- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 18 x CHL: CHLOROPHYLL B(Covalent)(Non-covalent)
- 24 x CLA: CHLOROPHYLL A(Non-covalent)(Covalent)
CLA.2: 23 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, N.48, R.49, E.52, H.55, R.172, M.175, F.176, F.179
- Ligands: CHL.1, CLA.3, LUT.16, CLA.23, CHL.29
16 PLIP interactions:16 interactions with chain A,- Hydrophobic interactions: A:Y.31, A:W.33, A:W.33, A:W.33, A:N.48, A:R.49, A:H.55, A:M.175, A:F.176, A:F.176, A:F.179
- Hydrogen bonds: A:Y.31, A:W.33
- Salt bridges: A:R.172
- pi-Cation interactions: A:R.172
- Metal complexes: A:E.52
CLA.3: 10 residues within 4Å:- Chain A: L.51, H.55
- Chain C: A.36, F.179
- Ligands: CLA.2, CHL.7, CHL.9, LUT.16, CLA.41, LUT.55
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain C,- Hydrophobic interactions: A:L.51, A:L.51, C:A.36, C:F.179
- Metal complexes: A:H.55
CLA.4: 18 residues within 4Å:- Chain A: L.61, L.64, G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106
- Ligands: CHL.6, CLA.10, LUT.16, NEX.18
10 PLIP interactions:10 interactions with chain A,- Hydrophobic interactions: A:L.61, A:L.61, A:L.64, A:A.87, A:L.97, A:Y.99, A:Y.99, A:L.100, A:V.106
- Hydrogen bonds: A:L.100
CLA.10: 19 residues within 4Å:- Chain A: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, K.164, E.167
- Ligands: CLA.4, CHL.8, CLA.12, LUT.15
10 PLIP interactions:10 interactions with chain A,- Hydrophobic interactions: A:R.57, A:R.57, A:L.61, A:L.64, A:A.154, A:L.163, A:E.167, A:E.167
- Hydrogen bonds: A:G.145
- Metal complexes: A:E.167
CLA.11: 9 residues within 4Å:- Chain A: W.3, L.64, K.166, K.169, N.170, L.173
- Ligands: CLA.12, LHG.19, XAT.20
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:W.3, A:L.64, A:K.169, A:K.169, A:K.169, A:L.173
CLA.12: 7 residues within 4Å:- Chain A: L.163, K.166, N.170, L.173
- Ligands: CLA.10, CLA.11, LUT.15
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:K.166, A:L.173
- Salt bridges: A:K.166, A:K.166
CLA.13: 16 residues within 4Å:- Chain A: F.176, G.180, V.183, Q.184, V.187, T.188, N.195, L.196, D.198, H.199, N.207, A.208
- Ligands: CLA.14, LUT.15, LHG.19, XAT.20
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:F.176, A:F.176, A:V.187, A:A.208
- Hydrogen bonds: A:T.188, A:A.208
CLA.14: 9 residues within 4Å:- Chain A: L.196, H.199, P.203, N.207, W.209
- Chain B: L.112, W.115
- Ligands: CLA.13, XAT.20
5 PLIP interactions:1 interactions with chain B, 4 interactions with chain A,- Hydrophobic interactions: B:L.112, A:P.203, A:P.203
- Hydrogen bonds: A:N.207
- Metal complexes: A:H.199
CLA.22: 22 residues within 4Å:- Chain B: L.23, P.28, G.29, D.30, Y.31, G.32, W.33, D.34, L.38, S.39, N.48, R.49, E.52, H.55, R.172, M.175, F.176, F.179
- Ligands: CHL.21, CLA.23, LUT.36, CLA.42
16 PLIP interactions:16 interactions with chain B,- Hydrophobic interactions: B:Y.31, B:W.33, B:W.33, B:L.38, B:N.48, B:R.49, B:H.55, B:F.176, B:F.176, B:F.179, B:F.179
- Hydrogen bonds: B:Y.31, B:G.32, B:W.33
- pi-Cation interactions: B:R.172
- Metal complexes: B:E.52
CLA.23: 13 residues within 4Å:- Chain A: A.36, L.38
- Chain B: L.51, H.55, F.182
- Ligands: CLA.2, LUT.16, LHG.19, CLA.22, CHL.27, CHL.29, LUT.36, CLA.42
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:L.51, B:L.51, B:F.182
- Metal complexes: B:H.55
CLA.24: 17 residues within 4Å:- Chain B: L.61, L.64, G.65, F.68, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106
- Ligands: CHL.25, CHL.26, LUT.36, NEX.37
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:L.61, B:L.64, B:A.87, B:L.97, B:Y.99, B:Y.99, B:L.100, B:L.105, B:L.105
- Hydrogen bonds: B:L.100
CLA.30: 20 residues within 4Å:- Chain B: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, K.164, K.166, E.167, N.170
- Ligands: CHL.28, CLA.32, LUT.35
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:R.57, B:L.61, B:L.64, B:F.148, B:A.154, B:L.163, B:K.166, B:E.167
- Hydrogen bonds: B:G.145
