- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
- 15 x CHL: CHLOROPHYLL B(Non-covalent)
CHL.4: 10 residues within 4Å:- Chain A: A.110, P.111, L.112, A.113, P.114, Y.119, N.124, V.125
- Ligands: CLA.3, CHL.5
7 PLIP interactions:7 interactions with chain A,- Hydrophobic interactions: A:L.112, A:L.112, A:P.114, A:Y.119, A:Y.119, A:V.125
- Metal complexes: A:L.112
CHL.5: 12 residues within 4Å:- Chain A: W.67, A.89, G.90, C.93, V.101, V.125, I.128, E.129
- Ligands: CLA.3, CHL.4, CHL.6, Q6L.16
7 PLIP interactions:7 interactions with chain A,- Hydrophobic interactions: A:W.67, A:V.101, A:V.125, A:V.125, A:E.129, A:E.129
- Metal complexes: A:E.129
CHL.6: 15 residues within 4Å:- Chain A: F.87, G.90, T.91, C.93, F.122, E.129
- Chain C: L.223, A.226, A.227
- Ligands: CLA.2, CHL.5, Q6L.16, Q6L.42, IWJ.59, Q6L.60
4 PLIP interactions:4 interactions with chain A,- Hydrophobic interactions: A:F.87, A:F.122
- Hydrogen bonds: A:T.91, A:T.91
CHL.7: 17 residues within 4Å:- Chain A: I.63, R.66, W.67, A.136, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, V.154, V.157, P.159, F.163
- Ligands: CLA.9, IWJ.17
14 PLIP interactions:14 interactions with chain A,- Hydrophobic interactions: A:I.63, A:Y.139, A:Y.139, A:R.140, A:P.147, A:F.148, A:F.148, A:L.152, A:V.154, A:P.159, A:F.163
- Hydrogen bonds: A:R.66
- pi-Stacking: A:F.163
- pi-Cation interactions: A:R.140
CHL.14: 8 residues within 4Å:- Chain A: A.77, N.80, F.105, P.106, G.107, V.109
- Ligands: CLA.3, IWJ.17
2 PLIP interactions:2 interactions with chain A,- Hydrophobic interactions: A:P.106
- Metal complexes: A:P.106
CHL.25: 8 residues within 4Å:- Chain B: A.110, L.112, A.113, P.114, Y.119, N.124, V.125
- Ligands: CHL.26
5 PLIP interactions:5 interactions with chain B,- Hydrophobic interactions: B:A.110, B:L.112, B:Y.119, B:V.125
- Metal complexes: B:L.112
CHL.26: 12 residues within 4Å:- Chain B: G.90, L.92, C.93, V.101, I.128, E.129, V.133
- Ligands: CLA.24, CHL.25, CHL.27, Q6L.37, NEX.38
4 PLIP interactions:4 interactions with chain B,- Hydrophobic interactions: B:L.92, B:V.101, B:E.129, B:V.133
CHL.27: 21 residues within 4Å:- Chain A: V.222, L.223, A.226, A.227, F.230
- Chain B: F.87, T.88, G.90, T.91, C.93, T.94, F.122, L.126, E.129
- Ligands: IWJ.18, Q6L.19, IWJ.20, Q6L.21, CLA.23, CHL.26, Q6L.37
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A,- Hydrophobic interactions: B:F.87, B:T.94, B:F.122, B:L.126, A:L.223
CHL.28: 22 residues within 4Å:- Chain B: I.63, R.66, W.67, A.136, E.137, Y.139, R.140, S.146, P.147, F.148, L.152, T.153, D.156, V.157, P.159, F.163, P.165
- Ligands: CLA.24, CLA.30, Q6L.36, NEX.38, IWJ.39
12 PLIP interactions:12 interactions with chain B,- Hydrophobic interactions: B:Y.139, B:Y.139, B:R.140, B:P.147, B:F.148, B:L.152, B:P.159, B:F.163, B:F.163, B:P.165
- Hydrogen bonds: B:R.66
- pi-Cation interactions: B:R.140
CHL.35: 9 residues within 4Å:- Chain B: A.77, F.105, P.106, G.107, A.108, V.109
- Ligands: CLA.24, NEX.38, IWJ.39
5 PLIP interactions:5 interactions with chain B,- Hydrophobic interactions: B:F.105, B:F.105, B:P.106, B:V.109
- Metal complexes: B:P.106
CHL.46: 9 residues within 4Å:- Chain C: P.111, L.112, A.113, P.114, Y.119, N.124, V.125
