- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-2-mer
- Ligands
- 18 x CHL: CHLOROPHYLL B(Non-covalent)
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
CLA.2: 25 residues within 4Å:- Chain A: L.53, G.59, D.60, Y.61, G.62, W.63, D.64, L.68, S.69, F.75, Y.78, R.79, L.81, E.82, R.202, M.205, F.206, F.209
- Ligands: CHL.1, CLA.3, CLA.13, LUT.16, LHG.19, CLA.41, CHL.47
20 PLIP interactions:20 interactions with chain A,- Hydrophobic interactions: A:Y.61, A:W.63, A:W.63, A:L.68, A:F.75, A:Y.78, A:R.79, A:L.81, A:E.82, A:E.82, A:R.202, A:M.205, A:F.209, A:F.209
- Hydrogen bonds: A:Y.61, A:G.62, A:W.63, A:L.68
- pi-Cation interactions: A:R.202
- Metal complexes: A:E.82
CLA.3: 16 residues within 4Å:- Chain A: Y.78, L.81, H.85, F.209, F.212
- Chain B: A.74, L.76, F.217
- Ligands: CLA.2, CHL.7, CHL.9, LUT.16, CLA.21, CLA.22, LUT.35, CLA.41
8 PLIP interactions:2 interactions with chain B, 6 interactions with chain A,- Hydrophobic interactions: B:F.217, B:F.217, A:L.81, A:F.209, A:F.212, A:F.212
- Hydrogen bonds: A:Y.78
- Metal complexes: A:H.85
CLA.4: 17 residues within 4Å:- Chain A: L.91, G.92, L.94, G.95, T.98, P.99, L.102, F.109, Q.120, L.127, N.128, Y.129, I.136
- Ligands: CHL.6, CLA.10, LUT.16, NEX.18
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:L.91, A:L.91, A:L.94, A:L.102, A:L.127, A:I.136
CLA.10: 19 residues within 4Å:- Chain A: R.87, M.90, L.91, H.173, P.174, G.175, F.178, D.179, L.183, A.184, F.190, L.193, K.194, K.196, E.197
- Ligands: CLA.4, CHL.8, CLA.12, LUT.15
18 PLIP interactions:18 interactions with chain A,- Hydrophobic interactions: A:R.87, A:R.87, A:M.90, A:L.91, A:L.91, A:F.178, A:L.183, A:F.190, A:L.193, A:L.193, A:K.194, A:K.196, A:E.197, A:E.197
- Hydrogen bonds: A:G.175
- Salt bridges: A:H.173
- pi-Stacking: A:H.173
- Metal complexes: A:E.197
CLA.11: 10 residues within 4Å:- Chain A: W.32, E.192, V.195, K.196, K.199, N.200, L.203
- Ligands: CLA.12, LHG.19, XAT.55
8 PLIP interactions:8 interactions with chain A,- Hydrophobic interactions: A:W.32, A:K.199, A:L.203
- Hydrogen bonds: A:N.200
- Salt bridges: A:K.196, A:K.199
- pi-Cation interactions: A:K.199, A:K.199
CLA.12: 6 residues within 4Å:- Chain A: L.193, K.196, N.200
- Ligands: CLA.10, CLA.11, LUT.15
3 PLIP interactions:3 interactions with chain A,- Hydrophobic interactions: A:L.193
- Hydrogen bonds: A:K.196
- Salt bridges: A:K.196
CLA.13: 19 residues within 4Å:- Chain A: F.206, G.210, V.213, Q.214, T.218, N.225, L.226, H.229, V.236, N.237, A.238, Y.241
- Chain C: A.154, V.157
- Ligands: CLA.2, CLA.14, LUT.15, LHG.19, XAT.55
11 PLIP interactions:9 interactions with chain A, 2 interactions with chain C,- Hydrophobic interactions: A:F.206, A:F.206, A:F.206, A:V.213, A:Q.214, A:L.226, A:A.238, C:A.154, C:V.157
- Hydrogen bonds: A:T.218, A:A.238
CLA.14: 9 residues within 4Å:- Chain A: L.226, H.229, L.230, P.233, N.237, F.239
