- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 19 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 3 residues within 4Å:- Chain A: A.319, S.320, R.321
Ligand excluded by PLIPSO4.6: 3 residues within 4Å:- Chain A: V.61, E.112, R.115
Ligand excluded by PLIPSO4.7: 4 residues within 4Å:- Chain A: T.191, N.196, K.198, R.199
Ligand excluded by PLIPSO4.8: 3 residues within 4Å:- Chain A: H.162, R.165
- Ligands: SO4.9
Ligand excluded by PLIPSO4.9: 4 residues within 4Å:- Chain A: T.161, H.162
- Chain C: S.273
- Ligands: SO4.8
Ligand excluded by PLIPSO4.10: 5 residues within 4Å:- Chain A: E.167, T.168, R.169, S.170
- Chain D: H.78
Ligand excluded by PLIPSO4.11: 3 residues within 4Å:- Chain A: P.4, H.24, A.26
Ligand excluded by PLIPSO4.14: 1 residues within 4Å:- Chain B: R.253
Ligand excluded by PLIPSO4.15: 6 residues within 4Å:- Chain B: R.33, R.37, Y.41, L.43, E.61
- Chain D: R.251
Ligand excluded by PLIPSO4.16: 4 residues within 4Å:- Chain B: Y.117, E.119, R.233, K.237
Ligand excluded by PLIPSO4.17: 3 residues within 4Å:- Chain B: H.72, D.129, G.130
Ligand excluded by PLIPSO4.25: 3 residues within 4Å:- Chain C: D.204, K.205, K.207
Ligand excluded by PLIPSO4.35: 4 residues within 4Å:- Chain C: N.199
- Chain D: H.143, R.265
- Ligands: SO4.40
Ligand excluded by PLIPSO4.36: 7 residues within 4Å:- Chain D: W.23, Y.50, G.52, A.53, S.54, S.133
- Ligands: LDA.43
Ligand excluded by PLIPSO4.37: 4 residues within 4Å:- Chain B: L.246
- Chain D: A.1, R.226
- Ligands: HTO.27
Ligand excluded by PLIPSO4.38: 3 residues within 4Å:- Chain D: S.35, Y.36, W.37
Ligand excluded by PLIPSO4.39: 2 residues within 4Å:- Chain D: P.15, H.16
Ligand excluded by PLIPSO4.40: 5 residues within 4Å:- Chain D: T.142, H.143, W.146, W.268
- Ligands: SO4.35
Ligand excluded by PLIPSO4.41: 3 residues within 4Å:- Chain D: P.106, L.107, H.108
Ligand excluded by PLIP- 5 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.12: 7 residues within 4Å:- Chain A: P.205, Q.206, T.207, L.209, P.210, L.211
- Chain D: D.290
7 PLIP interactions:5 interactions with chain A, 2 interactions with chain D- Hydrophobic interactions: A:L.211
- Hydrogen bonds: A:Q.206, A:T.207, A:T.207, A:L.211, D:D.290, D:D.290
HTO.13: 9 residues within 4Å:- Chain A: E.21, L.23, K.31, L.240, G.241, G.311, V.312, T.313, F.317
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:F.317, A:F.317
- Hydrogen bonds: A:E.21, A:K.31, A:G.311, A:T.313
- Water bridges: A:K.31
HTO.20: 9 residues within 4Å:- Chain B: P.71, A.121, V.123, V.124, D.125, A.126
- Chain D: E.234, T.237, D.238
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain B- Hydrophobic interactions: D:E.234, D:D.238, B:A.121
- Hydrogen bonds: B:D.125, B:A.126
HTO.26: 5 residues within 4Å:- Chain C: Y.29
- Chain D: I.254, F.256
- Ligands: LDA.18, MQ9.29
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.29, C:Y.29
HTO.27: 3 residues within 4Å:- Chain C: G.114, W.115
- Ligands: SO4.37
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:W.115
- Hydrogen bonds: C:W.115, C:W.115
- Water bridges: D:R.226
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.18: 6 residues within 4Å:- Chain B: L.29, R.33
- Chain D: F.206, F.256
- Ligands: HTO.26, MQ9.29
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.206
- pi-Cation interactions: D:F.256
LDA.19: 10 residues within 4Å:- Chain B: R.34, P.42, V.59, Y.60, L.62, P.63, Y.64, P.65, P.79, R.80
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.64, B:P.65
- Hydrogen bonds: B:Y.60
LDA.42: 13 residues within 4Å:- Chain B: W.17
- Chain C: D.60, F.62, L.151, L.154
- Chain D: Y.195, C.197, P.198, G.201, W.295, H.299, A.301
- Ligands: BCB.22
9 PLIP interactions:4 interactions with chain C, 2 interactions with chain B, 3 interactions with chain D- Hydrophobic interactions: C:L.151, C:L.154, B:W.17, B:W.17, D:P.198, D:W.295, D:A.301
- Hydrogen bonds: C:D.60
- Salt bridges: C:D.60
LDA.43: 4 residues within 4Å:- Chain D: W.23, S.126, S.133
- Ligands: SO4.36
No protein-ligand interaction detected (PLIP)- 3 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.21: 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, G.172, H.173, S.176, V.177, L.180, I.240, F.241, G.244, G.247, T.248
- Chain D: Y.195, Y.208
- Ligands: BCB.22, BPB.23, MQ9.29, BPB.32
18 PLIP interactions:18 interactions with chain C,- Hydrophobic interactions: C:F.97, C:F.97, C:P.124, C:M.127, C:F.128, C:F.160, C:Y.162, C:W.167, C:W.167, C:V.177, C:L.180, 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.22: 20 residues within 4Å:- Chain C: F.128, L.131, F.146, I.150, L.151, H.153, L.154, V.157
- Chain D: Y.195, L.200, G.201, I.204, G.205, Y.208, G.209