- Ligands: CHL.47, CHL.56
8 PLIP interactions:8 interactions with chain C,- Hydrophobic interactions: C:P.111, C:L.112, C:A.113, C:P.114, C:Y.119, C:V.125
- Hydrogen bonds: C:N.124
- Metal complexes: C:L.112
CHL.47: 12 residues within 4Å:- Chain C: W.67, A.89, C.93, V.101, L.112, V.125, I.128, E.129
- Ligands: CLA.45, CHL.46, CHL.48, Q6L.58
5 PLIP interactions:5 interactions with chain C,- Hydrophobic interactions: C:W.67, C:V.101, C:V.101, C:L.112, C:V.125
CHL.48: 17 residues within 4Å:- Chain B: V.222, L.223, A.226, A.227, F.230
- Chain C: W.86, F.87, G.90, T.91, F.122
- Ligands: IWJ.20, Q6L.40, Q6L.41, CLA.44, CHL.47, Q6L.58, IWJ.59
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain B,- Hydrophobic interactions: C:W.86, C:F.87, C:F.122, B:L.223, B:A.226
- Hydrogen bonds: C:T.91
CHL.49: 12 residues within 4Å:- Chain C: R.66, W.67, A.136, Y.139, R.140, P.147, F.148, L.152, T.153, P.159, F.163
- Ligands: CLA.51
10 PLIP interactions:10 interactions with chain C,- Hydrophobic interactions: C:Y.139, C:Y.139, C:Y.139, C:R.140, C:P.147, C:F.148, C:P.159, C:F.163
- Hydrogen bonds: C:R.66
- pi-Stacking: C:F.163
CHL.56: 8 residues within 4Å:- Chain C: A.77, G.81, F.105, P.106, G.107, A.108
- Ligands: CLA.45, CHL.46
3 PLIP interactions:3 interactions with chain C,- Hydrophobic interactions: C:F.105, C:P.106
- Metal complexes: C:P.106
- 3 x KC2: Chlorophyll c2(Non-covalent)
KC2.8: 12 residues within 4Å:- Chain A: E.59, R.60, I.63, H.64, W.67, V.133, E.137, R.140, T.141, I.143
- Ligands: CLA.2, Q6L.42
13 PLIP interactions:13 interactions with chain A,- Hydrophobic interactions: A:I.63, A:W.67, A:W.67, A:V.133, A:E.137, A:T.141, A:I.143
- Salt bridges: A:K.56, A:K.56, A:R.140
- pi-Cation interactions: A:R.140, A:R.140
- Metal complexes: A:E.137
KC2.29: 14 residues within 4Å:- Chain B: K.56, E.59, R.60, H.64, W.67, I.130, V.133, G.134, E.137, R.140, T.141, I.143
- Ligands: Q6L.21, CLA.23
12 PLIP interactions:12 interactions with chain B,- Hydrophobic interactions: B:W.67, B:W.67, B:I.130, B:E.137, B:E.137, B:I.143
- Hydrogen bonds: B:H.64
- Salt bridges: B:K.56, B:R.140
- pi-Cation interactions: B:R.140, B:R.140
- Metal complexes: B:E.137
KC2.50: 12 residues within 4Å:- Chain C: K.56, E.59, R.60, I.63, H.64, W.67, V.133, E.137, R.140, T.141
- Ligands: Q6L.41, CLA.44
10 PLIP interactions:10 interactions with chain C,- Hydrophobic interactions: C:I.63, C:W.67, C:V.133, C:E.137, C:T.141
- Salt bridges: C:K.56, C:R.140
- pi-Cation interactions: C:R.140, C:R.140
- Metal complexes: C:E.137
- 12 x Q6L: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol(Non-covalent)
Q6L.15: 21 residues within 4Å:- Chain A: M.69, T.73, W.76, D.164, P.165, L.166, G.167, L.168, H.184, L.187, S.188, A.191, C.195, Q.198, P.206, I.207, W.210
- Ligands: CLA.9, CLA.11, CLA.12, IWJ.17
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:M.69, A:W.76, A:L.166, A:L.187, A:A.191, A:P.206
- Hydrogen bonds: A:D.164, A:L.166, A:G.167, A:L.168
Q6L.16: 18 residues within 4Å:- Chain A: F.38, P.48, I.49, I.50, H.64, W.67, A.68, G.71, W.86, M.189, W.192, L.193
- Ligands: CLA.1, CLA.2, CLA.3, CHL.5, CHL.6, CLA.23
