- 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)(Covalent)
CLA.2: 21 residues within 4Å:- Chain A: L.23, P.28, G.29, Y.31, G.32, W.33, D.34, L.38, S.39, F.45, N.48, R.49, E.52, H.55, R.172, M.175, F.179
- Ligands: CHL.1, CLA.3, LUT.16, CLA.22
12 PLIP interactions:12 interactions with chain A,- Hydrophobic interactions: A:Y.31, A:N.48, A:R.49, A:E.52, A:H.55, A:F.179
- Hydrogen bonds: A:Y.31, A:G.32, A:W.33, A:N.48
- pi-Cation interactions: A:R.172
- Metal complexes: A:E.52
CLA.3: 7 residues within 4Å:- Chain A: H.55
- Chain C: T.35, A.36
- Ligands: CLA.2, CHL.7, CHL.9, LUT.16
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain C,- Metal complexes: A:H.55
- Hydrophobic interactions: C:A.36
CLA.4: 7 residues within 4Å:- Chain A: G.65, E.81, L.97, Y.99
- Ligands: CHL.6, LUT.16, NEX.17
2 PLIP interactions:2 interactions with chain A,- Hydrophobic interactions: A:Y.99, A:Y.99
CLA.10: 14 residues within 4Å:- Chain A: R.57, M.60, Y.143, P.144, G.145, F.148, D.149, L.153, F.160, L.163, E.167
- Ligands: CHL.8, CLA.12, LUT.15
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:F.148, A:F.160, A:L.163, A:E.167
- Hydrogen bonds: A:G.145
- Metal complexes: A:E.167
CLA.11: 5 residues within 4Å:- Chain A: W.3, K.169, N.170
- Ligands: CLA.12, LHG.18
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:K.169
- Salt bridges: A:K.169
- pi-Cation interactions: A:K.169, A:K.169
CLA.12: 5 residues within 4Å:- Chain A: N.170, L.173
- Ligands: CLA.10, CLA.11, LUT.15
3 PLIP interactions:3 interactions with chain A,- Hydrophobic interactions: A:L.173
- Salt bridges: A:K.166, A:K.166
CLA.13: 13 residues within 4Å:- Chain A: F.176, G.180, V.183, Q.184, T.188, N.195, H.199, N.207, A.208
- Ligands: CLA.14, LUT.15, LHG.18, XAT.19
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:F.176, A:V.183
- Hydrogen bonds: A:N.195, A:A.208
CLA.14: 3 residues within 4Å:- Chain A: H.199, P.203
- Ligands: CLA.13
3 PLIP interactions:3 interactions with chain A,- Hydrophobic interactions: A:P.203, A:P.203
- Metal complexes: A:H.199
CLA.21: 18 residues within 4Å:- Chain B: P.28, G.29, D.30, Y.31, G.32, W.33, S.39, N.48, R.49, E.52, H.55, R.172, F.176
- Ligands: CHL.20, CLA.22, LUT.35, CLA.43, CHL.48
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:Y.31, B:N.48, B:R.49, B:E.52, B:H.55, B:F.176
- Hydrogen bonds: B:Y.31, B:G.32, B:W.33
- pi-Cation interactions: B:R.172
- Metal complexes: B:E.52
CLA.22: 9 residues within 4Å:- Chain A: T.35, A.36
- Chain B: H.55
- Ligands: CLA.2, CLA.21, CHL.26, CHL.28, LUT.35, CLA.43
0 PLIP interactions:CLA.23: 7 residues within 4Å:- Chain B: G.62, G.65, L.97, Y.99
- Ligands: CHL.25, LUT.35, NEX.36
2 PLIP interactions:2 interactions with chain B,- Hydrophobic interactions: B:L.97, B:Y.99
CLA.29: 13 residues within 4Å:- Chain B: R.57, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, E.167
- Ligands: CHL.27, CLA.31, LUT.34
9 PLIP interactions:9 interactions with chain B,- Hydrophobic interactions: B:F.148, B:D.149, B:A.154, B:F.160, B:L.163, B:E.167
- Hydrogen bonds: B:G.145
- pi-Cation interactions: B:R.57
- Metal complexes: B:E.167
CLA.30: 6 residues within 4Å:- Chain B: K.166, K.169, N.170
- Ligands: CLA.31, LHG.37, XAT.39
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:K.169
- Hydrogen bonds: B:N.170
