SMTL ID : 4lcz.1

Crystal structure of a multilayer-packed major light-harvesting complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

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

LUT.1: 21 residues within 4Å: Chain A: M.65, A.68, F.153, D.154, P.155, L.156, L.158, N.175, L.178, A.179, S.182, F.186, Q.189, P.197, N.200, L.201 Ligands: CHL.12, CLA.14, CLA.16, CLA.17, CLA.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.65, A:A.68, A:L.178, A:A.179, A:F.186, A:L.201 Hydrogen bonds: A:D.154, A:L.156, A:Q.189, A:L.201 LUT.2: 21 residues within 4Å: Chain A: W.38, D.39, T.40, A.41, L.43, H.60, W.63, A.64, G.67, G.70, C.71, W.89, A.92, M.180, M.183 Ligands: CLA.6, CLA.7, CLA.8, CHL.10, CHL.11, CLA.29 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.38, A:W.38, A:W.38, A:A.41, A:A.64, A:W.89, A:W.89, A:M.180 Hydrogen bonds: A:D.39, A:T.40, A:A.41 Water bridges: A:T.40 LUT.23: 20 residues within 4Å: Chain B: M.65, A.68, L.69, F.153, D.154, P.155, L.156, G.157, L.158, N.175, S.182, F.186, Q.189, P.197, N.200 Ligands: CHL.34, CLA.36, CLA.38, CLA.39, CLA.40 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:M.65, B:A.68, B:L.69, B:L.156, B:L.158, B:F.186 Hydrogen bonds: B:D.154, B:L.156, B:G.157, B:Q.189, B:L.201 LUT.24: 22 residues within 4Å: Chain B: W.38, D.39, T.40, A.41, L.43, H.60, W.63, A.64, G.67, G.70, C.71, W.89, A.92, M.180, M.183 Ligands: CLA.28, CLA.29, CLA.30, CHL.32, CHL.33, CLA.51, CHL.57 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.38, B:W.38, B:W.38, B:A.41, B:A.64, B:W.89, B:W.89, B:M.180 Hydrogen bonds: B:D.39, B:T.40, B:A.41 LUT.45: 20 residues within 4Å: Chain C: M.65, A.68, L.69, F.153, D.154, P.155, L.156, L.158, N.175, L.178, A.179, S.182, F.186, Q.189, P.197, N.200 Ligands: CHL.56, CLA.58, CLA.60, CLA.61 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:M.65, C:A.68, C:L.69, C:L.178, C:A.179, C:F.186 Hydrogen bonds: C:D.154, C:L.156, C:Q.189, C:P.197 LUT.46: 22 residues within 4Å: Chain C: W.38, D.39, T.40, A.41, L.43, H.60, W.63, A.64, G.67, G.70, C.71, W.89, A.92, M.180, M.183, F.184 Ligands: CLA.7, CLA.50, CLA.51, CLA.52, CHL.54, CHL.55 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.38, C:W.38, C:A.41, C:L.43, C:W.63, C:A.64, C:W.89, C:W.89, C:M.180, C:F.184 Hydrogen bonds: C:D.39, C:T.40, C:A.41 Water bridges: C:T.40, C:W.89, C:G.93

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.3: 8 residues within 4Å: Chain A: W.63, Y.104, V.130, Y.133, P.139 Ligands: CLA.8, CHL.10, CHL.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.63, A:V.130, A:P.139 Hydrogen bonds: A:Y.104 NEX.25: 11 residues within 4Å: Chain B: W.63, Y.104, L.126, A.129, V.130, Y.133, P.139 Ligands: CLA.30, CHL.32, CHL.34, CLA.36 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.63, B:L.126, B:A.129, B:V.130, B:P.139 Hydrogen bonds: B:Y.104, B:Y.104 NEX.47: 9 residues within 4Å: Chain C: W.63, Y.104, L.126, V.130, Y.133, P.139 Ligands: CLA.52, CHL.54, CHL.56 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.63, C:L.126, C:P.139 Hydrogen bonds: C:Y.104, C:Y.104

