SMTL ID : 3d38.1

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: A.319, S.320, R.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.320 Salt bridges: A:R.321 SO4.2: 3 residues within 4Å: Chain A: V.61, E.112, R.115 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.115 SO4.3: 3 residues within 4Å: Chain A: N.196, K.198, R.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.196 Salt bridges: A:K.198, A:R.199 SO4.4: 3 residues within 4Å: Chain A: H.162, R.165 Ligands: SO4.5 No protein-ligand interaction detected (PLIP) SO4.5: 3 residues within 4Å: Chain A: T.161, H.162 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.162 Water bridges: A:V.163 SO4.6: 1 residues within 4Å: Chain A: K.258 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.258 SO4.7: 2 residues within 4Å: Chain A: P.160, R.165 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.165 SO4.14: 2 residues within 4Å: Chain B: T.250, R.253 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.253 SO4.15: 5 residues within 4Å: Chain B: R.37, Y.41, L.43, E.61 Chain D: R.251 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.33, B:Y.41, B:Y.41 Salt bridges: B:R.37, D:R.251 SO4.16: 5 residues within 4Å: Chain B: Y.117, E.119, E.122, R.233, K.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.117 Salt bridges: B:R.233, B:K.237 SO4.17: 2 residues within 4Å: Chain B: H.72, D.129 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.72 SO4.28: 4 residues within 4Å: Chain B: Y.31 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: 8 residues within 4Å: Chain D: W.23, Y.50, G.52, A.53, S.54, I.129, S.133 Ligands: LDA.37 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.50, D:Y.50, D:A.53, D:S.54, D:S.133 Water bridges: D:R.134, D:R.134 SO4.30: 3 residues within 4Å: Chain B: L.246 Chain D: A.1, R.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.1 Water bridges: D:R.226 Salt bridges: D:R.226 SO4.31: 3 residues within 4Å: Chain D: S.35, Y.36, W.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.36, D:W.37

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.8: 23 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, L.71, M.74, T.75, I.77, T.78, S.82, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108 Ligands: HEC.9 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.56, A:V.59, A:L.71, A:M.74, A:L.96, A:A.97, A:A.107 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.9: 24 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.282, L.289, R.293, P.301 Ligands: HEC.8, HEC.11 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.81, A:V.106, A:M.110, A:L.111, A:P.142, A:L.277, A:L.282, A:P.301 Hydrogen bonds: A:Y.89, A:Y.102 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEC.10: 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, W.256, R.264, A.267, W.268, R.272 Chain C: Y.162 Chain D: I.189 30 PLIP interactions: 28 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: A:V.201, A:V.204, 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:F.253, A:W.256, A:R.264, A:A.267, A:W.268, C:Y.162, D:I.189 Hydrogen bonds: A:V.203, A:V.204, A:E.254 Water bridges: A:R.202, A:R.272, A:R.272, A:R.272 Salt bridges: A:R.202, A:R.202, A:R.272 pi-Cation interactions: A:R.264 Metal complexes: A:H.248 HEC.11: 24 residues within 4Å: Chain A: I.117, 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.9 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.117, A:V.125, A:V.130, A:I.236, A:F.246, A:Q.263, A:I.266, A:A.267, A:I.271, A:V.274 Hydrogen bonds: A:T.128 Salt bridges: A:K.314, A:K.314 Metal complexes: A:H.124, A:H.309

3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.12: 6 residues within 4Å: Chain A: R.202, V.203, V.204, P.205, Q.206, R.221 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:R.190 Hydrophobic interactions: A:Q.206 Hydrogen bonds: A:V.203 HTO.13: 7 residues within 4Å: Chain A: E.21, L.240, G.241, G.311, V.312, T.313, F.317 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.317 Hydrogen bonds: A:E.21, A:G.311, A:T.313 HTO.20: 6 residues within 4Å: Chain B: P.71, H.72, V.123, V.124, D.125, A.126 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.72, B:V.123 Hydrogen bonds: B:H.72, B:D.125, B:D.125, B:A.126

4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.18: 4 residues within 4Å: Chain B: V.28, R.33 Chain D: F.256, W.266 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.256, D:W.266, B:V.28 pi-Cation interactions: D:F.256 Hydrogen bonds: B:R.33 LDA.19: 7 residues within 4Å: Chain B: R.34, P.42, V.59, Y.60, L.62, P.63, Y.64 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.42, B:V.59, B:L.62, B:Y.64, B:Y.64 Water bridges: B:R.34 LDA.26: 11 residues within 4Å: Chain B: W.17 Chain C: D.60, F.62 Chain D: Y.195, Y.196, C.197, P.198, W.295, C.296, H.299, A.301 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: C:F.62, D:W.295, D:H.299, D:A.301, B:W.17, B:W.17 Salt bridges: C:D.60 LDA.37: 5 residues within 4Å: Chain D: A.53, S.54, L.122, I.129 Ligands: SO4.29 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.53, D:L.122