- pi-Cation interactions: B:R.57
- Metal complexes: B:E.167
CLA.31: 10 residues within 4Å:- Chain B: W.3, L.64, V.67, K.166, K.169, N.170, L.173
- Ligands: CLA.32, LHG.38, XAT.39
7 PLIP interactions:7 interactions with chain B,- Hydrophobic interactions: B:W.3, B:L.64, B:V.67, B:K.169, B:L.173
- 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
5 PLIP interactions:5 interactions with chain B,- Hydrophobic interactions: B:L.163, B:K.166, B:L.173
- Salt bridges: B:K.166, B:K.166
CLA.33: 17 residues within 4Å:- Chain B: F.176, G.180, V.183, Q.184, V.187, T.188, N.195, L.196, D.198, H.199, N.207, A.208, F.211
- Ligands: CLA.34, LUT.35, LHG.38, XAT.39
8 PLIP interactions:8 interactions with chain B,- Hydrophobic interactions: B:F.176, B:F.176, B:F.176, B:Q.184, B:V.187, B:A.208
- Hydrogen bonds: B:Q.184, B:A.208
CLA.34: 9 residues within 4Å:- Chain B: L.196, H.199, L.200, P.203, N.207, W.209
- Chain C: L.112
- Ligands: CLA.33, XAT.39
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:L.196, B:L.200, B:P.203, B:P.203, C:L.112
- Metal complexes: B:H.199
CLA.41: 25 residues within 4Å:- Chain C: 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, L.51, E.52, H.55, R.172, M.175, F.176, F.179
- Ligands: CLA.3, CHL.9, CHL.40, CLA.42, LUT.55
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:Y.31, C:W.33, C:L.38, C:N.48, C:R.49, C:L.51, C:E.52, C:H.55, C:F.176, C:F.176, C:F.179
- Hydrogen bonds: C:D.30, C:Y.31, C:G.32, C:W.33
- pi-Cation interactions: C:R.172
- Metal complexes: C:E.52
CLA.42: 11 residues within 4Å:- Chain B: A.36
- Chain C: L.51, H.55
- Ligands: CLA.22, CLA.23, LUT.36, LHG.38, CLA.41, CHL.46, CHL.48, LUT.55
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B,- Hydrophobic interactions: C:L.51, B:A.36
- Metal complexes: C:H.55
CLA.43: 16 residues within 4Å:- Chain C: L.64, G.65, F.68, P.69, F.79, E.81, A.87, Q.90, L.97, Y.99, L.100, L.105, V.106
- Ligands: CHL.45, LUT.55, NEX.56
10 PLIP interactions:10 interactions with chain C,- Hydrophobic interactions: C:L.64, C:F.68, C:P.69, C:A.87, C:Y.99, C:Y.99, C:L.100, C:V.106
- Hydrogen bonds: C:Q.90, C:L.100
CLA.49: 18 residues within 4Å:- Chain C: R.57, M.60, L.61, L.64, Y.143, P.144, G.145, F.148, D.149, L.153, A.154, F.160, L.163, K.164, E.167
- Ligands: CHL.47, CLA.51, LUT.54
9 PLIP interactions:9 interactions with chain C,- Hydrophobic interactions: C:R.57, C:L.61, C:L.64, C:F.148, C:A.154, C:L.163, C:E.167
- Hydrogen bonds: C:G.145
- Metal complexes: C:E.167
CLA.50: 8 residues within 4Å:- Chain C: W.3, K.166, K.169, N.170, L.173
- Ligands: XAT.17, CLA.51, LHG.57
4 PLIP interactions:4 interactions with chain C,- Hydrophobic interactions: C:W.3, C:K.169, C:L.173
- pi-Cation interactions: C:K.169
CLA.51: 7 residues within 4Å:- Chain C: L.163, K.166, N.170, L.173
- Ligands: CLA.49, CLA.50, LUT.54
5 PLIP interactions:5 interactions with chain C,- Hydrophobic interactions: C:L.163, C:K.166, C:L.173
- Salt bridges: C:K.166, C:K.166
CLA.52: 18 residues within 4Å:- Chain C: F.176, S.177, F.179, G.180, V.183, Q.184, V.187, N.195, L.196, H.199, N.206, N.207, A.208, F.211
- Ligands: XAT.17, CLA.53, LUT.54, LHG.57
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:F.176, C:F.176, C:F.176, C:F.179, C:V.187, C:A.208
- Hydrogen bonds: C:A.208
CLA.53: 8 residues within 4Å:- Chain A: L.112, W.115
- Chain C: H.199, P.203, N.207, W.209
- Ligands: XAT.17, CLA.52
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain C,- Hydrophobic interactions: A:L.112, A:L.112, A:W.115, C:P.203
- 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: 17 residues within 4Å:- Chain A: M.60, A.63, F.148, D.149, P.150, L.151, L.153, N.170, S.177, F.181, Q.184, P.192, N.195
- Ligands: CHL.8, CLA.10, CLA.12, CLA.13
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:M.60, A:A.63, A:L.153, A:F.181
- Hydrogen bonds: A:L.151, A:Q.184, A:P.192
LUT.16: 21 residues within 4Å:- Chain A: W.33, D.34, T.35, A.36, H.55, W.58, A.59, G.62, G.65, W.84, A.87, M.175, M.178, F.179, F.182