- Chain C: V.150
- Ligands: CLA.13, XAT.55
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C,- Hydrophobic interactions: A:L.226, A:L.230, A:P.233, C:V.150
- Hydrogen bonds: A:N.237
- Metal complexes: A:H.229
CLA.21: 21 residues within 4Å:- Chain B: L.61, P.66, G.67, D.68, Y.69, G.70, W.71, D.72, L.76, S.77, F.83, Y.86, R.87, L.89, E.90, R.210, M.213
- Ligands: CLA.3, CHL.20, CLA.22, LUT.35
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:Y.69, B:W.71, B:L.76, B:Y.86, B:R.87, B:L.89, B:R.210, B:M.213
- Hydrogen bonds: B:Y.69, B:G.70, B:W.71
- Salt bridges: B:R.210
- pi-Stacking: B:W.71
- pi-Cation interactions: B:R.210
- Metal complexes: B:E.90
CLA.22: 15 residues within 4Å:- Chain B: Y.86, L.89, H.93, F.217, F.220
- Chain C: A.74, L.76
- Ligands: CLA.3, CLA.21, CHL.26, CHL.28, LUT.35, CLA.40, CLA.41, LUT.54
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:L.89, B:F.217, B:F.220, B:F.220, C:A.74
- Hydrogen bonds: B:Y.86
- Metal complexes: B:H.93
CLA.23: 21 residues within 4Å:- Chain B: W.96, L.99, G.100, L.102, G.103, T.106, P.107, L.110, F.117, E.119, A.125, Q.128, L.135, D.136, Y.137, L.138
- Ligands: CHL.24, CHL.25, CLA.29, LUT.35, NEX.37
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:W.96, B:L.99, B:L.99, B:L.102, B:L.102, B:L.110, B:L.135, B:Y.137, B:Y.137
- Hydrogen bonds: B:Q.128
CLA.29: 19 residues within 4Å:- Chain B: R.95, M.98, L.99, Y.181, P.182, G.183, F.186, D.187, L.191, A.192, F.198, L.201, K.202, E.205
- Ligands: CLA.23, CHL.27, CLA.31, LUT.34, NEX.37
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:R.95, B:R.95, B:M.98, B:L.99, B:L.99, B:F.198, B:L.201, B:K.202
- Hydrogen bonds: B:G.183
- Metal complexes: B:E.205
CLA.30: 8 residues within 4Å:- Chain B: F.40, V.203, K.204, K.207, N.208, L.211
- Ligands: CLA.31, LHG.38
6 PLIP interactions:6 interactions with chain B,- Hydrophobic interactions: B:K.207, B:L.211
- Hydrogen bonds: B:K.207
- Salt bridges: B:K.204, B:K.207
- pi-Cation interactions: B:K.207
CLA.31: 6 residues within 4Å:- Chain B: L.102, K.204, N.208
- Ligands: CLA.29, CLA.30, LUT.34
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:L.102, B:K.204
- Salt bridges: B:K.204, B:K.204
CLA.32: 21 residues within 4Å:- Chain A: I.142, L.145, A.146
- Chain B: F.214, S.215, G.218, V.221, Q.222, V.225, T.226, N.233, L.234, H.237, N.244, N.245, A.246, F.249
- Ligands: XAT.17, CLA.33, LUT.34, LHG.38
13 PLIP interactions:10 interactions with chain B, 3 interactions with chain A,- Hydrophobic interactions: B:F.214, B:F.214, B:V.221, B:Q.222, B:V.225, B:L.234, B:H.237, B:A.246, A:I.142, A:L.145, A:A.146
- Hydrogen bonds: B:A.246
- Salt bridges: B:H.237
CLA.33: 8 residues within 4Å:- Chain A: I.142
- Chain B: H.237, L.238, P.241, N.245, F.247
- Ligands: XAT.17, CLA.32
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain A,- Hydrophobic interactions: B:L.238, B:P.241, B:P.241, A:I.142
