- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 18 x CHL: CHLOROPHYLL B(Non-covalent)(Covalent)
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
CLA.2: 23 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, R.172, M.175, F.176, F.179
- Ligands: CHL.1, CLA.3, LUT.15, LHG.18, CHL.48
16 PLIP interactions:16 interactions with chain A,- Hydrophobic interactions: A:W.33, A:W.33, A:L.38, A:N.48, A:L.51, A:F.176, A:F.176, A:F.179, A:F.179
- Hydrogen bonds: A:Y.31, A:G.32, A:W.33, A:L.38
- pi-Stacking: A:W.33
- pi-Cation interactions: A:R.172
- Metal complexes: A:E.52
CLA.3: 7 residues within 4Å:- Chain A: H.55
- Ligands: CLA.2, CHL.8, LUT.15, CLA.22, LUT.36, CLA.43
0 PLIP interactions:CLA.4: 13 residues within 4Å:- Chain A: L.61, L.64, G.65, P.69, F.79, E.81, A.82, A.87, Q.90, L.97
- Ligands: CHL.6, LUT.15, NEX.17
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:L.64, A:P.69, A:A.87, A:L.97
CLA.9: 17 residues within 4Å:- Chain A: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, A.154, F.160, L.163, K.164, E.167, N.170
- Ligands: CHL.7, CLA.11, LUT.14
11 PLIP interactions:11 interactions with chain A,- Hydrophobic interactions: A:R.57, A:L.61, A:L.61, A:L.64, A:Y.143, A:F.148, A:K.164, A:E.167, A:N.170
- Hydrogen bonds: A:G.145
- Metal complexes: A:E.167
CLA.10: 9 residues within 4Å:- Chain A: W.3, V.165, K.166, K.169, N.170, L.173
- Ligands: CLA.11, XAT.16, LHG.18
5 PLIP interactions:5 interactions with chain A,- Hydrophobic interactions: A:K.166, A:K.169, A:K.169, A:L.173
- Salt bridges: A:K.169
CLA.11: 8 residues within 4Å:- Chain A: L.64, L.163, K.166, N.170, L.173
- Ligands: CLA.9, CLA.10, LUT.14
5 PLIP interactions:5 interactions with chain A,- Hydrophobic interactions: A:L.64, A:K.166, A:L.173
- Salt bridges: A:K.166, A:K.166
CLA.12: 16 residues within 4Å:- Chain A: F.176, S.177, F.179, G.180, V.183, Q.184, V.187, T.188, N.195, H.199, N.207, A.208
- Ligands: CLA.13, LUT.14, XAT.16, LHG.18
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:F.176, A:F.176, A:F.179, A:F.179, A:V.183, A:V.187
CLA.13: 6 residues within 4Å:- Chain A: H.199, P.203, A.208, W.209
- Ligands: CLA.12, LUT.14
3 PLIP interactions:3 interactions with chain A,- Hydrophobic interactions: A:P.203, A:W.209
- Metal complexes: A:H.199
CLA.22: 21 residues within 4Å:- Chain B: L.23, G.29, D.30, Y.31, G.32, W.33, D.34, L.38, F.45, N.48, R.49, E.52, H.55, R.172, M.175, F.176, F.179
- Ligands: CLA.3, CHL.21, CLA.23, LUT.36
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:Y.31, B:W.33, B:W.33, B:W.33, B:N.48, B:F.176, B:F.179, B:F.179, B:F.179
- Hydrogen bonds: B:Y.31, B:G.32, B:W.33
- pi-Stacking: B:W.33
- pi-Cation interactions: B:R.172
- Metal complexes: B:E.52
CLA.23: 9 residues within 4Å:- Chain B: H.55, F.179
- Chain C: A.36
- Ligands: CLA.22, CHL.27, CHL.29, LUT.36, CLA.42, LUT.55
1 PLIP interactions:1 interactions with chain B,- Hydrophobic interactions: B:F.179
CLA.24: 16 residues within 4Å:- Chain B: L.61, G.62, L.64, G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99
- Ligands: CHL.26, CLA.30, LUT.36, NEX.38
7 PLIP interactions:7 interactions with chain B,- Hydrophobic interactions: B:L.61, B:L.64, B:F.68, B:P.69, B:L.97, B:Y.99, B:Y.99
CLA.30: 19 residues within 4Å:- Chain B: R.57, M.60, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, K.164, E.167, N.170
- Ligands: CLA.24, CHL.28, CLA.32, LUT.35
9 PLIP interactions:9 interactions with chain B,- Hydrophobic interactions: B:R.57, B:L.64, B:F.148, B:A.154, B:F.160, B:L.163, B:K.164, B:E.167
- Hydrogen bonds: B:G.145
CLA.31: 8 residues within 4Å:- Chain B: W.3, V.165, K.166, K.169, N.170, L.173
