SMTL ID : 3g7f.1

Crystal structure of Blastochloris viridis heterodimer mutant reaction center

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)

HEC.1: 23 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, M.74, T.75, I.77, T.78, S.82, G.86, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108 Ligands: HEC.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.56, A:V.59, A:F.70, A:F.70, A:M.74, A:I.77, A:L.96, A:L.96, A:A.107, A:R.108 Hydrogen bonds: A:K.57, A:N.58, A:N.58, A:K.60, A:V.61, A:L.62 Salt bridges: A:R.108 pi-Stacking: A:F.70, A:Y.104 Metal complexes: A:H.91 HEC.2: 23 residues within 4Å: Chain A: I.77, V.81, Y.89, Y.102, P.103, V.106, M.110, L.111, M.113, T.114, T.131, C.132, C.135, H.136, P.140, L.141, P.142, L.277, L.289, R.293, P.301 Ligands: HEC.1, HEC.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.81, A:V.81, A:P.103, A:V.106, A:M.110, A:L.111, A:L.141, A:L.277, A:P.301 Hydrogen bonds: A:P.140 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEC.3: 25 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, I.236, S.237, L.240, T.242, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, I.271, R.272 Chain D: I.189 Ligands: HEC.4 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:V.201, A:T.229, A:F.230, A:M.233, A:I.236, A:L.240, A:T.242, A:F.253, A:F.253, A:F.253, A:R.264, A:A.267, A:W.268, A:I.271, D:I.189 Hydrogen bonds: A:V.203, A:V.204 Water bridges: A:R.202, A:R.202, A:R.264, A:R.272, A:R.272, A:R.272 Salt bridges: A:R.202, A:R.272 pi-Cation interactions: A:R.264 Metal complexes: A:H.248 HEC.4: 24 residues within 4Å: Chain A: H.124, V.125, T.128, G.129, V.130, I.236, L.240, F.246, Q.263, I.266, A.267, G.270, I.271, M.273, V.274, D.304, C.305, C.308, H.309, T.313, K.314, P.315 Ligands: HEC.2, HEC.3 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.125, A:V.125, A:V.130, A:I.236, A:L.240, A:I.266, A:A.267, A:I.271, A:V.274 Hydrogen bonds: A:T.128, A:Q.263 Water bridges: A:K.314, A:K.314, A:K.314 Salt bridges: A:K.314, A:K.314 Metal complexes: A:H.124, A:H.309

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 PLIP SO4.6: 3 residues within 4Å: Chain A: V.61, E.112, R.115 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.191, N.196, K.198, R.199 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: H.162, R.165 Ligands: SO4.9 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: T.161, H.162 Chain C: S.273 Ligands: SO4.8 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: E.167, T.168, R.169, S.170 Chain D: H.78 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: P.4, H.24, A.26 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain B: R.253 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain B: R.33, R.37, Y.41, L.43, E.61 Chain D: R.251 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: Y.117, E.119, R.233, K.237 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: H.72, D.129, G.130 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: D.204, K.205, K.207 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain C: N.199 Chain D: H.143, R.265 Ligands: SO4.40 Ligand excluded by PLIP SO4.36: 7 residues within 4Å: Chain D: W.23, Y.50, G.52, A.53, S.54, S.133 Ligands: LDA.43 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain B: L.246 Chain D: A.1, R.226 Ligands: HTO.27 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain D: S.35, Y.36, W.37 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain D: P.15, H.16 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain D: T.142, H.143, W.146, W.268 Ligands: SO4.35 Ligand excluded by PLIP SO4.41: 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)

FE2.28: 5 residues within 4Å: Chain C: H.190, H.230 Chain D: H.217, E.232, H.264 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.190, C:H.230, D:H.217, D:E.232, D:H.264

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
C

B
H

C
L

D
M

Membrane

We predict this structure to be a membrane protein.
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Photosynthetic reaction center cytochrome c subunit

Photosynthetic reaction center H subunit

Photosynthetic reaction center L subunit

Photosynthetic reaction center M subunit

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