- Hydrogen bonds: B:N.245
- Metal complexes: B:H.237
CLA.40: 20 residues within 4Å:- Chain C: L.61, G.67, D.68, Y.69, G.70, W.71, D.72, L.76, S.77, F.83, Y.86, R.87, L.89, E.90, R.210, M.213
- Ligands: CLA.22, CHL.39, CLA.41, LUT.54
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:Y.69, C:W.71, C:W.71, C:L.76, C:Y.86, C:R.87, C:L.89, C:R.210, C:R.210, C:M.213
- Hydrogen bonds: C:Y.69, C:G.70, C:W.71
- Salt bridges: C:R.210
- pi-Stacking: C:W.71
- pi-Cation interactions: C:R.210
- Metal complexes: C:E.90
CLA.41: 17 residues within 4Å:- Chain A: T.65, A.66, L.68
- Chain C: Y.86, L.89, H.93, F.217, F.220
- Ligands: CHL.1, CLA.2, CLA.3, LUT.16, CLA.22, CLA.40, CHL.45, CHL.47, LUT.54
9 PLIP interactions:6 interactions with chain C, 3 interactions with chain A,- Hydrophobic interactions: C:L.89, C:L.89, C:F.217, C:F.220, C:F.220, A:A.66, A:L.68
- Metal complexes: C:H.93
- Hydrogen bonds: A:T.65
CLA.42: 19 residues within 4Å:- Chain C: W.96, L.99, G.100, L.102, G.103, T.106, P.107, L.110, F.117, E.119, A.120, Q.128, L.135, Y.137, V.144
- Ligands: CHL.44, CLA.48, LUT.54, NEX.56
7 PLIP interactions:7 interactions with chain C,- Hydrophobic interactions: C:W.96, C:L.99, C:L.102, C:L.110, C:F.117, C:V.144
- Hydrogen bonds: C:Q.128
CLA.48: 20 residues within 4Å:- Chain C: R.95, M.98, L.99, Y.181, P.182, G.183, F.186, D.187, L.191, A.192, F.198, L.201, K.202, K.204, E.205
- Ligands: CLA.42, CHL.46, CLA.50, LUT.53, NEX.56
13 PLIP interactions:13 interactions with chain C,- Hydrophobic interactions: C:R.95, C:R.95, C:M.98, C:F.186, C:L.191, C:F.198, C:L.201, C:K.202, C:K.204, C:E.205
- Hydrogen bonds: C:G.183
- pi-Cation interactions: C:R.95
- Metal complexes: C:E.205
CLA.49: 10 residues within 4Å:- Chain C: I.38, F.40, V.203, K.204, K.207, N.208, L.211
- Ligands: XAT.36, CLA.50, LHG.57
8 PLIP interactions:8 interactions with chain C,- Hydrophobic interactions: C:I.38, C:K.207, C:L.211, C:L.211
- Salt bridges: C:K.204, C:K.207
- pi-Cation interactions: C:K.207, C:K.207
CLA.50: 8 residues within 4Å:- Chain C: L.102, L.201, K.204, N.208, L.211
- Ligands: CLA.48, CLA.49, LUT.53
6 PLIP interactions:6 interactions with chain C,- Hydrophobic interactions: C:L.102, C:L.201, C:L.211
- Hydrogen bonds: C:K.204
- Salt bridges: C:K.204, C:K.204
CLA.51: 21 residues within 4Å:- Chain B: V.150, L.153, A.154
- Chain C: F.214, S.215, F.217, G.218, V.221, Q.222, V.225, T.226, N.233, H.237, N.244, N.245, A.246, F.249
- Ligands: XAT.36, CLA.52, LUT.53, LHG.57
9 PLIP interactions:6 interactions with chain C, 3 interactions with chain B,- Hydrophobic interactions: C:F.217, C:V.221, C:V.225, B:V.150, B:L.153, B:A.154
- Hydrogen bonds: C:Q.222, C:A.246
- Salt bridges: C:H.237
CLA.52: 9 residues within 4Å:- Chain C: L.234, H.237, L.238, P.241, N.245, F.247
- Ligands: XAT.36, CLA.51, LUT.53