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

LHG.4: 11 residues within 4Å: Chain A: W.8, Y.36, K.174, R.177, L.178, F.181 Ligands: CHL.5, CLA.6, CLA.15, CLA.17, CLA.29 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.177, A:F.181, A:F.181 Salt bridges: A:K.174, A:K.174 LHG.26: 11 residues within 4Å: Chain B: W.8, Y.36, K.174, R.177, L.178, F.181 Ligands: CHL.27, CLA.28, CLA.37, CLA.39, CLA.51 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.177, B:F.181, B:F.181, B:F.181 Hydrogen bonds: B:Y.36 Salt bridges: B:K.174, B:K.174 LHG.48: 11 residues within 4Å: Chain C: W.8, Y.36, K.174, R.177, L.178, F.181 Ligands: CLA.7, CHL.49, CLA.50, CLA.59, CLA.61 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.177, C:F.181, C:F.181, C:F.181 Salt bridges: C:K.174, C:K.174

18 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.5: 15 residues within 4Å: Chain A: V.14, K.15, Y.16, L.17, G.18, P.19, F.20, Y.36, W.38, F.181 Chain B: W.120 Ligands: LHG.4, CLA.6, CHL.33, CHL.35 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:V.14, A:Y.16, A:Y.16, A:L.17, A:P.19, A:F.20, A:F.20, A:W.38 Metal complexes: A:Y.16 CHL.9: 12 residues within 4Å: Chain A: P.108, S.109, L.110, V.111, H.112, A.113, Q.114, S.115, A.118, I.119, C.122 Ligands: CHL.10 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:V.111, A:A.113, A:Q.114, A:I.119 Hydrogen bonds: A:V.111, A:Q.114, A:S.115 Metal complexes: A:V.111 CHL.10: 15 residues within 4Å: Chain A: W.63, G.93, L.102, V.111, A.113, I.119, C.122, Q.123, L.126 Ligands: LUT.2, NEX.3, CLA.8, CHL.9, CHL.11, CHL.13 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.63, A:L.102, A:V.111, A:A.113, A:I.119, A:I.119, A:L.126 Metal complexes: H2O.1 CHL.11: 15 residues within 4Å: Chain A: W.89, F.90, K.91, G.93, S.94, I.96, F.97, I.116, Q.123, F.187 Ligands: LUT.2, CLA.7, CHL.10, CHL.13, CHL.49 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.89, A:F.90, A:I.96, A:F.97, A:F.187 Hydrogen bonds: A:G.93, A:S.94, A:Q.123 Metal complexes: H2O.1 CHL.12: 21 residues within 4Å: Chain A: I.59, R.62, W.63, L.66, V.130, Y.133, R.134, G.137, G.138, P.139, L.140, G.141, P.146, L.147, P.149, S.152, F.153, P.155 Ligands: LUT.1, NEX.3, CLA.14 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.66, A:V.130, A:Y.133, A:R.134, A:P.139, A:L.140, A:L.140, A:P.149, A:P.149, A:F.153, A:F.153, A:F.153, A:F.153, A:P.155 Hydrogen bonds: A:R.62, A:L.140 Metal complexes: H2O.1 CHL.13: 20 residues within 4Å: Chain A: E.55, L.56, I.59, H.60, W.63, Q.123, M.127, G.128, E.131, R.134, I.135, F.184, I.191 Chain C: W.38, T.40 Ligands: CLA.7, CHL.10, CHL.11, CHL.49, CLA.50 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:I.59, A:W.63, A:W.63, A:I.135, A:F.184, A:I.191 Hydrogen bonds: A:Q.123 Salt bridges: A:R.134 pi-Cation interactions: A:R.134 Metal complexes: A:E.131 Water bridges: C:T.40 CHL.27: 15 residues within 4Å: Chain B: V.14, K.15, Y.16, L.17, G.18, P.19, F.20, Y.36, W.38, F.181 Chain C: W.120 Ligands: LHG.26, CLA.28, CHL.55, CHL.57 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:V.14, B:Y.16, B:Y.16, B:L.17, B:F.20, B:Y.36, B:W.38 Metal complexes: B:Y.16 CHL.31: 11 residues within 4Å: Chain B: P.108, S.109, L.110, V.111, H.112, A.113, Q.114, S.115, A.118, C.122 Ligands: CHL.32 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.111, B:H.112, B:A.113, B:Q.114, B:Q.114 Hydrogen bonds: B:V.111, B:Q.114, B:S.115 Metal complexes: B:V.111 CHL.32: 15 residues within 4Å: Chain B: W.63, G.93, L.102, V.111, A.113, I.119, C.122, Q.123, L.126 Ligands: LUT.24, NEX.25, CLA.30, CHL.31, CHL.33, CHL.35 