- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.25 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
DGA.5: 13 residues within 4Å:- Chain A: C.1, F.2
- Chain C: P.171, S.175, S.178, F.246, A.250, W.262, W.265
- Chain D: F.89
- Ligands: BCB.22, NS5.25, UQ2.34
5 PLIP interactions:2 interactions with chain A, 1 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: A:F.2, A:F.2, D:F.89, C:F.246, C:A.250
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.6: 8 residues within 4Å:- Chain B: I.24, R.33, R.37
- Chain D: F.256, F.270
- Ligands: SO4.8, MQ9.21, LDA.29
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain B- Hydrophobic interactions: D:F.256, D:F.270, B:I.24
LDA.7: 6 residues within 4Å:- Chain B: Y.31
- Chain D: R.265, W.268
- Ligands: HTO.26, OLC.32, SO4.35
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:Y.31
LDA.20: 7 residues within 4Å:- Chain C: R.231, F.235
- Chain D: T.5, I.6, I.41
- Ligands: HTO.15, HTO.18
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:F.235, D:I.41
LDA.27: 7 residues within 4Å:- Chain D: A.53, A.57, S.126, I.129
- Ligands: LDA.30, SO4.36, SO4.38
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:A.53, D:A.57
LDA.29: 13 residues within 4Å:- Chain B: W.17
- Chain C: L.151
- Chain D: Y.195, Y.196, C.197, P.198, G.201, F.202, G.205, F.206, C.296
- Ligands: LDA.6, BCB.10
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:F.202, D:F.202, D:F.206
LDA.30: 3 residues within 4Å:- Chain D: W.23, W.128
- Ligands: LDA.27
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:W.128
LDA.31: 3 residues within 4Å:- Chain D: D.27, I.56
- Ligands: OLC.28
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:D.27
- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 5 residues within 4Å:- Chain B: R.33, R.37, Y.41
- Chain D: R.251
- Ligands: LDA.6
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:R.33, B:Y.41, D:R.251, D:R.251
- Water bridges: B:E.61, B:E.61
- Salt bridges: B:R.37
SO4.35: 5 residues within 4Å:- Chain C: N.199
- Chain D: H.143, R.265
- Ligands: LDA.7, HTO.26
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:H.143, D:R.265
SO4.36: 7 residues within 4Å:- Chain D: W.23, Y.50, G.52, A.53, S.54, S.133
- Ligands: LDA.27
7 PLIP interactions:7 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, D:R.134
SO4.37: 4 residues within 4Å:- Chain B: L.246
- Chain D: A.1, R.226
- Ligands: HTO.18
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:R.226
SO4.38: 4 residues within 4Å:- Chain D: F.61, L.122
- Ligands: LDA.27, OLC.28
No protein-ligand interaction detected (PLIP)- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.9: 28 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, BCB.22, BCB.23
15 PLIP interactions:15 interactions with chain C,- Hydrophobic interactions: C:F.97, 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: 18 residues within 4Å:- Chain C: I.49, 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
- Ligands: BCB.9, BPB.11, MQ9.21, BCB.23, LDA.29
10 PLIP interactions:6 interactions with chain C, 4 interactions with chain D,- Hydrophobic interactions: C:I.49, C:F.128, C:F.146, C:L.154, C:V.157, D:Y.195, D:I.204, D:I.204
- Metal complexes: C:H.153
- pi-Stacking: D:Y.208
BCB.22: 22 residues within 4Å:- Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220
- Chain D: F.154, V.155, I.158, I.177, W.178, H.180, I.181, L.184
- Ligands: DGA.5, BCB.9, UQ2.17, BCB.23, BPB.24, NS5.25
10 PLIP interactions:6 interactions with chain D, 4 interactions with chain C,- Hydrophobic interactions: D:F.154, D:V.155, D:I.158, D:I.181, D:L.184, C:V.177, C:V.182, C:V.220
- Metal complexes: D:H.180
- pi-Stacking: C:F.181
BCB.23: 26 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: I.69, L.124, F.148, F.154, V.155, W.183, L.184, 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.22, BPB.24
16 PLIP interactions:16 interactions with chain D,- Hydrophobic interactions: D:I.69, D:L.124, D:F.148, 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, D:Y.208
- 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: I.42, I.49, A.93, A.96, F.97, W.100, E.104, V.117, A.120, F.121, P.124, F.128, Y.148, G.149, I.150, A.237, F.241