- Ligands: CLA.2, CLA.3, CLA.4, CHL.7, CLA.23, CHL.29
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:W.33, A:W.33, A:A.36, A:A.59, A:W.84, A:M.175, A:M.178, A:F.179, A:F.182
- Hydrogen bonds: A:T.35, A:A.36, A:A.36
LUT.35: 19 residues within 4Å:- Chain B: M.60, A.63, L.64, F.148, D.149, P.150, L.151, L.153, N.170, A.174, S.177, F.181, Q.184, P.192, N.195
- Ligands: CHL.28, CLA.30, CLA.32, CLA.33
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:M.60, B:A.63, B:L.64, B:L.151, B:L.153, B:A.174, B:F.181, B:P.192
- Hydrogen bonds: B:D.149, B:L.151, B:Q.184
LUT.36: 19 residues within 4Å:- Chain B: W.33, D.34, T.35, A.36, H.55, W.58, A.59, G.62, G.65, C.66, W.84, M.175, M.178, F.179
- Ligands: CLA.22, CLA.23, CLA.24, CHL.27, CLA.42
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:W.33, B:W.33, B:W.33, B:A.59, 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.54: 18 residues within 4Å:- Chain C: M.60, A.63, F.148, D.149, P.150, L.151, N.170, A.174, S.177, F.181, Q.184, P.192, N.195, L.196
- Ligands: CHL.47, CLA.49, CLA.51, CLA.52
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:M.60, C:A.174, C:F.181, C:F.181
- Hydrogen bonds: C:L.151, C:Q.184
LUT.55: 22 residues within 4Å:- Chain C: W.33, D.34, T.35, A.36, H.55, W.58, A.59, G.62, G.65, C.66, W.84, A.87, M.175, M.178, F.179, F.182
- Ligands: CLA.3, CHL.9, CLA.41, CLA.42, CLA.43, CHL.46
11 PLIP interactions:11 interactions with chain C- Hydrophobic interactions: C:W.33, C:W.33, C:W.33, C:A.59, C:W.84, C:M.178, C:F.179, C:F.182
- Hydrogen bonds: C:T.35, 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.17: 10 residues within 4Å:- Chain A: W.115
- Chain C: A.208, W.209, A.212
- Ligands: CHL.7, CHL.40, CLA.50, CLA.52, CLA.53, LHG.57
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:A.212, A:W.115
XAT.20: 10 residues within 4Å:- Chain A: A.208, W.209, A.212
- Chain B: W.115
- Ligands: CHL.1, CLA.11, CLA.13, CLA.14, LHG.19, CHL.27
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:W.209, A:A.212
XAT.39: 10 residues within 4Å:- Chain B: A.208, W.209, A.212
- Chain C: W.115
- Ligands: CHL.21, CLA.31, CLA.33, CLA.34, LHG.38, CHL.46
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:A.212
- 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: 8 residues within 4Å:- Chain A: Y.99, L.121, V.125, Y.128, P.134
- Ligands: CLA.4, CHL.6, CHL.8
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.121, A:V.125, A:P.134
- Hydrogen bonds: A:Y.99
NEX.37: 8 residues within 4Å:- Chain B: W.58, Y.99, V.125, Y.128, P.134
- Ligands: CLA.24, CHL.26, CHL.28
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:W.58, B:P.134
- Hydrogen bonds: B:Y.99
NEX.56: 10 residues within 4Å:- Chain C: W.58, Y.99, L.121, M.122, V.125, Y.128, P.134
- Ligands: CLA.43, CHL.45, CHL.47
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:W.58, C:L.121, 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, R.172, L.173, F.176
- Ligands: CHL.1, CLA.11, CLA.13, XAT.20, CLA.23
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:R.172, A:L.173, A:L.173, A:F.176, A:F.176, A:F.176
- Salt bridges: A:K.169
LHG.38: 11 residues within 4Å:- Chain B: W.3, Y.31, K.169, R.172, L.173, F.176
- Ligands: CHL.21, CLA.31, CLA.33, XAT.39, CLA.42
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:R.172, B:F.176, B:F.176
- Hydrogen bonds: B:Y.31
- Salt bridges: B:K.169, B:K.169
LHG.57: 11 residues within 4Å:- Chain C: W.3, Y.31, K.169, R.172, L.173, F.176
- Ligands: CHL.7, XAT.17, CHL.40, 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
- Salt bridges: C:K.169, 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
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(Covalent)(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 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
NB
GC
Y - Membrane
-
We predict this structure to be a membrane protein.