SMTL ID : 2wjm.1

Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, M.74, 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 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.56, A:Y.56, A:V.59, A:F.70, A:F.70, A:M.74, A:I.77, A:L.96, A:A.107, A:R.108 Hydrogen bonds: A:K.57, 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.282, L.289, R.293, P.301, T.307 Ligands: HEC.1 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.81, A:P.103, A:V.106, A:M.110, A:L.111, A:L.141, A:L.282, A:P.301, A:T.307 Hydrogen bonds: A:Y.102 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEC.3: 24 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, S.237, 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 C: Y.163 Chain D: I.190 Ligands: HEC.4 27 PLIP interactions: 25 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: A:V.201, A:T.229, A:F.230, A:M.233, A:T.242, A:F.253, A:F.253, A:F.253, A:F.253, A:A.267, A:W.268, A:I.271, D:I.190, C:Y.163 Hydrogen bonds: A:V.203, A:V.204, A:E.254 Water bridges: A:Q.206, A:R.264, A:R.272, 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: 23 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.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.125, A:V.130, A:I.236, A:I.266, A:A.267, A:I.271, A:K.314 Hydrogen bonds: A:T.128, A:Q.263 Water bridges: A:K.314, A:K.314 Salt bridges: A:K.314, A:K.314 pi-Stacking: A:H.124 Metal complexes: A:H.124, A:H.309

1 x DGA: DIACYL GLYCEROL(Covalent)

DGA.5: 10 residues within 4Å: Chain A: C.1 Chain C: P.172, M.175, S.176, S.179, W.263, W.266 Ligands: MPG.10, BCB.12, NS5.16 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:M.175, C:W.266

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.6: 33 residues within 4Å: Chain C: F.98, F.122, P.125, I.126, M.128, F.129, L.132, V.158, N.159, F.161, G.162, Y.163, W.168, H.169, G.173, H.174, S.177, V.178, L.181, F.182, I.241, F.242, G.245, G.248, T.249 Chain D: L.185, Y.196, Y.209 Ligands: BCB.7, BPB.8, BCB.12, BCB.13, MQ7.15 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:F.98, C:F.122, C:P.125, C:V.158, C:F.161, C:Y.163, C:W.168, C:W.168, C:V.178, C:L.181, C:F.182, C:I.241, C:F.242, C:F.242, C:F.242 Hydrogen bonds: C:S.177, C:T.249 pi-Stacking: C:W.168 Metal complexes: C:H.174 BCB.7: 21 residues within 4Å: Chain C: V.47, I.50, F.129, F.147, I.151, L.152, H.154, L.155, V.158 Chain D: Y.196, G.202, I.205, G.206, Y.209, G.210, L.213, F.271 Ligands: BCB.6, BPB.8, BCB.13, MQ7.15 15 PLIP interactions: 6 interactions with chain D, 9 interactions with chain C, Hydrophobic interactions: D:Y.196, D:I.205, D:I.205, D:L.213, D:F.271, C:V.47, C:I.50, C:F.129, C:F.147, C:F.147, C:I.151, C:L.155, C:V.158 pi-Stacking: D:Y.209 Metal complexes: C:H.154 BCB.12: 23 residues within 4Å: Chain C: H.169, M.175, V.178, S.179, F.182, V.183, M.186 Chain D: M.121, F.155, V.156, I.159, V.174, I.178, W.179, H.181, I.182, W.184, L.185 Ligands: DGA.5, BCB.6, BCB.13, BPB.14, NS5.16 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:V.178, C:F.182, C:V.183, C:V.183, D:F.155, D:V.156, D:I.159, D:V.174, D:I.178, D:I.182, D:W.184, D:L.185 pi-Stacking: C:F.182 Metal complexes: D:H.181 BCB.13: 34 residues within 4Å: Chain C: V.158, Y.163, F.182 Chain D: G.63, I.67, I.70, M.121, L.125, F.149, A.152, F.155, V.156, I.159, W.184, L.185, T.186, F.188, S.189, F.195, Y.196, H.201, S.204, I.205, A.208, Y.209, V.275, M.276, A.279, G.282, I.283 Ligands: BCB.6, BCB.7, BCB.12, BPB.14 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:I.67, D:I.70, D:L.125, D:F.149, D:A.152, D:F.155, D:V.156, D:W.184, D:L.185, D:F.188, D:F.195, D:Y.196, D:Y.196, D:I.205, D:A.208, D:Y.209, D:A.279 Hydrogen bonds: D:Y.196, D:S.204 Metal complexes: D:H.201