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:F.38, A:I.50, A:W.67, A:W.67, A:A.68, A:W.86, A:W.86, A:M.189, A:W.192, A:W.192, A:W.192, A:W.192, A:W.192, A:L.193
- Hydrogen bonds: A:I.49
Q6L.19: 20 residues within 4Å:- Chain A: Y.35, E.37, F.38, K.183, R.186, L.187, F.190, V.218, N.221, L.223
- Chain B: P.95, F.122, W.123, L.126
- Ligands: CLA.1, CLA.10, CLA.12, CLA.13, IWJ.18, CHL.27
10 PLIP interactions:3 interactions with chain B, 7 interactions with chain A- Hydrophobic interactions: B:P.95, B:F.122, B:W.123, A:E.37, A:R.186, A:L.187, A:F.190, A:F.190, A:L.223
- Hydrogen bonds: A:F.38
Q6L.21: 17 residues within 4Å:- Chain A: F.38, A.226, G.229, F.230, Y.233
- Chain B: W.86, F.87, W.192, I.196, A.199, L.200
- Ligands: CLA.12, IWJ.18, IWJ.20, CLA.23, CHL.27, KC2.29
12 PLIP interactions:7 interactions with chain B, 5 interactions with chain A- Hydrophobic interactions: B:W.86, B:F.87, B:F.87, B:I.196, B:I.196, B:A.199, B:L.200, A:F.38, A:F.38, A:F.230, A:F.230, A:Y.233
Q6L.36: 21 residues within 4Å:- Chain B: M.69, V.72, T.73, F.163, D.164, P.165, L.166, G.167, H.184, S.188, A.191, C.195, Q.198, P.206, N.209, W.210
- Ligands: CHL.28, CLA.30, CLA.32, CLA.33, IWJ.39
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:L.166, B:L.166, B:A.191, B:P.206, B:W.210, B:W.210
- Hydrogen bonds: B:D.164, B:L.166, B:G.167, B:Q.198, B:P.206, B:W.210
Q6L.37: 18 residues within 4Å:- Chain B: S.47, I.49, I.50, H.64, W.67, A.68, G.71, G.74, A.75, W.86, A.89, M.189, W.192
- Ligands: CLA.22, CLA.23, CLA.24, CHL.26, CHL.27
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:I.49, B:I.49, B:W.67, B:W.67, B:A.68, B:W.86, B:M.189, B:W.192, B:W.192
- Hydrogen bonds: B:S.47
Q6L.40: 20 residues within 4Å:- Chain B: Y.35, E.37, F.38, K.183, R.186, L.187, F.190, V.218, N.221, L.223
- Chain C: P.95, F.122, L.126
- Ligands: IWJ.20, CLA.22, CLA.31, CLA.33, CLA.34, CLA.44, CHL.48
15 PLIP interactions:3 interactions with chain C, 12 interactions with chain B- Hydrophobic interactions: C:P.95, C:F.122, C:F.122, B:Y.35, B:E.37, B:F.38, B:K.183, B:R.186, B:L.187, B:F.190, B:F.190, B:L.223
- Hydrogen bonds: B:F.38, B:V.218, B:N.221
Q6L.41: 16 residues within 4Å:- Chain B: F.38, A.226, G.229, F.230, Y.233
- Chain C: R.60, W.86, F.87, W.192, I.196, A.199
- Ligands: IWJ.20, CLA.33, CLA.44, CHL.48, KC2.50
9 PLIP interactions:4 interactions with chain C, 5 interactions with chain B- Hydrophobic interactions: C:W.86, C:I.196, C:A.199, B:F.38, B:F.38, B:F.230, B:Y.233, B:Y.233
- Hydrogen bonds: C:R.60
Q6L.42: 13 residues within 4Å:- Chain A: F.87, W.192, I.196, A.199, L.200
- Chain C: F.38, A.226, F.230, Y.233
- Ligands: CLA.2, CHL.6, KC2.8, IWJ.59
10 PLIP interactions:6 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: C:F.38, C:A.226, C:F.230, C:F.230, C:Y.233, C:Y.233, A:F.87, A:F.87, A:I.196, A:L.200
Q6L.57: 15 residues within 4Å:- Chain C: L.70, V.72, T.73, F.163, D.164, L.168, H.184, L.187, A.191, C.195, Q.198, P.206
- Ligands: CLA.51, CLA.53, CLA.54
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:L.70, C:T.73, C:L.168, C:L.187, C:L.187, C:A.191, C:P.206
Q6L.58: 18 residues within 4Å:- Chain C: I.49, H.64, W.67, A.68, G.71, G.74, A.75, W.86, A.89, M.189, W.192, L.193
- Ligands: CLA.2, CLA.43, CLA.44, CLA.45, CHL.47, CHL.48