- Ligands: CLA.32, LHG.39
5 PLIP interactions:5 interactions with chain B,- Hydrophobic interactions: B:W.3, B:L.173
- Salt bridges: B:K.169
- pi-Cation interactions: B:K.169, B:K.169
CLA.32: 7 residues within 4Å:- Chain B: L.163, K.166, N.170, L.173
- Ligands: CLA.30, CLA.31, LUT.35
2 PLIP interactions:2 interactions with chain B,- Hydrophobic interactions: B:L.173
- Salt bridges: B:K.166
CLA.33: 15 residues within 4Å:- Chain B: F.176, S.177, G.180, V.183, Q.184, V.187, T.188, N.195, H.199, N.207, A.208
- Ligands: CLA.34, LUT.35, LHG.39, XAT.40
7 PLIP interactions:7 interactions with chain B,- Hydrophobic interactions: B:F.176, B:F.176, B:V.183, B:V.183, B:V.187
- Hydrogen bonds: B:T.188, B:N.207
CLA.34: 5 residues within 4Å:- Chain B: H.199, P.203, W.209
- Ligands: CLA.33, XAT.40
2 PLIP interactions:2 interactions with chain B,- Hydrophobic interactions: B:P.203
- Metal complexes: B:H.199
CLA.42: 24 residues within 4Å:- Chain C: 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: CLA.23, CHL.29, CHL.41, CLA.43, LUT.55
15 PLIP interactions:15 interactions with chain C,- Hydrophobic interactions: C:Y.31, C:W.33, C:W.33, C:W.33, C:N.48, C:R.49, C:L.51, C:F.176, C:F.176, C:F.179
- Hydrogen bonds: C:Y.31, C:G.32, C:W.33
- pi-Cation interactions: C:R.172
- Metal complexes: C:E.52
CLA.43: 7 residues within 4Å:- Chain C: L.51, H.55
- Ligands: CLA.3, LUT.15, CLA.42, CHL.48, LUT.55
1 PLIP interactions:1 interactions with chain C,- Hydrophobic interactions: C:L.51
CLA.44: 14 residues within 4Å:- Chain C: W.58, L.61, G.62, G.65, F.68, F.79, A.87, Q.90, L.97, Y.99
- Ligands: CHL.46, CLA.49, LUT.55, NEX.56
4 PLIP interactions:4 interactions with chain C,- Hydrophobic interactions: C:L.61, C:F.68, C:L.97, C:Y.99
CLA.49: 16 residues within 4Å:- Chain C: R.57, M.60, L.61, Y.143, P.144, F.148, D.149, A.154, F.160, L.163, K.164, E.167
- Ligands: CLA.44, CHL.47, CLA.51, LUT.54
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:M.60, C:L.61, C:L.61, C:F.148, C:K.164, C:E.167
- pi-Cation interactions: C:R.57
CLA.50: 7 residues within 4Å:- Chain C: K.166, K.169, N.170, L.173
- Ligands: XAT.37, CLA.51, LHG.57
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:K.169, C:K.169, C:L.173
- Hydrogen bonds: C:N.170
- Salt bridges: C:K.169
- pi-Cation interactions: C:K.169, C:K.169
CLA.51: 7 residues within 4Å:- Chain C: L.64, L.163, K.166, N.170
- Ligands: CLA.49, CLA.50, LUT.54
2 PLIP interactions:2 interactions with chain C,- Hydrophobic interactions: C:L.64
- Salt bridges: C:K.166
CLA.52: 15 residues within 4Å:- Chain C: F.176, S.177, F.179, G.180, V.183, Q.184, V.187, T.188, N.195, N.207, A.208
- Ligands: XAT.37, CLA.53, LUT.54, LHG.57
8 PLIP interactions:8 interactions with chain C,- Hydrophobic interactions: C:F.176, C:F.176, C:F.176, C:F.179, C:F.179, C:Q.184, C:V.187
- Hydrogen bonds: C:T.188
CLA.53: 7 residues within 4Å:- Chain B: W.115
- Chain C: H.199, P.203, W.209
- Ligands: XAT.37, CLA.52, LUT.54
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain B,- Hydrophobic interactions: C:P.203, C:W.209, B:W.115
- pi-Stacking: 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.14: 14 residues within 4Å:- Chain A: M.60, D.149, P.150, N.170, A.174, S.177, F.181, Q.184, L.196
- Ligands: CHL.7, CLA.9, CLA.11, CLA.12, CLA.13
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:M.60, A:A.174, A:F.181, A:F.181, A:L.196
- Hydrogen bonds: A:Q.184
LUT.15: 18 residues within 4Å:- Chain A: W.33, D.34, T.35, A.36, L.38, H.55, G.62, W.84, M.175, M.178, F.179
- Ligands: CLA.2, CLA.3, CLA.4, CHL.6, CHL.20, CLA.43, CHL.48
