- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 9 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.6: 2 residues within 4Å:- Chain B: W.21, W.25
No protein-ligand interaction detected (PLIP)HTO.12: 4 residues within 4Å:- Chain C: L.75, Q.87, V.91, W.142
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:W.142
- Hydrogen bonds: C:Q.87
HTO.13: 4 residues within 4Å:- Chain C: A.77, A.78, L.80, Q.87
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.80
HTO.14: 7 residues within 4Å:- Chain C: W.115, H.116, L.119
- Chain D: A.1, D.2
- Ligands: LDA.19, HTO.20
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:D.2, C:W.115
HTO.15: 3 residues within 4Å:- Chain C: S.175, N.239
- Ligands: DGA.5
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:S.175, C:N.239
HTO.20: 7 residues within 4Å:- Chain C: L.119, A.120, C.122, V.123, L.234
- Ligands: HTO.14, LDA.19
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.123
HTO.27: 5 residues within 4Å:- Chain D: G.141, T.142, H.143, W.146
- Ligands: SO4.32
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:T.142
HTO.28: 6 residues within 4Å:- Chain C: V.220
- Chain D: G.30, K.31, I.46, G.47, I.49
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:I.46
- Hydrogen bonds: D:K.31
HTO.29: 2 residues within 4Å:- Chain D: F.71, W.112
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:F.71
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 6 residues within 4Å:- Chain B: R.33, R.37, Y.41, Q.58
- Chain D: R.251
- Ligands: OLC.7
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:R.33, B:Y.41, D:R.251
- Water bridges: B:R.33, B:Y.41
- Salt bridges: B:R.37
SO4.16: 5 residues within 4Å:- Chain C: P.61, I.64, Y.148, I.150
- Ligands: BCB.10
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:I.150
- Water bridges: C:P.61, C:I.64
SO4.31: 4 residues within 4Å:- Chain B: L.246
- Chain D: A.1, D.2, R.226
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:R.226
SO4.32: 4 residues within 4Å:- Chain C: N.199
- Chain D: H.143, R.265
- Ligands: HTO.27
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:H.143, D:R.265
SO4.33: 4 residues within 4Å:- Chain B: D.202
- Chain D: Y.3, Y.7, Q.9
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:Y.7, D:Y.7, D:Q.9
SO4.34: 9 residues within 4Å:- Chain D: W.23, Y.50, L.51, G.52, A.53, S.54, I.129, S.133
- Ligands: LDA.30
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:Y.50, D:A.53, D:S.54, D:S.133, D:S.133
- Water bridges: D:R.134
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.9: 29 residues within 4Å:- Chain C: F.97, P.124, M.127, F.128, L.131, V.157, N.158, F.160, G.161, Y.162, W.167, H.168, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, T.248
- Chain D: L.184, Y.195, Y.208
- Ligands: BCB.10, BPB.11, MQ7.22, BCB.23, BCB.24
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:F.97, C:F.97, C:V.157, C:F.160, C:Y.162, C:W.167, C:W.167, C:V.177, C:L.180, C:F.181, C:I.240, C:F.241, C:F.241
- Hydrogen bonds: C:S.176, C:T.248
- pi-Stacking: C:W.167
- Metal complexes: C:H.173
BCB.10: 19 residues within 4Å:- Chain C: F.128, F.146, I.150, H.153, L.154, V.157
- Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212
- Ligands: OLC.7, BCB.9, BPB.11, SO4.16, MQ7.22, BCB.24
10 PLIP interactions:5 interactions with chain C, 5 interactions with chain D,- Hydrophobic interactions: C:F.128, C:F.146, C:L.154, C:V.157, D:Y.195, D:I.204, D:I.204, D:L.212
- Metal complexes: C:H.153
- pi-Stacking: D:Y.208
BCB.23: 20 residues within 4Å:- Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220
- Chain D: V.155, I.158, I.177, W.178, H.180, I.181, L.184
- Ligands: DGA.5, BCB.9, BCB.24, BPB.25, NS5.26
