- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 15 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 5 residues within 4Å:- Chain A: E.167, T.168, R.169, S.170
- Chain D: H.78
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:R.169, A:S.170
- Salt bridges: D:H.78
SO4.7: 2 residues within 4Å:- Chain A: H.162, R.165
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:H.162, A:R.165
SO4.8: 2 residues within 4Å:- Chain A: T.161, H.162
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.162
SO4.10: 6 residues within 4Å:- Chain B: R.33, R.37, Y.41, L.43, E.61
- Chain D: R.251
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:Y.41
- Water bridges: B:R.33, B:R.33, B:R.37
- Salt bridges: B:R.33, B:R.37, D:R.251
SO4.11: 4 residues within 4Å:- Chain B: Y.117, E.122, R.233, K.237
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.117, B:E.122
- Salt bridges: B:R.233, B:K.237
SO4.12: 2 residues within 4Å:- Chain B: W.25, T.26
No protein-ligand interaction detected (PLIP)SO4.13: 6 residues within 4Å:- Chain B: D.202, V.203, K.204
- Chain D: Y.3, Y.7, Q.9
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.202
- Salt bridges: B:K.204
SO4.14: 2 residues within 4Å:- Chain B: R.34
- Ligands: LDA.16
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.34
SO4.31: 7 residues within 4Å:- Chain D: W.23, Y.50, G.52, A.53, S.54, S.133
- Ligands: LDA.38
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:Y.50, D:A.53, D:S.54, D:S.133
- Water bridges: D:G.55, D:R.134
SO4.32: 3 residues within 4Å:- Chain B: L.246
- Chain D: A.1, R.226
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:A.1, D:A.1
- Water bridges: D:R.226
- Salt bridges: D:R.226
SO4.33: 4 residues within 4Å:- Chain C: N.199
- Chain D: H.143, R.265
- Ligands: SO4.35
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:H.143, D:R.265
SO4.34: 4 residues within 4Å:- Chain D: Y.34, S.35, Y.36, W.37
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Y.36, D:W.37
SO4.35: 4 residues within 4Å:- Chain D: T.142, H.143, W.146
- Ligands: SO4.33
2 PLIP interactions:2 interactions with chain D- Water bridges: D:T.142
- Salt bridges: D:H.143
SO4.36: 3 residues within 4Å:- Chain D: P.106, L.107, H.108
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:L.107, D:H.108
- Salt bridges: D:H.108
SO4.37: 5 residues within 4Å:- Chain D: G.14, P.15, H.16, P.32, Y.34
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:H.16, D:Y.34
- Salt bridges: D:H.16
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.9: 4 residues within 4Å:- Chain B: L.29, R.33
- Chain D: F.256
- Ligands: LDA.23
1 PLIP interactions:1 interactions with chain D- pi-Cation interactions: D:F.256
LDA.15: 11 residues within 4Å:- Chain B: Q.14, W.17, Y.18
- Chain C: F.62, L.151
- Chain D: Y.195, P.198, C.296, H.299, A.301
- Ligands: BCB.20
5 PLIP interactions:1 interactions with chain B, 2 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: B:W.17, D:A.301, C:F.62, C:L.151
- Hydrogen bonds: D:H.299
LDA.16: 9 residues within 4Å:- Chain B: R.34, P.42, V.59, Y.60, L.62, Y.64, P.65, P.79
- Ligands: SO4.14
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.64, B:P.65
- pi-Cation interactions: B:Y.64
LDA.23: 6 residues within 4Å:- Chain C: Y.29
- Chain D: I.254, F.256
- Ligands: LDA.9, BCB.19, BCB.20
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Y.29
LDA.24: 3 residues within 4Å:- Chain C: F.134, L.137, L.138
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:F.134, C:L.137, C:L.138
LDA.38: 3 residues within 4Å:- Chain D: W.23, S.126
- Ligands: SO4.31
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:W.23
LDA.39: 5 residues within 4Å:- Chain C: R.231
- Chain D: I.6, Y.7, K.40, I.41
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:I.6, D:I.41
- 3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.17: 1 residues within 4Å:- Chain B: V.27
No protein-ligand interaction detected (PLIP)HTO.18: 4 residues within 4Å:- Chain A: R.216
- Chain B: H.3, G.4, A.5
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:H.3, A:R.216
HTO.25: 3 residues within 4Å:- Chain C: L.75, Q.87, W.142