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.63, B:L.102, B:V.111, B:A.113, B:I.119, B:I.119, B:L.126 Metal complexes: H2O.3 CHL.33: 15 residues within 4Å: Chain B: W.89, F.90, K.91, G.93, S.94, I.96, F.97, I.116, Q.123, F.187 Ligands: CHL.5, LUT.24, CLA.29, CHL.32, CHL.35 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.89, B:F.90, B:I.96, B:F.97, B:I.116, B:F.187 Hydrogen bonds: B:G.93, B:S.94, B:Q.123 Water bridges: B:A.92 Metal complexes: H2O.3 CHL.34: 21 residues within 4Å: Chain B: I.59, R.62, W.63, L.66, V.130, Y.133, R.134, G.137, G.138, P.139, L.140, G.141, E.142, P.146, P.149, S.152, F.153, P.155 Ligands: LUT.23, NEX.25, CLA.36 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.66, B:V.130, B:Y.133, B:R.134, B:P.139, B:L.140, B:L.140, B:P.149, B:F.153, B:F.153, B:F.153, B:P.155 Hydrogen bonds: B:R.62, B:L.140, B:G.141 pi-Cation interactions: B:R.134 Metal complexes: H2O.3 CHL.35: 21 residues within 4Å: Chain A: Y.16, W.38, T.40 Chain B: E.55, L.56, I.59, H.60, W.63, Q.123, M.127, G.128, E.131, R.134, I.135, F.184, I.191 Ligands: CHL.5, CLA.6, CLA.29, CHL.32, CHL.33 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.59, B:W.63, B:M.127, B:I.135, B:F.184, B:I.191 Hydrogen bonds: B:Q.123 Salt bridges: B:R.134 pi-Cation interactions: B:R.134 Metal complexes: B:E.131 Water bridges: A:T.40 CHL.49: 16 residues within 4Å: Chain A: W.120, Q.123, G.128 Chain C: V.14, K.15, Y.16, L.17, G.18, P.19, F.20, Y.36, W.38 Ligands: CHL.11, CHL.13, LHG.48, CLA.50 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:V.14, C:Y.16, C:L.17, C:P.19, C:F.20, C:Y.36, C:W.38 Metal complexes: C:Y.16 CHL.53: 12 residues within 4Å: Chain C: P.108, S.109, L.110, V.111, H.112, A.113, Q.114, S.115, A.118, I.119, C.122 Ligands: CHL.54 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:V.111, C:H.112, C:A.113, C:Q.114, C:I.119 Hydrogen bonds: C:V.111, C:Q.114, C:S.115 pi-Stacking: C:H.112 Metal complexes: C:V.111 CHL.54: 15 residues within 4Å: Chain C: W.63, G.93, L.102, V.111, A.113, I.119, C.122, Q.123, L.126 Ligands: LUT.46, NEX.47, CLA.52, CHL.53, CHL.55, CHL.57 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.63, C:L.102, C:V.111, C:A.113, C:I.119, C:I.119, C:L.126 Water bridges: C:G.93 Metal complexes: H2O.6 CHL.55: 15 residues within 4Å: Chain C: W.89, F.90, K.91, G.93, S.94, I.96, F.97, I.116, Q.123, F.187 Ligands: CHL.27, LUT.46, CLA.51, CHL.54, CHL.57 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.89, C:F.90, C:I.96, C:F.97, C:I.116, C:F.187 Hydrogen bonds: C:G.93, C:S.94, C:Q.123 Metal complexes: H2O.5 CHL.56: 22 residues within 4Å: Chain C: I.59, R.62, W.63, L.66, V.130, Y.133, R.134, G.137, G.138, P.139, L.140, G.141, E.142, P.146, L.147, P.149, S.152, F.153, P.155 Ligands: LUT.45, NEX.47, CLA.58 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:L.66, C:V.130, C:V.130, C:Y.133, C:R.134, C:R.134, C:P.139, C:L.140, C:L.140, C:L.140, C:P.149, C:P.149, C:F.153, C:F.153, C:F.153, C:F.153, C:P.155 Hydrogen bonds: C:R.62, C:L.140, C:G.141 pi-Cation interactions: C:R.134 Metal complexes: H2O.5 CHL.57: 23 residues within 4Å: Chain B: Y.16, L.17, W.38, T.40 Chain C: E.55, L.56, I.59, H.60, W.63, Q.123, M.127, G.128, E.131, R.134, I.135, F.184, I.191 Ligands: LUT.24, CHL.27, CLA.28, CLA.51, CHL.54, CHL.55 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:I.59, C:W.63, C:M.127, C:E.131, C:I.135, C:F.184, C:I.191, B:L.17, B:T.40 Hydrogen bonds: C:Q.123 Salt bridges: C:R.134 pi-Cation interactions: C:R.134 Metal complexes: C:E.131 Water bridges: B:T.40