11 PLIP interactions:6 interactions with chain C, 5 interactions with chain D,- Hydrophobic interactions: C:V.177, C:F.181, C:V.182, C:V.182, C:V.220, D:V.155, D:I.158, D:I.181, D:L.184
- pi-Stacking: C:F.181
- Metal complexes: D:H.180
BCB.24: 29 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: I.69, L.124, F.148, F.154, V.155, I.158, W.183, L.184, T.185, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, A.207, Y.208, M.275, A.278, I.282
- Ligands: BCB.9, BCB.10, BCB.23, BPB.25, NS5.26
16 PLIP interactions:16 interactions with chain D,- Hydrophobic interactions: D:I.69, D:L.124, D:F.148, D:F.154, D:F.154, D:V.155, D:W.183, D:L.184, D:F.187, D:F.194, D:Y.195, D:Y.195, D:I.204, D:A.207
- Hydrogen bonds: D:S.203
- Metal complexes: D:H.200
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.11: 24 residues within 4Å:- Chain C: F.41, I.42, A.93, A.96, F.97, W.100, E.104, V.117, A.120, F.121, P.124, Y.148, G.149, I.150, H.153, A.237, F.241
- Chain D: Y.208, L.212, W.250, I.254
- Ligands: BCB.9, BCB.10, MQ7.22
13 PLIP interactions:1 interactions with chain D, 12 interactions with chain C- Hydrophobic interactions: D:Y.208, C:I.42, C:A.96, C:A.120, C:F.121, C:F.121, C:F.121, C:P.124, C:Y.148, C:Y.148, C:I.150, C:F.241, C:F.241
BPB.25: 21 residues within 4Å:- Chain C: F.181, M.185, L.189, V.219, V.220
- Chain D: A.58, F.59, G.62, S.63, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, M.275
- Ligands: BCB.23, BCB.24
9 PLIP interactions:6 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:I.66, D:W.127, D:N.147, D:F.148, D:F.148, C:F.181, C:M.185, C:L.189
- pi-Stacking: D:F.148
- 2 x UQ1: UBIQUINONE-1(Non-covalent)
UQ1.17: 13 residues within 4Å:- Chain C: L.189, H.190, L.193, E.212, N.213, F.216, V.220, Y.222, S.223, I.224, G.225, A.226, I.229
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:L.189, C:F.216, C:F.216, C:F.216, C:F.216, C:V.220, C:I.224, C:I.229
- Hydrogen bonds: C:I.224, C:G.225
UQ1.18: 5 residues within 4Å:- Chain C: W.263, W.266
- Chain D: F.85, F.88, F.89
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:F.88, D:F.88
- Water bridges: D:F.89
- pi-Stacking: C:W.266
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
MQ7.22: 23 residues within 4Å:- Chain C: Y.29, G.35, I.39, W.100, R.103
- Chain D: A.216, H.217, T.220, A.246, A.247, W.250, I.254, F.256, N.257, A.258, T.259, I.260, V.263, W.266, F.270
- Ligands: BCB.9, BCB.10, BPB.11
20 PLIP interactions:14 interactions with chain D, 6 interactions with chain C- Hydrophobic interactions: D:A.216, D:T.220, D:A.246, D:W.250, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:W.266, D:F.270, C:Y.29, C:Y.29, C:I.39, C:W.100, C:W.100, C:W.100
- Hydrogen bonds: D:A.258
- pi-Stacking: D:W.250
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bath, P. et al., Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Acta Crystallogr D Struct Biol (2022)
- Release Date
- 2022-06-22
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Reaction center protein H chain: B
Reaction center protein L chain: C
Reaction center protein M chain: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
HHHC
LLLD
MMM - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 9 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 2 x UQ1: UBIQUINONE-1(Non-covalent)
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bath, P. et al., Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Acta Crystallogr D Struct Biol (2022)
- Release Date
- 2022-06-22
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Reaction center protein H chain: B
Reaction center protein L chain: C
Reaction center protein M chain: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
HHHC
LLLD
MMM - Membrane
-
We predict this structure to be a membrane protein.