- Ligands: BCB.21, BPB.23, MQ9.29, BPB.32, LDA.42
12 PLIP interactions:4 interactions with chain D, 8 interactions with chain C,- Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, C:F.128, C:L.131, C:F.146, C:F.146, C:I.150, C:L.154, C:V.157
- pi-Stacking: D:Y.208
- Metal complexes: C:H.153
BCB.31: 20 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, W.183, L.184
- Ligands: BPB.32, BPB.33, NS5.34
14 PLIP interactions:6 interactions with chain C, 8 interactions with chain D,- Hydrophobic interactions: C:V.177, C:F.181, C:V.182, C:V.182, C:V.220, D:F.154, D:V.155, D:I.158, D:I.177, D:I.181, D:W.183, D:L.184
- pi-Stacking: C:F.181
- Metal complexes: D:H.180
- 3 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.23: 28 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, F.128, Y.148, G.149, I.150, H.153, A.237, S.238, F.241
- Chain D: Y.208, G.211, L.212, A.215, W.250, I.254
- Ligands: BCB.21, BCB.22, MQ9.29
16 PLIP interactions:14 interactions with chain C, 2 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:F.128, C:Y.148, C:Y.148, C:F.241, D:Y.208, D:A.215
- Hydrogen bonds: C:E.104
BPB.32: 31 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: G.62, I.69, M.120, L.124, F.148, A.151, F.154, V.155, L.184, T.185, F.187, S.188, F.194, Y.195, W.199, L.200, S.203, I.204, A.207, Y.208, M.275, A.278, G.281, I.282
- Ligands: BCB.21, BCB.22, BCB.31, BPB.33
17 PLIP interactions:17 interactions with chain D- Hydrophobic interactions: D:I.69, D:L.124, D:F.148, D:A.151, D:F.154, D:V.155, D:F.187, D:F.194, D:Y.195, D:Y.195, D:L.200, D:I.204, D:I.204, D:A.207, D:Y.208
- Hydrogen bonds: D:Y.195, D:S.203
BPB.33: 23 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, A.151, S.271, V.274, M.275
- Ligands: BCB.31, BPB.32
14 PLIP interactions:11 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:F.59, D:F.59, D:F.59, D:I.66, D:W.127, D:N.147, D:F.148, D:F.148, D:A.151, D:V.274, C:F.181, C:M.185, C:L.189
- pi-Stacking: D:F.148
- 2 x UQ1: UBIQUINONE-1(Non-covalent)
UQ1.24: 12 residues within 4Å:- Chain C: L.189, H.190, L.193, I.194, E.212, N.213, F.216, Y.222, S.223, I.224, G.225, I.229
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:L.189, C:F.216, C:F.216, C:I.229, C:I.229
- Hydrogen bonds: C:I.224, C:G.225
UQ1.30: 4 residues within 4Å:- Chain C: W.266
- Chain D: F.85, F.88, F.89
6 PLIP interactions:3 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:F.89, D:F.89, C:W.266, C:W.266
- Water bridges: D:F.89
- pi-Stacking: C:W.266
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ9: MENAQUINONE-9(Non-covalent)
MQ9.29: 27 residues within 4Å:- Chain C: Y.29, F.30, G.35, I.39, I.42, F.43, W.100, R.103
- Chain D: 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.18, BCB.21, BCB.22, BPB.23, HTO.26
20 PLIP interactions:8 interactions with chain C, 12 interactions with chain D- Hydrophobic interactions: C:Y.29, C:Y.29, C:Y.29, C:I.39, C:I.42, C:W.100, C:W.100, C:W.100, D:A.246, D:W.250, 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
- Hydrogen bonds: D:A.258
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
NS5.34: 16 residues within 4Å:- Chain D: I.66, F.88, W.113, G.117, L.118, T.121, I.158, G.159, C.160, V.173, P.174, F.175, G.176, I.177, H.180
- Ligands: BCB.31
9 PLIP interactions:9 interactions with chain D- Hydrophobic interactions: D:I.66, D:F.88, D:W.113, D:I.158, D:V.173, D:V.173, D:F.175, D:I.177, D:H.180
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ponomarenko, N.S. et al., Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center. Biochim.Biophys.Acta (2009)
- Release Date
- 2009-09-22
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Photosynthetic reaction center H subunit: B
Photosynthetic reaction center L subunit: C
Photosynthetic reaction center M subunit: 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 2.50 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 5 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 3 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 3 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 2 x UQ1: UBIQUINONE-1(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)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ponomarenko, N.S. et al., Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center. Biochim.Biophys.Acta (2009)
- Release Date
- 2009-09-22
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Photosynthetic reaction center H subunit: B
Photosynthetic reaction center L subunit: C
Photosynthetic reaction center M subunit: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
HC
LD
M - Membrane
-
We predict this structure to be a membrane protein.