- Salt bridges: B:K.169
- pi-Cation interactions: B:K.169
CLA.31: 5 residues within 4Å:- Chain B: K.166, N.170
- Ligands: CLA.29, CLA.30, LUT.34
2 PLIP interactions:2 interactions with chain B,- Salt bridges: B:K.166, B:K.166
CLA.32: 14 residues within 4Å:- Chain B: V.183, Q.184, V.187, T.188, N.195, H.199, N.207, A.208, F.211
- Chain C: W.115
- Ligands: CLA.33, LUT.34, LHG.37, XAT.39
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:V.183, B:V.187, B:A.208, C:W.115
- Hydrogen bonds: B:N.195, B:A.208
CLA.33: 4 residues within 4Å:- Chain B: H.199, P.203, W.209
- Ligands: CLA.32
2 PLIP interactions:2 interactions with chain B,- Hydrophobic interactions: B:P.203
- Metal complexes: B:H.199
CLA.42: 20 residues within 4Å:- Chain C: L.23, P.28, G.29, D.30, Y.31, G.32, W.33, L.38, S.39, F.45, N.48, R.49, E.52, H.55, R.172, M.175, F.176, F.179
- Ligands: CHL.41, LUT.55
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:W.33, C:N.48, C:E.52, C:H.55, C:F.176, C:F.179
- Hydrogen bonds: C:Y.31, C:G.32, C:W.33, C:N.48
- pi-Cation interactions: C:R.172
- Metal complexes: C:E.52
CLA.43: 10 residues within 4Å:- Chain B: A.36
- Chain C: H.55, W.58
- Ligands: CLA.21, CLA.22, CHL.28, LUT.35, CHL.38, CHL.48, LUT.55
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:A.36
- Metal complexes: C:H.55
CLA.44: 10 residues within 4Å:- Chain C: L.61, G.62, G.65, F.68, F.79, L.97, Y.99
- Ligands: CHL.46, LUT.55, NEX.56
1 PLIP interactions:1 interactions with chain C,- Hydrophobic interactions: C:F.68
CLA.49: 14 residues within 4Å:- Chain C: R.57, L.61, Y.143, P.144, G.145, F.148, D.149, L.153, L.163, K.164, E.167
- Ligands: CHL.47, CLA.51, LUT.54
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:L.61, C:F.148, C:L.163, C:E.167, C:E.167
- Hydrogen bonds: C:G.145
- Metal complexes: C:E.167
CLA.50: 7 residues within 4Å:- Chain C: W.3, K.169, N.170, L.173
- Ligands: XAT.40, CLA.51, LHG.57
6 PLIP interactions:6 interactions with chain C,- Hydrophobic interactions: 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: 6 residues within 4Å:- Chain C: L.64, K.166, N.170
- Ligands: CLA.49, CLA.50, LUT.54
3 PLIP interactions:3 interactions with chain C,- Hydrophobic interactions: C:L.64
- Salt bridges: C:K.166, C:K.166
CLA.52: 13 residues within 4Å:- Chain C: G.180, V.183, Q.184, V.187, T.188, N.195, H.199, N.207, A.208
- Ligands: XAT.40, CLA.53, LUT.54, LHG.57
6 PLIP interactions:6 interactions with chain C,- Hydrophobic interactions: C:V.183, C:Q.184, C:V.187, C:A.208
- Hydrogen bonds: C:Q.184, C:A.208
CLA.53: 4 residues within 4Å:- Chain C: H.199, P.203, N.207
- Ligands: CLA.52
3 PLIP interactions:3 interactions with chain C,- Hydrophobic interactions: C:P.203
- Hydrogen bonds: C:N.207
- 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: 12 residues within 4Å:- Chain A: M.60, A.63, L.64, D.149, P.150, L.151, S.177, F.181, P.192
- Ligands: CLA.10, CLA.12, CLA.13
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:A.63, A:L.64, A:F.181
- Hydrogen bonds: A:P.192
LUT.16: 15 residues within 4Å:- Chain A: W.33, D.34, T.35, A.36, H.55, A.59, G.62, C.66, W.84, M.175, M.178
- Ligands: CLA.2, CLA.3, CLA.4, CHL.7
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:W.33, A:W.33, A:A.36, A:A.59, A:W.84
- Hydrogen bonds: A:A.36
