- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 18 x CHL: CHLOROPHYLL B(Non-covalent)
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
CLA.2: 24 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, LUT.16, LHG.19, CLA.41, CHL.47
14 PLIP interactions:14 interactions with chain A,- Hydrophobic interactions: A:Y.31, A:W.33, A:W.33, A:N.48, A:F.179, A:F.179, A:F.179
- Hydrogen bonds: A:Y.31, A:G.32, A:W.33
- Salt bridges: A:R.172
- pi-Stacking: A:W.33
- pi-Cation interactions: A:R.172
- Metal complexes: A:E.52
CLA.3: 11 residues within 4Å:- Chain A: L.51, H.55
- Chain B: F.179
- Ligands: CLA.2, CHL.7, CHL.9, LUT.16, CLA.22, LUT.36, LHG.38, CLA.41
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B,- Hydrophobic interactions: A:L.51, B: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, P.69, F.79, A.87, Q.90, L.97, D.98, Y.99, L.100, L.105
- Ligands: CHL.6, CLA.10, LUT.16, NEX.18
7 PLIP interactions:7 interactions with chain A,- Hydrophobic interactions: A:L.61, A:F.68, A:A.87, A:L.97, A:Y.99, A:Y.99
- Hydrogen bonds: A:L.100
CLA.10: 18 residues within 4Å:- Chain A: R.57, M.60, 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.4, CHL.8, CLA.12, LUT.15
7 PLIP interactions:7 interactions with chain A,- Hydrophobic interactions: A:R.57, A:F.148, A:A.154, A:F.160, A:L.163, A:E.167
- Hydrogen bonds: A:G.145
CLA.11: 8 residues within 4Å:- Chain A: W.3, K.166, K.169, N.170, L.173
- Ligands: CLA.12, XAT.17, LHG.19
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:K.169, A:L.173
- Salt bridges: A:K.169
- pi-Cation interactions: A:K.169
CLA.12: 9 residues within 4Å:- Chain A: L.64, F.68, L.163, K.166, N.170, L.173
- Ligands: CLA.10, CLA.11, LUT.15
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:L.64, A:F.68, A:K.166, A:L.173
- Salt bridges: A:K.166, A:K.166
CLA.13: 14 residues within 4Å:- Chain A: F.176, F.179, G.180, V.183, Q.184, T.188, N.195, H.199, N.207, A.208
- Ligands: CLA.14, LUT.15, XAT.17, LHG.19
3 PLIP interactions:3 interactions with chain A,- Hydrophobic interactions: A:F.176, A:F.179, A:F.179
CLA.14: 7 residues within 4Å:- Chain A: L.196, H.199, L.200, P.203, A.208, W.209
- Ligands: CLA.13
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:L.196, A:L.200, A:P.203
- Metal complexes: A:H.199
CLA.22: 24 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.9, CHL.21, CLA.23, CLA.33, LUT.36, LHG.38
12 PLIP interactions:12 interactions with chain B,- Hydrophobic interactions: B:Y.31, B:W.33, B:W.33, B:L.38, B:F.45, B:N.48
- 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: 11 residues within 4Å:- Chain B: L.51, H.55
- Ligands: CLA.22, CHL.27, CHL.29, LUT.36, CHL.39, CLA.40, CLA.41, CHL.47, LUT.54
2 PLIP interactions:2 interactions with chain B,- Hydrophobic interactions: B:L.51
- Metal complexes: B:H.55
CLA.24: 15 residues within 4Å:- Chain B: L.61, G.62, L.64, G.65, F.68, P.69, F.79, A.87, Q.90, L.97, Y.99, L.100
- Ligands: CHL.26, LUT.36, NEX.37
7 PLIP interactions:7 interactions with chain B,- Hydrophobic interactions: B:L.61, B:L.64, B:L.97, B:Y.99, B:Y.99
- Hydrogen bonds: B:Q.90, B:L.100
CLA.30: 15 residues within 4Å:- Chain B: R.57, M.60, L.61, Y.143, G.145, D.149, L.153, A.154, F.160, L.163, K.164, E.167
- Ligands: CHL.28, CLA.32, LUT.35
8 PLIP interactions:8 interactions with chain B,- Hydrophobic interactions: B:R.57, B:L.61, B:A.154, B:L.163, B:E.167
- Hydrogen bonds: B:G.145, B:D.149
- Metal complexes: B:E.167