24 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.6: 27 residues within 4Å: Chain A: L.28, P.33, G.34, D.35, Y.36, G.37, W.38, D.39, L.43, S.44, F.50, N.53, R.54, L.56, E.57, H.60, R.177, M.180, F.181, F.184 Ligands: LUT.2, LHG.4, CHL.5, CLA.7, CLA.17, CLA.29, CHL.35 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.36, A:W.38, A:W.38, A:W.38, A:L.43, A:R.54, A:L.56, A:H.60, A:R.177, A:M.180, A:F.181, A:F.184 Hydrogen bonds: A:Y.36, A:W.38, A:N.53 Salt bridges: A:R.177 pi-Stacking: A:W.38 pi-Cation interactions: A:R.177 Metal complexes: A:E.57 CLA.7: 13 residues within 4Å: Chain A: L.56, H.60, F.187 Chain C: A.41 Ligands: LUT.2, CLA.6, CHL.11, CHL.13, CLA.29, LUT.46, LHG.48, CLA.50, CLA.51 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:L.56, A:F.187, C:A.41 Metal complexes: A:H.60 CLA.8: 17 residues within 4Å: Chain A: L.66, G.67, L.69, G.70, F.73, P.74, F.84, E.86, Q.95, L.102, Y.104, L.105, L.110, V.111 Ligands: LUT.2, NEX.3, CHL.10 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.66, A:L.69, A:L.102, A:Y.104, A:Y.104, A:L.105, A:L.105, A:L.110 Hydrogen bonds: A:Q.95, A:L.105 Water bridges: A:G.106 pi-Stacking: A:Y.104 Metal complexes: H2O.2 CLA.14: 19 residues within 4Å: Chain A: R.62, M.65, L.66, Y.148, P.149, G.150, F.153, D.154, L.158, A.159, F.165, L.168, K.169, K.171, E.172, N.175 Ligands: LUT.1, CHL.12, CLA.16 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:R.62, A:R.62, A:M.65, A:F.153, A:F.165, A:L.168, A:K.171, A:N.175 Hydrogen bonds: A:G.150 pi-Cation interactions: A:R.62 Metal complexes: A:E.172 CLA.15: 10 residues within 4Å: Chain A: W.8, L.69, V.72, E.167, K.171, K.174, N.175, L.178 Ligands: LHG.4, CLA.16 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:W.8, A:L.69, A:V.72, A:K.174, A:L.178 Hydrogen bonds: A:N.175 Salt bridges: A:K.174 pi-Cation interactions: A:K.174, A:K.174 CLA.16: 6 residues within 4Å: Chain A: K.171, N.175, L.178 Ligands: LUT.1, CLA.14, CLA.15 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:K.171, A:L.178 Salt bridges: A:K.171, A:K.171 CLA.17: 17 residues within 4Å: Chain A: F.181, S.182, G.185, V.188, Q.189, V.192, T.193, N.200, L.201, H.204, N.212, A.213 Chain B: W.120 Ligands: LUT.1, LHG.4, CLA.6, CLA.18 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.181, A:F.181, A:V.188, A:Q.189, A:V.192, A:A.213, B:W.120, B:W.120 Hydrogen bonds: A:Q.189, A:A.213 pi-Stacking: A:H.204 CLA.18: 8 residues within 4Å: Chain A: H.204, L.205, P.208, V.209, N.212 Chain B: L.117 Ligands: LUT.1, CLA.17 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:V.209 Metal complexes: A:H.204 CLA.28: 27 residues within 4Å: Chain B: L.28, P.33, G.34, D.35, Y.36, G.37, W.38, D.39, L.43, S.44, F.50, N.53, R.54, L.56, E.57, H.60, R.177, M.180, F.181, F.184 Ligands: LUT.24, LHG.26, CHL.27, CLA.29, CLA.39, CLA.51, CHL.57 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:Y.36, B:W.38, B:W.38, B:D.39, B:L.43, B:F.50, B:N.53, B:R.54, B:L.56, B:H.60, B:R.177, B:R.177, B:M.180, B:F.181, B:F.184 Hydrogen bonds: B:Y.36, B:G.37, B:W.38, B:N.53 Salt bridges: B:R.177 pi-Stacking: B:W.38 pi-Cation interactions: B:R.177 Metal complexes: B:E.57 CLA.29: 13 residues within 4Å: Chain A: A.41 Chain B: L.56, H.60, F.187 Ligands: LUT.2, LHG.4, CLA.6, CLA.7, LUT.24, CLA.28, CHL.33, CHL.35, CLA.51 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:A.41, B:L.56, B:L.56, B:F.187, B:F.187 Water bridges: B:N.53 Metal complexes: B:H.60 CLA.30: 16 residues within 4Å: Chain B: L.66, L.69, G.70, F.73, P.74, F.84, E.86, Q.95, L.102, Y.104, L.105, L.110 Ligands: LUT.24, NEX.25, CHL.32, CLA.36 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.66, B:L.69, B:F.73, B:P.74, B:L.102, B:Y.104, B:Y.104, B:Y.104, B:L.105, B:L.110 Hydrogen bonds: B:Q.95, B:L.105 pi-Stacking: B:Y.104 Metal complexes: H2O.4 CLA.36: 21 residues within 4Å: Chain B: R.62, M.65, L.66, Y.148, P.149, G.150, F.153, D.154, L.158, A.159, F.165, L.168, K.169, K.171, E.172, N.175 Ligands: LUT.23, NEX.25, CLA.30, CHL.34, CLA.38 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:R.62, B:M.65, B:L.66, B:L.66, B:L.66, B:F.153, B:F.165, B:L.168, B:K.171, B:N.175 Hydrogen bonds: B:G.150 pi-Cation interactions: B:R.62 Metal complexes: B:E.172 CLA.37: 9 residues within 4Å: Chain B: W.8, L.69, V.170, K.171, K.174, N.175, L.178 Ligands: LHG.26, CLA.38 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:W.8, B:L.69, B:K.174, B:L.178 Hydrogen bonds: B:N.175 Salt bridges: B:K.174 pi-Cation interactions: B:K.174, B:K.174 CLA.38: 6 residues within 4Å: Chain B: K.171, N.175, L.178 Ligands: LUT.23, CLA.36, CLA.37 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:K.171, B:L.178 Salt bridges: B:K.171, B:K.171 CLA.39: 17 residues within 4Å: Chain B: F.181, S.182, G.185, V.188, Q.189, V.192, T.193, N.200, L.201, H.204, N.212, A.213 Chain C: W.120 Ligands: LUT.23, LHG.26, CLA.28, CLA.40 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:W.120, B:F.181, B:F.181, B:Q.189, B:V.192, B:L.201 Hydrogen bonds: B:Q.189, B:A.213 CLA.40: 8 residues within 4Å: Chain B: L.201, H.204, L.205, P.208, N.212, A.213 Ligands: LUT.23, CLA.39 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.201, B:P.208 Metal complexes: B:H.204 CLA.50: 25 residues within 4Å: Chain C: L.28, P.33, G.34, D.35, Y.36, G.37, W.38, D.39, L.43, S.44, F.50, N.53, R.54, L.56, E.57, H.60, R.177, M.180, F.181 Ligands: CLA.7, CHL.13, LUT.46, LHG.48, CHL.49, CLA.51 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Y.36, C:W.38, C:W.38, C:L.43, C:F.50, C:N.53, C:R.54, C:L.56, C:H.60, C:R.177, C:R.177, C:M.180 Hydrogen bonds: C:Y.36, C:W.38, C:N.53 Salt bridges: C:R.177 pi-Stacking: C:W.38 pi-Cation interactions: C:R.177 Metal complexes: C:E.57 CLA.51: 12 residues within 4Å: Chain C: L.56, H.60, F.187 Ligands: CLA.7, LUT.24, LHG.26, CLA.28, CLA.29, LUT.46, CLA.50, CHL.55, CHL.57 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.56, C:L.56, C:F.187, C:F.187 Metal complexes: C:H.60 CLA.52: 16 residues within 4Å: Chain C: L.66, G.67, L.69, G.70, F.73, P.74, F.84, E.86, Q.95, L.102, Y.104, L.105, L.110 Ligands: LUT.46, NEX.47, CHL.54 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:L.66, C:L.69, C:L.102, C:Y.104, C:Y.104, C:L.105, C:L.105, C:L.110 Hydrogen bonds: C:Q.95, C:L.105 pi-Stacking: C:Y.104 Metal complexes: H2O.5 CLA.58: 18 residues within 4Å: Chain C: R.62, M.65, L.66, Y.148, P.149, G.150, F.153, L.158, A.159, F.165, L.168, K.169, K.171, E.172, N.175 Ligands: LUT.45, CHL.56, CLA.60 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:R.62, C:R.62, C:M.65, C:L.66, C:F.153, C:L.168, C:K.171, C:E.172, C:N.175 Hydrogen bonds: C:G.150 pi-Cation interactions: C:R.62 Metal complexes: C:E.172 CLA.59: 9 residues within 4Å: Chain C: W.8, V.72, L.76, K.171, K.174, N.175, L.178 Ligands: LHG.48, CLA.60 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:W.8, C:V.72, C:L.76, C:K.174, C:L.178 Hydrogen bonds: C:N.175 Salt bridges: C:K.174 pi-Cation interactions: C:K.174, C:K.174 CLA.60: 6 residues within 4Å: Chain C: K.171, N.175, L.178 Ligands: LUT.45, CLA.58, CLA.59 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.178 Salt bridges: C:K.171, C:K.171 CLA.61: 17 residues within 4Å: Chain A: W.120 Chain C: F.181, S.182, F.184, G.185, V.188, Q.189, V.192, T.193, N.200, L.201, H.204, N.212, A.213 Ligands: LUT.45, LHG.48, CLA.62 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain C, Hydrophobic interactions: A:W.120, C:F.181, C:F.181, C:F.184, C:F.184, C:Q.189, C:V.192, C:A.213 Hydrogen bonds: C:A.213 CLA.62: 6 residues within 4Å: Chain C: H.204, L.205, P.208, N.212, A.213 Ligands: CLA.61 1 PLIP interactions: 1 interactions with chain C, Metal complexes: C:H.204

