within 4Å: Chain D: S.79, F.80, V.82, K.84, A.87 Ligands: A86.39, A86.62 3 PLIP interactions: 3 interactions with chain D, Hydrophobic interactions: D:A.87 Hydrogen bonds: D:S.79 Salt bridges: D:K.84

3 x KC1: Chlorophyll c1(Covalent)(Non-covalent)

KC1.9: 7 residues within 4Å: Chain A: K.166, Q.169, H.173, L.176 Ligands: CLA.7, CLA.8, A86.13 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.176 Salt bridges: A:K.166 Metal complexes: A:H.173 KC1.53: 5 residues within 4Å: Chain C: I.138, Q.142 Ligands: A86.43, A86.45, CLA.46 0 PLIP interactions: KC1.72: 6 residues within 4Å: Chain D: K.135, I.138, N.142 Ligands: A86.63, A86.64, CLA.65 2 PLIP interactions: 2 interactions with chain D, Hydrophobic interactions: D:I.138 Salt bridges: D:K.135

17 x A86: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate(Non-covalent)

A86.13: 14 residues within 4Å: Chain A: Q.69, V.72, L.145, A.146, P.153, F.154, L.176, A.177, G.180, L.184, Q.187 Ligands: CLA.7, KC1.9, CLA.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.72, A:P.153, A:L.176, A:A.177, A:L.184 Hydrogen bonds: A:Q.187 A86.21: 6 residues within 4Å: Chain B: P.9, Q.124, L.128, L.131 Ligands: CLA.26, CLA.33 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.131 Hydrogen bonds: B:Q.124 A86.22: 13 residues within 4Å: Chain B: K.36, R.39, A.40, L.43, Y.58, D.59, P.62 Ligands: CLA.6, CLA.28, CLA.29, CLA.30, CLA.34, A86.60 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.36, B:Y.58, B:P.62 Hydrogen bonds: B:R.39 A86.24: 18 residues within 4Å: Chain A: F.32, F.37 Chain B: M.42, V.45, T.105, G.106, H.125, L.128, A.132, L.136, I.156, T.157, G.158 Ligands: CLA.3, CLA.31, CLA.32, CLA.33, CLA.34 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.105, B:L.128, B:A.132, A:F.32, A:F.32, A:F.37 Hydrogen bonds: B:G.158 A86.39: 7 residues within 4Å: Chain C: Q.7, M.148 Chain D: W.76 Ligands: CLA.46, CLA.47, CLA.54, CLA.74 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.76 Hydrogen bonds: C:Q.7 A86.40: 13 residues within 4Å: Chain C: K.36, I.40, L.43, D.60, I.61, F.94, I.95, M.103 Ligands: CLA.49, CLA.50, CLA.51, CLA.52, LMT.58 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.40, C:I.40, C:F.94, C:I.95, C:I.95 Hydrogen bonds: C:K.36 A86.41: 12 residues within 4Å: Chain C: W.13, L.16, H.37, G.73, I.74, M.147, L.151 Ligands: CLA.47, KC2.48, CLA.49, CLA.51, LHG.56 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.13, C:L.16, C:I.74, C:L.151 Hydrogen bonds: C:G.73, C:G.73 A86.42: 10 residues within 4Å: Chain C: V.102, F.116, R.117, N.118, F.120, F.122, W.131 Ligands: A86.43, A86.45, CLA.52 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.116, C:F.120, C:F.122, C:W.131 A86.43: 9 residues within 4Å: Chain C: Q.42, F.45, V.46, A.146, G.149 Ligands: A86.42, CLA.52, KC1.53, CLA.54 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.42, C:F.45, C:F.45, C:V.46, C:A.146 A86.44: 6 residues within 4Å: Chain C: M.155, Q.158 Ligands: KC2.48, CLA.51, LHG.56, A86.59 No protein-ligand interaction detected (PLIP) A86.45: 5 residues within 4Å: Chain C: R.52, A.53 Ligands: A86.42, KC1.53, CLA.55 No protein-ligand interaction detected (PLIP) A86.59: 9 residues within 4Å: Chain C: L.16, F.18, R.21 Chain D: R.27, M.154, V.155 Ligands: A86.44, KC2.67, CLA.70 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.18, D:V.155 Salt bridges: C:R.21, D:R.27 Hydrogen bonds: D:R.27 A86.60: 12 residues within 4Å: Chain D: Q.8, P.10, N.141, A.145, M.148 Ligands: CLA.11, A86.22, LMT.37, A86.63, CLA.65, CLA.66, CLA.73 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:M.148 A86.61: 8 residues within 4Å: Chain D: I.41, I.62, S.63, I.90, M.102 Ligands: CLA.68, CLA.69, CLA.70 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.41, D:I.62, D:I.90, D:I.90 Hydrogen bonds: D:S.63 A86.62: 17 residues within 4Å: Chain D: F.14, P.16, L.17, H.38, I.41, C.42, A.45, N.49, G.75, M.147, L.151 Ligands: CLA.11, CLA.12, CLA.66, KC2.67, CLA.68, CLA.74 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.14, D:L.17, D:I.41, D:A.45, D:L.151 Hydrogen bonds: D:G.75, D:G.75 A86.63: 15 residues within 4Å: Chain D: Q.43, F.46, L.47, N.142, A.145, A.146, G.149, L.163, P.164, I.165, V.166 Ligands: A86.60, CLA.71, KC1.72, CLA.73 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.46, D:F.46, D:F.46, D:L.47, D:A.145, D:A.146, D:L.163, D:I.165 Hydrogen bonds: D:P.164 A86.64: 6 residues within 4Å: Chain D: I.50, R.53, A.54, I.165, V.166 Ligands: KC1.72 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.166