CLA.31: 7 residues within 4Å:- Chain B: W.3, K.166, K.169, N.170
- Ligands: XAT.20, CLA.32, LHG.38
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:W.3, B:N.170
- Salt bridges: B:K.169
- pi-Cation interactions: 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
3 PLIP interactions:3 interactions with chain B,- Hydrophobic interactions: B:L.173
- Salt bridges: B:K.166, B:K.166
CLA.33: 15 residues within 4Å:- Chain B: F.176, F.179, G.180, V.183, T.188, N.195, L.196, H.199, N.207, A.208
- Ligands: XAT.20, CLA.22, CLA.34, LUT.35, LHG.38
3 PLIP interactions:3 interactions with chain B,- Hydrophobic interactions: B:F.176, B:F.179, B:V.183
CLA.34: 8 residues within 4Å:- Chain B: L.196, H.199, L.200, P.203, V.204, W.209
- Ligands: XAT.20, CLA.33
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:L.196, B:L.200, B:V.204
- Metal complexes: B:H.199
CLA.40: 23 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, F.176, F.179
- Ligands: CLA.23, CHL.29, CHL.39, CLA.41, LUT.54
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:Y.31, C:W.33, C:W.33, C:W.33, C:N.48, C:L.51, C:F.176, C:F.179
- Hydrogen bonds: C:Y.31, C:G.32, C:W.33
- pi-Cation interactions: C:R.172
CLA.41: 12 residues within 4Å:- Chain A: A.36
- Chain C: L.51, H.55
- Ligands: CLA.2, CLA.3, LUT.16, LHG.19, CLA.23, CLA.40, CHL.45, CHL.47, LUT.54
3 PLIP interactions:3 interactions with chain C,- Hydrophobic interactions: C:L.51, C:L.51
- Metal complexes: C:H.55
CLA.42: 15 residues within 4Å:- Chain C: L.61, G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105
- Ligands: CHL.44, LUT.54, NEX.56
9 PLIP interactions:9 interactions with chain C,- Hydrophobic interactions: C:A.87, C:L.97, C:Y.99, C:Y.99, C:Y.99, C:L.100, C:L.105
- Hydrogen bonds: C:Q.90, C:L.100
CLA.48: 16 residues within 4Å:- Chain C: R.57, M.60, L.61, Y.143, P.144, G.145, F.148, D.149, L.153, F.160, L.163, E.167, N.170
- Ligands: CHL.46, CLA.50, LUT.53
6 PLIP interactions:6 interactions with chain C,- Hydrophobic interactions: C:R.57, C:L.61, C:F.148, C:L.163, C:E.167, C:N.170
CLA.49: 6 residues within 4Å:- Chain C: W.3, K.166, K.169
- Ligands: CLA.50, XAT.55, LHG.57
2 PLIP interactions:2 interactions with chain C,- Salt bridges: C:K.169
- pi-Cation interactions: C:K.169
CLA.50: 8 residues within 4Å:- Chain C: L.64, L.163, K.166, N.170, L.173
- Ligands: CLA.48, CLA.49, LUT.53
4 PLIP interactions:4 interactions with chain C,- Hydrophobic interactions: C:L.64, C:L.173
- Salt bridges: C:K.166, C:K.166
CLA.51: 17 residues within 4Å:- Chain B: W.115
- Chain C: F.176, G.180, V.183, Q.184, V.187, T.188, N.195, L.196, H.199, N.206, N.207, A.208
- Ligands: CLA.52, LUT.53, XAT.55, LHG.57
7 PLIP interactions:6 interactions with chain C, 1 interactions with chain B,- Hydrophobic interactions: C:F.176, C:F.176, C:Q.184, C:V.187, C:L.196, B:W.115
- Hydrogen bonds: C:T.188
CLA.52: 8 residues within 4Å:- Chain B: L.112, W.115
- Chain C: H.199, L.200, P.203, A.208, W.209
- Ligands: CLA.51
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain B,- Hydrophobic interactions: C:L.200, C:P.203, B:L.112
- Metal complexes: 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.15: 15 residues within 4Å:- Chain A: M.60, L.61, A.63, L.64, L.151, N.170, A.174, S.177, F.181, Q.184, P.192, L.196
- Ligands: CLA.10, CLA.12, CLA.13
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:M.60, A:L.64, A:A.174, A:F.181, A:F.181, A:L.196
- Hydrogen bonds: A:Q.184, A:P.192