No protein-ligand interaction detected (PLIP)- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.19: 31 residues within 4Å:- Chain C: F.97, P.124, I.125, 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, G.247, T.248
- Chain D: L.184, Y.195, Y.208
- Ligands: BCB.20, BPB.21, BCB.22, LDA.23, BCB.28
19 PLIP interactions:19 interactions with chain C,- Hydrophobic interactions: C:F.97, C:P.124, C:V.157, C:F.160, C:Y.162, C:W.167, C:W.167, C:V.177, C:L.180, C:L.180, C:F.181, C:I.240, C:F.241, 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.20: 19 residues within 4Å:- Chain C: F.128, F.146, I.150, L.151, H.153, L.154, V.157
- Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209
- Ligands: LDA.15, BCB.19, BPB.21, LDA.23, MQ7.27, BCB.28
10 PLIP interactions:6 interactions with chain C, 4 interactions with chain D,- Hydrophobic interactions: C:F.128, C:F.146, C:I.150, 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, Y.222
- Chain D: L.38, F.154, V.155, I.158, I.177, W.178, H.180, I.181, L.184
- Ligands: BCB.19, BCB.28, BPB.29, NS5.30
12 PLIP interactions:8 interactions with chain D, 4 interactions with chain C,- Hydrophobic interactions: D:L.38, D:F.154, D:V.155, D:I.158, D:I.177, D:I.181, D:L.184, C:V.177, C:F.181, C:Y.222
- Metal complexes: D:H.180
- pi-Stacking: C:F.181
BCB.28: 29 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: I.69, M.120, 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.19, BCB.20, BCB.22, BPB.29
22 PLIP interactions:22 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:L.184, D:F.187, D:F.194, D:F.194, D:F.194, D:Y.195, D:Y.195, D:I.204, D:A.207, D:Y.208
- Hydrogen bonds: D:Y.195, D:S.203
- Salt bridges: D:H.200
- Metal complexes: D:H.200
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.21: 24 residues within 4Å:- Chain C: F.41, I.42, I.49, A.96, F.97, W.100, E.104, V.117, A.120, F.121, P.124, Y.148, G.149, I.150, A.237, F.241
- Chain D: Y.208, G.211, L.212, W.250, I.254
- Ligands: BCB.19, BCB.20, MQ7.27
15 PLIP interactions:14 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:I.42, C:I.42, C:I.49, 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, D:Y.208
- Hydrogen bonds: C:E.104
BPB.29: 18 residues within 4Å:- Chain C: F.181, M.185, L.189, V.220
- Chain D: I.49, F.59, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, V.274, M.275
- Ligands: BCB.22, BCB.28
10 PLIP interactions:7 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:I.49, D:F.59, D:N.147, D:F.148, D:F.148, D:V.274, C:F.181, C:M.185, C:L.189
- pi-Stacking: D:F.148
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
MQ7.27: 21 residues within 4Å:- Chain C: Y.29, 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: BCB.20, BPB.21
15 PLIP interactions:5 interactions with chain C, 10 interactions with chain D- Hydrophobic interactions: C:Y.29, C:Y.29, C:Y.29, C:W.100, C:W.100, D:A.216, D:A.246, D:W.250, D:I.254, D:I.254, D:F.256, D:W.266, D:W.266, D:F.270
- Hydrogen bonds: D:A.258
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
NS5.30: 19 residues within 4Å:- Chain D: I.66, I.69, M.73, L.114, G.117, L.118, M.120, T.121, V.155, G.159, C.160, W.169, V.173, P.174, F.175, G.176, I.177, H.180
- Ligands: BCB.22
12 PLIP interactions:12 interactions with chain D- Hydrophobic interactions: D:I.66, D:I.69, D:L.114, D:L.114, D:W.169, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:I.177, D:H.180
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dods, R. et al., Ultrafast structural changes within a photosynthetic reaction centre. Nature (2021)
- Release Date
- 2020-12-09
- 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
CB
HC
LD
M - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 15 x SO4: SULFATE ION(Non-functional Binders)
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 1 x FE: FE (III) 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
- Dods, R. et al., Ultrafast structural changes within a photosynthetic reaction centre. Nature (2021)
- Release Date
- 2020-12-09
- 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
CB
HC
LD
M - Membrane
-
We predict this structure to be a membrane protein.