2 x DD6: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol(Non-covalent)

DD6.14: 14 residues within 4Å: Chain A: F.27, P.29, I.30, H.64, I.67, A.71, F.75, P.101, M.178 Ligands: CLA.2, CLA.3, CLA.4, CLA.5, DGD.20 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.27, A:I.30, A:I.67, A:A.71, A:F.75 Hydrogen bonds: A:I.30, A:P.101 DD6.23: 16 residues within 4Å: Chain B: F.13, D.14, P.15, A.16, L.18, H.37, A.40, A.44, G.73, M.130, F.133, L.134 Ligands: CLA.26, KC2.27, CLA.28, LHG.38 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.13, B:L.18, B:A.40, B:M.130, B:F.133, B:F.133, B:F.133, B:L.134 Hydrogen bonds: B:D.14, B:D.14, B:A.16, B:G.73, B:G.73

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

LMG.15: 7 residues within 4Å: Chain A: F.10, G.11, S.12 Chain B: I.114, K.117, R.118 Ligands: CLA.32 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.118, B:R.118, A:F.10, A:F.10, A:S.12, A:S.12 Salt bridges: B:K.117 LMG.16: 4 residues within 4Å: Chain A: Q.198, L.199, A.202 Ligands: CLA.10 No protein-ligand interaction detected (PLIP) LMG.57: 6 residues within 4Å: Chain B: K.78 Chain C: S.62, S.84, Q.90 Ligands: LHG.38, CLA.50 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.84, C:S.84, B:K.78

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

LHG.17: 4 residues within 4Å: Chain A: R.6, K.172 Ligands: CLA.1, CLA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.6 Salt bridges: A:K.172 LHG.18: 6 residues within 4Å: Chain A: N.190 Chain B: F.161 Ligands: CLA.1, CLA.2, CLA.10, CLA.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.161 LHG.38: 11 residues within 4Å: Chain B: I.77, W.85, S.141, L.144 Chain C: A.86 Ligands: DD6.23, KC2.27, CLA.28, CLA.30, CLA.51, LMG.57 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.77, B:W.85 LHG.56: 5 residues within 4Å: Chain C: Q.158 Ligands: CLA.29, A86.41, A86.44, CLA.51 No protein-ligand interaction detected (PLIP)

1 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.20: 6 residues within 4Å: Chain A: F.182, F.185 Chain B: Y.54 Ligands: CLA.3, DD6.14, LMT.37 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.54, A:F.182, A:F.185, A:F.185

3 x KC2: Chlorophyll c2(Covalent)(Non-covalent)

KC2.27: 8 residues within 4Å: Chain B: Y.30, H.37 Chain C: F.97, R.101 Ligands: DD6.23, CLA.26, CLA.30, LHG.38 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:F.97 Hydrogen bonds: C:R.101 Salt bridges: C:R.101 Metal complexes: B:H.37 KC2.48: 10 residues within 4Å: Chain B: Y.98, W.100 Chain C: R.29, V.33, H.37 Ligands: CLA.29, A86.41, A86.44, CLA.47, CLA.51 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:V.33 Salt bridges: C:R.29 Metal complexes: C:H.37 KC2.67: 7 residues within 4Å: Chain C: L.16 Chain D: R.30, H.38 Ligands: A86.59, A86.62, CLA.66, CLA.70 3 PLIP interactions: 3 interactions with chain D, Salt bridges: D:R.30, D:R.30 pi-Stacking: D:H.38

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.37: 6 residues within 4Å: Chain B: G.57, D.59 Ligands: CLA.3, DGD.20, CLA.28, A86.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.57 LMT.58: 4 residues within 4Å: Chain C: L.57, P.58, D.60 Ligands: A86.40 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.57 Hydrogen bonds: C:D.60, C:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Y. et al., Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Sci Adv (2023)

Release Date

2023-10-25

Peptides

Fucoxanthin chl a/c protein, lhca clade: A
Fucoxanthin-chlorophyll a-c binding protein, plastid: B
Fucoxanthin chlorophyll a/c protein 6: C
Fucoxanthin chlorophyll a/c protein 5: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
4

C
5

D
6

Membrane

We predict this structure to be a membrane protein.
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Fucoxanthin chl a/c protein, lhca clade

Fucoxanthin-chlorophyll a-c binding protein, plastid

Fucoxanthin chlorophyll a/c protein 6

Fucoxanthin chlorophyll a/c protein 5

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