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.19: 3 residues within 4Å: Chain A: E.99, G.100 Ligands: ZN.21 No protein-ligand interaction detected (PLIP) CAC.41: 3 residues within 4Å: Chain B: E.99, G.100 Ligands: ZN.43 No protein-ligand interaction detected (PLIP) CAC.63: 3 residues within 4Å: Chain C: E.99, G.100 Ligands: ZN.65 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.20: 3 residues within 4Å: Chain A: D.46 Chain B: D.46 Chain C: D.46 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.46, H2O.6 ZN.21: 3 residues within 4Å: Chain A: E.99, G.100 Ligands: CAC.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.99 ZN.22: 3 residues within 4Å: Chain A: K.195, E.199, D.203 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.199, A:D.203, H2O.3 ZN.43: 2 residues within 4Å: Chain B: E.99 Ligands: CAC.41 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.99 ZN.65: 3 residues within 4Å: Chain C: E.99, G.100 Ligands: CAC.63 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.99

5 x NA: SODIUM ION(Non-functional Binders)

NA.42: 3 residues within 4Å: Chain B: K.195, E.199, D.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.195, B:E.199 Water bridges: B:D.203 NA.44: 2 residues within 4Å: Chain A: S.26 Chain B: E.48 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.26, B:E.48 NA.64: 3 residues within 4Å: Chain C: K.195, E.199, D.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.195, C:E.199 NA.66: 1 residues within 4Å: Chain C: E.163 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.163 NA.67: 2 residues within 4Å: Chain B: A.45 Chain C: D.46 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, T. et al., Crystal structure of a multilayer packed major light-harvesting complex: implications for grana stacking in higher plants. Mol Plant (2014)

Release Date

2014-05-07

Peptides

Major chlorophyll a/b binding protein LHCb1.3: 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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Major chlorophyll a/b binding protein LHCb1.3