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:W.33, A:A.36, A:L.38, A:W.84, A:F.179
- Hydrogen bonds: A:T.35, A:T.35, A:A.36
LUT.35: 13 residues within 4Å:- Chain B: D.149, P.150, L.151, G.152, N.170, S.177, F.181, Q.184, P.192
- Ligands: CHL.28, CLA.30, CLA.32, CLA.33
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:D.149, B:L.151, B:F.181, B:F.181
- Hydrogen bonds: B:L.151, B:G.152, B:Q.184, B:P.192
LUT.36: 16 residues within 4Å:- Chain B: W.33, D.34, T.35, A.36, G.62, W.84, F.85, M.175, M.178, F.179
- Ligands: CLA.3, CLA.22, CLA.23, CLA.24, CHL.26, CHL.27
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:W.33, B:W.84, B:W.84, B:F.179
- Hydrogen bonds: B:D.34, B:T.35, B:T.35, B:A.36, B:W.84
LUT.54: 10 residues within 4Å:- Chain C: M.60, L.151, A.174, S.177, Q.184, L.196
- Ligands: CLA.49, CLA.51, CLA.52, CLA.53
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.151, C:A.174, C:L.196
- Hydrogen bonds: C:L.151, C:Q.184
LUT.55: 16 residues within 4Å:- Chain C: W.33, D.34, T.35, A.36, L.38, G.62, W.84, M.175, M.178
- Ligands: CHL.19, CLA.23, CHL.29, CLA.42, CLA.43, CLA.44, CHL.46
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:W.33, C:A.36, C:L.38, C:W.84
- Hydrogen bonds: C:T.35, C:A.36
- 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.16: 7 residues within 4Å:- Chain A: V.216
- Ligands: CHL.1, CLA.10, CLA.12, LHG.18, CHL.19, CHL.48
No protein-ligand interaction detected (PLIP)XAT.37: 9 residues within 4Å:- Chain B: W.115
- Chain C: V.216
- Ligands: CHL.27, CHL.29, CHL.41, CLA.50, CLA.52, CLA.53, LHG.57
No protein-ligand interaction detected (PLIP)XAT.40: 6 residues within 4Å:- Chain B: V.216
- Ligands: CHL.20, CHL.21, CLA.33, CLA.34, LHG.39
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.216
- 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: 8 residues within 4Å:- Chain A: W.58, Y.99, L.121, V.125, Y.128, P.134
- Ligands: CLA.4, CHL.6
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:W.58, A:L.121
- Hydrogen bonds: A:Y.99, A:Y.99
NEX.38: 8 residues within 4Å:- Chain B: W.58, Y.99, L.121, V.125, Y.128, P.134
- Ligands: CLA.24, CHL.26
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:W.58, B:L.121, B:Y.128, B:P.134
- Hydrogen bonds: B:Y.99
NEX.56: 11 residues within 4Å:- Chain C: W.58, Y.99, L.121, M.122, A.124, V.125, Y.128, P.134
- Ligands: CLA.44, CHL.46, CHL.47
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:W.58, 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: 10 residues within 4Å:- Chain A: Y.31, K.169, R.172, L.173, F.176
- Ligands: CHL.1, CLA.2, CLA.10, CLA.12, XAT.16
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:R.172, A:L.173, A:F.176, A:F.176, A:F.176
- Salt bridges: A:K.169
LHG.39: 9 residues within 4Å:- Chain B: Y.31, K.169, R.172, L.173, F.176
- Ligands: CHL.21, CLA.31, CLA.33, XAT.40
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:R.172, B:F.176, 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.37, CHL.41, 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, C:F.176
- Salt bridges: C:K.169
- 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
GB
NC
Y - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 18 x CHL: CHLOROPHYLL B(Non-covalent)(Covalent)
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
- 6 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)
- 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)
- 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)
- 3 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
- 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
GB
NC
Y - Membrane
-
We predict this structure to be a membrane protein.