- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.30 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 10 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 4 residues within 4Å:- Chain A: T.168, R.169, S.170
- Chain D: H.78
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:R.169, A:S.170, A:S.170
- Salt bridges: D:H.78
SO4.9: 5 residues within 4Å:- Chain B: R.32, R.36, Y.40, E.60
- Chain D: R.251
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain B- Salt bridges: D:R.251, B:R.36
- Hydrogen bonds: B:R.32
SO4.10: 2 residues within 4Å:- Chain B: R.33
- Ligands: LDA.13
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.33
SO4.11: 4 residues within 4Å:- Chain B: Y.116, E.121, R.232, K.236
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.121
- Salt bridges: B:R.232, B:K.236
SO4.26: 7 residues within 4Å:- Chain D: W.23, Y.50, G.52, A.53, S.54, S.133
- Ligands: LDA.32
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Y.50, D:A.53, D:S.54, D:S.133
SO4.27: 4 residues within 4Å:- Chain B: L.245
- Chain D: A.1, R.226
- Ligands: HTO.19
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:A.1, D:A.1
- Salt bridges: D:R.226
SO4.28: 4 residues within 4Å:- Chain B: Y.30
- Chain C: N.199
- Chain D: H.143, R.265
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:H.143, D:R.265
SO4.29: 4 residues within 4Å:- Chain D: S.35, Y.36, W.37, L.38
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:S.35, D:Y.36, D:W.37, D:L.38
SO4.30: 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
SO4.31: 5 residues within 4Å:- Chain B: D.201, V.202
- Chain D: Y.3, Y.7, Q.9
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.201
- 1 x FME: N-FORMYLMETHIONINE(Covalent)
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.8: 2 residues within 4Å:- Chain B: R.32
- Chain D: F.256
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:R.32
- Water bridges: B:R.36
- Hydrophobic interactions: D:F.256
- pi-Cation interactions: D:F.256
LDA.12: 11 residues within 4Å:- Chain B: Q.13, W.16, Y.17
- Chain C: F.62, L.151
- Chain D: Y.195, C.197, P.198, W.295, H.299, A.301
9 PLIP interactions:5 interactions with chain D, 3 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: D:P.198, D:W.295, D:W.295, D:A.301, C:F.62, C:F.62, C:L.151
- Hydrogen bonds: D:H.299, B:Q.13
LDA.13: 10 residues within 4Å:- Chain B: R.33, V.58, Y.59, L.61, Y.63, P.64, P.78, R.79, R.80
- Ligands: SO4.10
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.63, B:P.64
- pi-Cation interactions: B:Y.63
LDA.32: 3 residues within 4Å:- Chain D: W.23, S.133
- Ligands: SO4.26
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:W.23
- 3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.14: 4 residues within 4Å:- Chain A: R.216
- Chain B: H.2, G.3, A.4
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:H.2, A:R.216
HTO.18: 4 residues within 4Å:- Chain C: L.75, Q.87, V.91, W.142
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Q.87
HTO.19: 6 residues within 4Å:- Chain C: G.114, W.115, H.116
- Chain D: A.1, I.6
- Ligands: SO4.27
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:W.115
- Hydrophobic interactions: D:I.6
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.15: 29 residues within 4Å:- Chain C: F.97, P.124, I.125, M.127, F.128, L.131, V.157, N.158, F.160, 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.16, BPB.17, MQ7.21, BCB.22, BCB.23
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:F.97, C:M.127, 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.16: 17 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: BCB.15, BPB.17, MQ7.21, BCB.23
12 PLIP interactions:5 interactions with chain D, 7 interactions with chain C,- Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, D:L.212, C:F.128, C:F.146, C:I.150, C:L.154, C:V.157
- pi-Stacking: D:Y.208, C:H.153
- Metal complexes: C:H.153
BCB.22: 21 residues within 4Å:- Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, Y.222
- Chain D: M.120, V.155, I.158, V.173, I.177, H.180, I.181, L.184
- Ligands: DGA.5, BCB.15, BCB.23, BPB.24, NS5.25
15 PLIP interactions:7 interactions with chain C, 8 interactions with chain D,- Hydrophobic interactions: C:V.177, C:V.182, C:Y.222, D:V.155, D:I.158, D:V.173, D:I.177, D:I.181, D:L.184, D:L.184
- Hydrogen bonds: C:S.178
- Water bridges: C:H.173
- pi-Stacking: C:F.181, C:F.181
- Metal complexes: D:H.180
BCB.23: 31 residues within 4Å:- Chain C: V.157, Y.162, H.168, F.181
- Chain D: I.69, M.120, L.124, F.148, A.151, 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.15, BCB.16, BCB.22, BPB.24
21 PLIP interactions:21 interactions with chain D,- Hydrophobic interactions: D:I.69, D:L.124, D:F.148, D:A.151, D:F.154, 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, 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.17: 27 residues within 4Å:- Chain C: I.42, I.49, C.92, 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, G.211, L.212, A.215, W.250, I.254
- Ligands: BCB.15, BCB.16, MQ7.21
16 PLIP interactions:13 interactions with chain C, 3 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:F.121, C:P.124, C:Y.148, C:I.150, C:F.241, D:Y.208, D:L.212, D:A.215
BPB.24: 19 residues within 4Å:- Chain C: F.181, M.185, L.189, V.219, V.220
- Chain D: I.46, I.49, F.59, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, M.275
- Ligands: BCB.22, BCB.23
12 PLIP interactions:9 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:I.46, D:I.49, D:F.59, D:F.59, 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
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
MQ7.21: 23 residues within 4Å:- Chain C: Y.29, V.31, G.35, I.39, W.100
- 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.15, BCB.16, BPB.17
23 PLIP interactions:14 interactions with chain D, 9 interactions with chain C- Hydrophobic interactions: D:A.216, D:A.246, D:W.250, D:I.254, D:I.254, 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:Y.29, C:Y.29, C:V.31, C:I.39, 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.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, 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.118, D:V.155, D:W.169, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:H.180
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dods, R. et al., From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Structure (2017)
- Release Date
- 2017-08-16
- 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 3.30 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 10 x SO4: SULFATE ION(Non-functional Binders)
- 1 x FME: N-FORMYLMETHIONINE(Covalent)
- 4 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 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
- Dods, R. et al., From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Structure (2017)
- Release Date
- 2017-08-16
- 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.