LUT.16: 16 residues within 4Å:- Chain A: W.33, D.34, T.35, A.36, H.55, G.62, C.66, W.84, M.175, M.178, F.179
- Ligands: CLA.2, CLA.3, CLA.4, CLA.41, CHL.47
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:W.33, A:W.33, A:W.84, A:M.175, A:F.179
- Hydrogen bonds: A:T.35, A:T.35, A:A.36, A:W.84
LUT.35: 13 residues within 4Å:- Chain B: M.60, A.63, L.151, N.170, A.174, S.177, F.181, Q.184, P.192
- Ligands: CHL.28, CLA.30, CLA.32, CLA.33
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:M.60, B:A.63, B:L.151, B:A.174, B:F.181
- Hydrogen bonds: B:Q.184
LUT.36: 18 residues within 4Å:- Chain B: W.33, D.34, T.35, A.36, H.55, A.59, G.62, W.84, M.175, M.178, F.179
- Ligands: CLA.3, CHL.9, CLA.22, CLA.23, CLA.24, CHL.26, CHL.27
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:W.33, B:W.33, B:A.59, B:W.84, B:W.84, B:M.175, B:F.179
- Hydrogen bonds: B:D.34, B:T.35, B:T.35, B:A.36, B:W.84
LUT.53: 15 residues within 4Å:- Chain C: M.60, L.61, L.64, D.149, L.151, N.170, A.174, S.177, F.181, Q.184, P.192
- Ligands: CHL.46, CLA.48, CLA.50, CLA.51
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:M.60, C:L.64, C:A.174, C:F.181
- Hydrogen bonds: C:Q.184
LUT.54: 19 residues within 4Å:- Chain C: W.33, D.34, T.35, A.36, L.38, H.55, W.58, A.59, G.62, C.66, W.84, M.175, M.178
- Ligands: CLA.23, CLA.40, CLA.41, CLA.42, CHL.44, CHL.45
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:W.33, C:A.36, C:L.38, C:A.59, C:W.84
- Hydrogen bonds: C:T.35, C:A.36, C:W.84
- 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.17: 7 residues within 4Å:- Chain A: V.216
- Chain C: W.115
- Ligands: CHL.1, CLA.11, CLA.13, LHG.19, CHL.45
No protein-ligand interaction detected (PLIP)XAT.20: 9 residues within 4Å:- Chain A: W.115
- Chain B: A.212, V.216
- Ligands: CHL.7, CHL.21, CLA.31, CLA.33, CLA.34, LHG.38
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:A.212, A:W.115
XAT.55: 9 residues within 4Å:- Chain B: W.115, V.119
- Chain C: V.216
- Ligands: CHL.27, CHL.29, CHL.39, CLA.49, CLA.51, LHG.57
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.115
- 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.18: 7 residues within 4Å:- Chain A: Y.99, V.125, Y.128, P.134
- Ligands: CLA.4, CHL.6, CHL.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.99, A:Y.99
NEX.37: 7 residues within 4Å:- Chain B: Y.99, V.125, Y.128, P.134
- Ligands: CLA.24, CHL.26, CHL.28
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:P.134, B:P.134
NEX.56: 7 residues within 4Å:- Chain C: Y.99, V.125, Y.128, P.134
- Ligands: CLA.42, CHL.44, CHL.46
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:V.125, C:P.134
- Hydrogen bonds: C:Y.99, C:Y.99
- 3 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.19: 11 residues within 4Å:- Chain A: W.3, Y.31, K.169, L.173, F.176
- Ligands: CHL.1, CLA.2, CLA.11, CLA.13, XAT.17, CLA.41
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:F.176, A:F.176, A:F.176
- Salt bridges: A:K.169, A:K.169
LHG.38: 11 residues within 4Å:- Chain B: W.3, Y.31, K.169, L.173, F.176
- Ligands: CLA.3, XAT.20, CHL.21, CLA.22, CLA.31, CLA.33
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.173, B:F.176
LHG.57: 8 residues within 4Å:- Chain C: W.3, Y.31, L.173, F.176
- Ligands: CHL.39, CLA.49, CLA.51, XAT.55
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.173, C:L.173, C:F.176, C:F.176
- Hydrogen bonds: C:Y.31
- 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)
- 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.