4 PLIP interactions:4 interactions with chain C,- Hydrophobic interactions: C:L.234, C:L.238, C:P.241
- Metal complexes: C:H.237
- 6 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)
LUT.15: 20 residues within 4Å:- Chain A: M.90, A.93, L.94, I.97, F.178, D.179, L.181, L.183, N.200, L.203, S.207, F.211, Q.214, P.222, I.223, L.226
- Ligands: CHL.8, CLA.10, CLA.12, CLA.13
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:M.90, A:L.94, A:I.97, A:L.181, A:L.183, A:L.203, A:F.211, A:I.223, A:L.226
- Hydrogen bonds: A:D.179, A:Q.214, A:P.222, A:L.226
LUT.16: 23 residues within 4Å:- Chain A: W.63, D.64, T.65, A.66, L.68, H.85, W.88, A.89, G.92, G.95, C.96, W.114, A.117, M.205, M.208, F.209
- Ligands: CLA.2, CLA.3, CLA.4, CHL.6, CHL.7, CLA.41, CHL.47
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:W.63, A:W.63, A:W.63, A:A.66, A:L.68, A:A.89, A:W.114, A:W.114, A:M.205, A:F.209
- Hydrogen bonds: A:T.65, A:A.66
LUT.34: 18 residues within 4Å:- Chain B: M.98, L.99, A.101, L.102, D.187, L.189, N.208, L.211, A.212, S.215, F.219, Q.222, P.230, L.234
- Ligands: CHL.27, CLA.29, CLA.31, CLA.32
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:M.98, B:L.102, B:D.187, B:A.212, B:F.219, B:F.219
- Hydrogen bonds: B:Q.222
LUT.35: 23 residues within 4Å:- Chain B: W.71, D.72, T.73, A.74, L.76, H.93, W.96, A.97, G.100, G.103, C.104, W.122, A.125, M.213, M.216, F.217
- Ligands: CLA.3, CHL.9, CLA.21, CLA.22, CLA.23, CHL.25, CHL.26
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:W.71, B:W.71, B:W.71, B:A.74, B:L.76, B:W.96, B:A.97, B:W.122, B:M.216, B:F.217
- Hydrogen bonds: B:A.74, B:W.122
LUT.53: 20 residues within 4Å:- Chain C: M.98, L.99, A.101, L.102, F.186, D.187, P.188, L.189, N.208, A.212, S.215, F.219, Q.222, P.230, L.234
- Ligands: CHL.46, CLA.48, CLA.50, CLA.51, CLA.52
13 PLIP interactions:13 interactions with chain C- Hydrophobic interactions: C:M.98, C:L.99, C:A.101, C:L.102, C:L.189, C:A.212, C:F.219, C:F.219, C:P.230, C:L.234
- Hydrogen bonds: C:L.189, C:Q.222, C:P.230
LUT.54: 23 residues within 4Å:- Chain C: W.71, D.72, T.73, A.74, G.75, H.93, W.96, A.97, G.100, G.103, C.104, W.122, A.125, M.213, M.216, F.217
- Ligands: CLA.22, CHL.28, CLA.40, CLA.41, CLA.42, CHL.44, CHL.45
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:W.71, C:W.71, C:A.74, C:A.97, C:W.122, C:W.122, C:M.213, C:F.217
- Hydrogen bonds: C:A.74, C:G.75
- 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: 12 residues within 4Å:- Chain A: L.145, V.149
- Chain B: A.246, F.247, A.250, F.253
- Ligands: CHL.7, CHL.9, CHL.20, CLA.32, CLA.33, LHG.38
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain B- Hydrophobic interactions: A:L.145, A:V.149, B:A.246, B:F.247, B:A.250
XAT.36: 14 residues within 4Å:- Chain B: L.153, V.157
- Chain C: A.246, F.247, F.249, A.250, F.253
- Ligands: CHL.26, CHL.28, CHL.39, CLA.49, CLA.51, CLA.52, LHG.57