LUT.34: 10 residues within 4Å:- Chain B: M.60, L.64, D.149, L.151, S.177, F.181, P.192
- Ligands: CLA.29, CLA.31, CLA.32
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.64, B:L.151, B:F.181
- Hydrogen bonds: B:D.149
LUT.35: 15 residues within 4Å:- Chain B: W.33, T.35, A.36, H.55, A.59, G.62, C.66, W.84, M.175
- Ligands: CLA.21, CLA.22, CLA.23, CHL.25, CHL.26, CLA.43
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:W.33, B:W.33, B:A.59
- Hydrogen bonds: B:T.35, B:T.35, B:A.36
LUT.54: 14 residues within 4Å:- Chain C: M.60, L.64, F.148, D.149, P.150, L.151, L.173, S.177, F.181, P.192, L.196
- Ligands: CLA.49, CLA.51, CLA.52
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.64, C:L.151, C:L.173, C:F.181, C:L.196
- Hydrogen bonds: C:D.149
LUT.55: 15 residues within 4Å:- Chain C: W.33, D.34, T.35, A.36, H.55, A.59, G.62, C.66, W.84, M.175, M.178
- Ligands: CHL.38, CLA.42, CLA.43, CLA.44
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:W.33, C:W.33, C:A.36, C:A.59, C:W.84
- Hydrogen bonds: C:T.35, C:A.36
- 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: 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- Hydrophobic interactions: A:P.134
- Hydrogen bonds: A:Y.99
NEX.36: 6 residues within 4Å:- Chain B: Y.99, L.121, P.134
- Ligands: CLA.23, CHL.25, CHL.27
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.121, B:P.134
- Hydrogen bonds: B:Y.99, B:Y.99
NEX.56: 7 residues within 4Å:- Chain C: Y.99, V.125, Y.128, P.134
- Ligands: CLA.44, CHL.46, CHL.47
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:V.125, C:P.134
- Hydrogen bonds: C:Y.99
- 3 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.18: 9 residues within 4Å:- Chain A: Y.31, K.169, R.172, L.173, F.176
- Ligands: CHL.1, CLA.11, CLA.13, XAT.19
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:R.172, A:F.176, A:F.176
- Hydrogen bonds: A:Y.31
- Salt bridges: A:K.169, A:K.169
LHG.37: 8 residues within 4Å:- Chain B: K.169, L.173, F.176
- Ligands: CHL.20, CLA.30, CLA.32, CHL.38, XAT.39
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:F.176
- Salt bridges: B:K.169, B:K.169
LHG.57: 6 residues within 4Å:- Chain C: K.169, F.176
- Ligands: XAT.40, CHL.41, CLA.50, CLA.52
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:F.176
- Salt bridges: C:K.169, C:K.169
- 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.19: 7 residues within 4Å:- Chain A: W.209, A.212, F.215
- Chain B: W.115
- Ligands: CHL.1, CLA.13, LHG.18
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:W.115, A:W.209
XAT.39: 7 residues within 4Å:- Chain B: W.209, A.212
- Chain C: W.115
- Ligands: CHL.20, CLA.30, CLA.32, LHG.37
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.209
XAT.40: 7 residues within 4Å:- Chain A: W.115
- Chain C: W.209, A.212
- Ligands: CHL.41, CLA.50, CLA.52, LHG.57
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:W.209
- 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
NB
GC
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)(Covalent)
- 6 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-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)
- 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)
- 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
NB
GC
Y - Membrane
-
We predict this structure to be a membrane protein.