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.21: 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.22, BPB.23, MQ9.32, BCB.33, BCB.34 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:F.97, C:F.97, C:F.97, C:P.124, C:I.125, C:F.128, C:V.157, C:F.160, C:Y.162, C:W.167, C:W.167, C:L.180, C:F.181, C:I.240, C:F.241, C:F.241, C:F.241 pi-Stacking: C:W.167 Metal complexes: C:H.173 BCB.22: 19 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, G.201, I.204, G.205, Y.208, G.209, L.212 Ligands: BCB.21, BPB.23, MQ9.32, BCB.34 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, D:L.212, C:F.146, C:I.150, C:L.154, C:V.157 pi-Stacking: D:Y.208 Metal complexes: C:H.153 BCB.33: 21 residues within 4Å: Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, Y.222 Chain D: F.154, V.155, I.158, I.177, W.178, H.180, I.181, W.183, L.184 Ligands: BCB.21, BCB.34, BPB.35, NS5.36 14 PLIP interactions: 8 interactions with chain D, 6 interactions with chain C, Hydrophobic interactions: D:F.154, D:V.155, D:I.158, D:I.177, D:I.181, D:W.183, D:L.184, C:V.177, C:F.181, C:V.182, C:Y.222 Metal complexes: D:H.180 Water bridges: C:H.168 pi-Stacking: C:F.181 BCB.34: 32 residues within 4Å: Chain C: V.157, Y.162, F.181 Chain D: G.62, A.65, I.69, M.120, L.124, A.151, I.152, 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.21, BCB.22, BCB.33, BPB.35 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:A.65, D:I.69, D:L.124, D:A.151, D:F.154, D:V.155, D:V.155, D:W.183, 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.23: 31 residues within 4Å: Chain C: F.41, I.42, G.45, I.49, I.89, C.92, A.93, A.96, F.97, W.100, E.104, V.117, F.121, V.123, P.124, 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, MQ9.32 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:Y.208, D:A.215, C:I.42, C:I.49, C:I.89, C:A.96, C:F.121, C:F.121, C:F.121, C:F.121, C:V.123, C:Y.148, C:F.241, C:F.241 BPB.35: 20 residues within 4Å: Chain C: F.181, A.184, M.185, L.189, V.220 Chain D: A.58, F.59, S.63, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, A.151, S.271 Ligands: BCB.33, BCB.34 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.181, C:A.184, C:L.189, D:F.59, D:F.59, D:W.127, D:F.148 pi-Stacking: D:F.148

2 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.24: 11 residues within 4Å: Chain C: L.189, H.190, L.193, E.212, N.213, F.216, S.223, I.224, G.225, A.226, I.229 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.189, C:F.216, C:F.216, C:I.229 Hydrogen bonds: C:I.224, C:G.225 UQ1.25: 4 residues within 4Å: Chain C: W.266 Chain D: F.85, F.88, F.89 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.89, C:W.266, C:W.266 pi-Stacking: C:W.266

1 x FE2: FE (II) ION(Non-covalent)

FE2.27: 5 residues within 4Å: Chain C: H.190, H.230 Chain D: H.217, E.232, H.264 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.217, D:E.232, D:H.264, C:H.190, C:H.230

1 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.32: 21 residues within 4Å: Chain C: Y.29, 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, N.257, A.258, I.260, V.263, W.266 Ligands: BCB.21, BCB.22, BPB.23 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:Y.29, C:Y.29, C:I.42, C:W.100, C:W.100, C:W.100, D:A.246, D:W.250, D:I.254, D:I.260, D:V.263, D:W.266, D:W.266 Hydrogen bonds: D:T.220, D:A.258

1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)

NS5.36: 17 residues within 4Å: Chain D: I.66, L.70, F.88, L.114, G.117, L.118, M.120, T.121, V.155, G.159, C.160, V.173, F.175, G.176, I.177, H.180 Ligands: BCB.33 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.66, D:L.70, D:F.88, D:L.114, D:L.118, D:V.173, D:V.173, D:I.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device. J.Am.Chem.Soc. (2008)

Release Date

2008-07-08

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
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

Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

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