- Chain D: Y.208, L.212, W.250, I.254
- Ligands: BCB.9, BCB.10, MQ9.21
16 PLIP interactions:15 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:I.42, C:I.49, C:A.93, C:A.96, C:A.120, C:F.121, C:F.121, C:F.121, C:F.121, C:P.124, C:F.128, C:Y.148, C:I.150, C:F.241, C:F.241, D:Y.208
BPB.24: 18 residues within 4Å:- Chain C: F.181, M.185, L.189, V.219, V.220
- Chain D: G.62, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, M.275
- Ligands: BCB.22, BCB.23
10 PLIP interactions:6 interactions with chain D, 4 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, C:V.220
- pi-Stacking: D:F.148
- 8 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.12: 5 residues within 4Å:- Chain C: G.84, Q.87, A.88
- Ligands: HTO.13, HTO.14
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:A.78, C:G.84
HTO.13: 4 residues within 4Å:- Chain C: Q.87, V.91, W.142
- Ligands: HTO.12
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:V.91, C:W.142
HTO.14: 5 residues within 4Å:- Chain C: L.44, A.88, V.91, C.92
- Ligands: HTO.12
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:L.44, C:V.91
HTO.15: 4 residues within 4Å:- Chain C: L.119, F.235, L.242
- Ligands: LDA.20
No protein-ligand interaction detected (PLIP)HTO.16: 2 residues within 4Å:- Chain C: L.102, W.115
No protein-ligand interaction detected (PLIP)HTO.18: 9 residues within 4Å:- Chain C: G.114, W.115, H.116, L.119
- Chain D: A.1, D.2, T.5
- Ligands: LDA.20, SO4.37
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:D.2, C:W.115
HTO.26: 7 residues within 4Å:- Chain D: G.141, T.142, H.143, W.146
- Ligands: LDA.7, OLC.32, SO4.35
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:W.146
- Hydrogen bonds: D:T.142, D:T.142, D:T.142
HTO.33: 3 residues within 4Å:- Chain D: F.71, N.72, W.112
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:F.71, D:W.112
- Hydrogen bonds: D:F.71
- 2 x UQ2: UBIQUINONE-2(Non-covalent)
UQ2.17: 14 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
- Ligands: BCB.22
11 PLIP interactions:11 interactions with chain C- Hydrophobic interactions: C:L.189, C:L.189, C:F.216, C:F.216, C:V.220, C:I.224, C:I.224, C:I.229, C:I.229
- Hydrogen bonds: C:I.224, C:G.225
UQ2.34: 8 residues within 4Å:- Chain C: W.263, W.265, W.266
- Chain D: F.85, F.88, F.89
- Ligands: DGA.5, NS5.25
6 PLIP interactions:4 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:F.88, D:F.88, D:F.89, D:F.89, C:W.266
- pi-Stacking: C:W.266
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ9: MENAQUINONE-9(Non-covalent)
MQ9.21: 23 residues within 4Å:- Chain C: Y.29, F.30, G.35, 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: LDA.6, BCB.10, BPB.11
17 PLIP interactions:12 interactions with chain D, 5 interactions with chain C- Hydrophobic interactions: D:A.216, D:A.246, D:W.250, D:W.250, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:F.270, C:Y.29, C:Y.29, C:W.100, C:W.100, C:W.100
- Hydrogen bonds: D:A.258
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
NS5.25: 18 residues within 4Å:- Chain D: I.69, I.104, G.117, L.118, M.120, T.121, V.155, G.159, C.160, V.173, P.174, F.175, G.176, I.177, H.180
- Ligands: DGA.5, BCB.22, UQ2.34
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:I.69, D:I.104, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:I.177
- 2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
OLC.28: 6 residues within 4Å:- Chain D: I.104, P.105, P.106, L.107
- Ligands: LDA.31, SO4.38
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:I.104
OLC.32: 5 residues within 4Å:- Chain D: W.146, A.149, F.153
- Ligands: LDA.7, HTO.26
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:F.153
- 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 2.25 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 5 x SO4: SULFATE ION(Non-functional Binders)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 8 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 2 x UQ2: UBIQUINONE-2(Non-covalent)
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ9: MENAQUINONE-9(Non-covalent)
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- 2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(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.