7 PLIP interactions:4 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:A.246, C:F.247, C:A.250, B:L.153, B:V.157, B:V.157
- Hydrogen bonds: C:F.253
XAT.55: 14 residues within 4Å:- Chain A: A.238, F.239, Y.241, A.242, F.245
- Chain C: L.153, V.157
- Ligands: CHL.1, CLA.11, CLA.13, CLA.14, LHG.19, CHL.45, CHL.47
6 PLIP interactions:3 interactions with chain C, 3 interactions with chain A- Hydrophobic interactions: C:L.153, C:V.157, C:V.157, A:A.238, A:F.239, A:A.242
- 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: 9 residues within 4Å:- Chain A: W.88, Y.129, V.151, L.154, Y.158, P.164
- Ligands: CLA.4, CHL.6, CHL.8
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.88, A:V.151, A:L.154, A:P.164
- Hydrogen bonds: A:Y.129
NEX.37: 12 residues within 4Å:- Chain B: W.96, Y.137, L.159, M.160, L.162, V.163, Y.166, P.172
- Ligands: CLA.23, CHL.25, CHL.27, CLA.29
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:W.96, B:L.159, B:L.159, B:L.162
NEX.56: 10 residues within 4Å:- Chain C: W.96, Y.137, L.159, L.162, Y.166, P.172
- Ligands: CLA.42, CHL.44, CHL.46, CLA.48
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:W.96, C:L.162, C:Y.166, C:P.172
- Hydrogen bonds: C:Y.137
- 3 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.19: 11 residues within 4Å:- Chain A: W.32, Y.61, K.199, L.203, F.206
- Ligands: CHL.1, CLA.2, CLA.11, CLA.13, CHL.45, XAT.55
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:L.203, A:F.206
- Hydrogen bonds: A:Y.61
- Salt bridges: A:K.199, A:K.199
LHG.38: 9 residues within 4Å:- Chain B: Y.69, K.207, R.210, L.211, F.214
- Ligands: XAT.17, CHL.20, CLA.30, CLA.32
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:R.210, B:F.214, B:F.214, B:F.214
- Hydrogen bonds: B:Y.69
- Salt bridges: B:K.207
LHG.57: 12 residues within 4Å:- Chain C: I.38, F.40, Y.69, K.207, R.210, L.211, F.214
- Ligands: CHL.26, XAT.36, CHL.39, CLA.49, CLA.51
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:L.211, C:F.214, C:F.214
- Salt bridges: C:K.207
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pan, X. et al., Structural basis of LhcbM5-mediated state transitions in green algae. Nat.Plants (2021)
- Release Date
- 2021-06-30
- Peptides
- Chlorophyll a-b binding protein, chloroplastic: A
Chlorophyll a-b binding protein, chloroplastic: BC - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
XB
YC
Z - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-2-mer
- 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
- Pan, X. et al., Structural basis of LhcbM5-mediated state transitions in green algae. Nat.Plants (2021)
- Release Date
- 2021-06-30
- Peptides
- Chlorophyll a-b binding protein, chloroplastic: A
Chlorophyll a-b binding protein, chloroplastic: BC - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
XB
YC
Z - Membrane
-
We predict this structure to be a membrane protein.