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:I.49, C:I.49, C:W.67, C:A.68, C:W.86, C:W.192, C:W.192, C:L.193, C:L.193
- Hydrogen bonds: C:I.49
Q6L.60: 15 residues within 4Å:- Chain A: P.95, F.122, L.126
- Chain C: Y.35, E.37, F.38, F.190, V.218, N.221, L.223, T.224
- Ligands: CHL.6, CLA.43, CLA.55, IWJ.59
12 PLIP interactions:3 interactions with chain A, 9 interactions with chain C- Hydrophobic interactions: A:P.95, A:F.122, A:L.126, C:Y.35, C:E.37, C:F.38, C:F.190, C:V.218, C:L.223
- Hydrogen bonds: C:V.218, C:N.221, C:T.224
- 5 x IWJ: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one(Non-covalent)
IWJ.17: 8 residues within 4Å:- Chain A: T.73, W.76, N.80, R.162
- Ligands: CLA.3, CHL.7, CHL.14, Q6L.15
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:T.73, A:R.162
- Hydrogen bonds: A:N.80, A:R.162
IWJ.18: 15 residues within 4Å:- Chain A: F.197, L.200, V.222, L.223, F.230, F.232
- Chain C: F.197, Y.233
- Ligands: CLA.12, CLA.13, Q6L.19, IWJ.20, Q6L.21, CHL.27, IWJ.59
11 PLIP interactions:2 interactions with chain C, 9 interactions with chain A- Hydrophobic interactions: C:F.197, C:Y.233, A:F.197, A:F.197, A:L.200, A:L.200, A:V.222, A:V.222, A:L.223, A:F.230, A:F.232
IWJ.20: 17 residues within 4Å:- Chain A: Y.233
- Chain B: F.197, L.200, A.201, V.222, L.223, F.230, F.232
- Ligands: IWJ.18, Q6L.21, CHL.27, CLA.33, CLA.34, Q6L.40, Q6L.41, CHL.48, IWJ.59
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:F.197, B:F.197, B:L.200, B:L.200, B:L.200, B:A.201, B:V.222, B:V.222, B:L.223, B:F.230
IWJ.39: 13 residues within 4Å:- Chain B: L.70, T.73, W.76, N.80, R.162, F.163, P.165
- Ligands: CLA.24, CHL.28, CLA.30, CHL.35, Q6L.36, NEX.38
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:L.70, B:T.73, B:W.76, B:F.163, B:P.165
- Hydrogen bonds: B:N.80, B:R.162
IWJ.59: 13 residues within 4Å:- Chain B: Y.233
- Chain C: L.200, A.201, F.230, F.232
- Ligands: CHL.6, IWJ.18, IWJ.20, Q6L.42, CHL.48, CLA.54, CLA.55, Q6L.60
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.200, C:L.200, C:A.201, C:F.230, C:F.232
- 1 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)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ishii, A. et al., The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers. Elife (2023)
- Release Date
- 2023-04-26
- Peptides
- Chlorophyll a-b binding protein, chloroplastic: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
VB
WC
X - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 24 x CLA: CHLOROPHYLL A(Non-covalent)
- 15 x CHL: CHLOROPHYLL B(Non-covalent)
- 3 x KC2: Chlorophyll c2(Non-covalent)
- 12 x Q6L: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol(Non-covalent)
- 5 x IWJ: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one(Non-covalent)
- 1 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)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ishii, A. et al., The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers. Elife (2023)
- Release Date
- 2023-04-26
- Peptides
- Chlorophyll a-b binding protein, chloroplastic: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
VB
WC
X - Membrane
-
We predict this structure to be a membrane protein.