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.8: 28 residues within 4Å: Chain C: F.42, I.43, G.46, I.50, A.94, A.97, F.98, W.101, E.105, V.118, A.121, F.122, P.125, F.129, Y.149, G.150, I.151, H.154, A.238, F.242 Chain D: Y.209, G.212, L.213, W.251, I.255 Ligands: BCB.6, BCB.7, MQ7.15 18 PLIP interactions: 2 interactions with chain D, 16 interactions with chain C Hydrophobic interactions: D:Y.209, D:L.213, C:I.43, C:I.43, C:I.50, C:A.94, C:A.121, C:F.122, C:F.122, C:F.122, C:P.125, C:F.129, C:Y.149, C:Y.149, C:F.242, C:F.242, C:F.242 Hydrogen bonds: C:E.105 BPB.14: 23 residues within 4Å: Chain C: F.182, A.185, M.186, L.190, V.220, V.221 Chain D: A.59, F.60, G.63, S.64, I.67, S.124, L.125, W.128, V.132, I.145, N.148, F.149, S.272, M.276 Ligands: BCB.12, BCB.13, NS5.16 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.59, D:F.60, D:I.67, D:W.128, D:W.128, D:N.148, D:F.149, D:F.149, C:F.182, C:A.185, C:M.186, C:L.190 pi-Stacking: D:F.149

3 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.9: 8 residues within 4Å: Chain C: W.116, H.117, L.120, R.232, F.236, S.239 Chain D: A.2, T.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.120, C:R.232, C:F.236 Hydrogen bonds: D:A.2 MPG.10: 15 residues within 4Å: Chain C: F.180, V.183, A.187, L.190, H.191, L.194, F.217, S.224, I.225, G.226, I.230, F.236, L.237 Ligands: DGA.5, MPG.17 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.180, C:V.183, C:A.187, C:L.190, C:F.236, C:L.237 Hydrogen bonds: C:I.225, C:G.226, C:G.226 Water bridges: C:H.191, C:E.213, C:S.224 MPG.17: 7 residues within 4Å: Chain C: V.221, G.222 Chain D: G.31, K.32, I.47, G.48 Ligands: MPG.10 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.47

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

FE2.11: 5 residues within 4Å: Chain C: H.191, H.231 Chain D: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.191, C:H.231, D:H.218, D:E.233, D:H.265

1 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.15: 28 residues within 4Å: Chain C: V.27, Y.30, V.32, G.36, I.40, I.43, W.101, R.104 Chain D: L.213, L.214, H.218, T.221, V.244, A.247, A.248, W.251, I.255, F.257, N.258, A.259, T.260, I.261, V.264, W.267, F.271 Ligands: BCB.6, BCB.7, BPB.8 26 PLIP interactions: 16 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:L.213, D:L.214, D:A.247, D:A.248, D:W.251, D:I.255, D:I.255, D:F.257, D:F.257, D:I.261, D:V.264, D:W.267, D:W.267, D:F.271, C:V.27, C:Y.30, C:Y.30, C:Y.30, C:Y.30, C:V.32, C:I.40, C:I.43, C:W.101, C:W.101 Hydrogen bonds: D:T.221, D:A.259

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

NS5.16: 22 residues within 4Å: Chain D: I.67, I.70, L.71, M.74, F.89, L.115, G.118, L.119, T.122, V.156, G.160, C.161, W.170, V.174, P.175, F.176, G.177, I.178, H.181 Ligands: DGA.5, BCB.12, BPB.14 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.67, D:I.70, D:L.115, D:W.170, D:V.174, D:F.176, D:F.176, D:F.176, D:I.178, D:H.181

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 6 residues within 4Å: Chain D: W.24, Y.51, G.53, A.54, S.55, S.134 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.54, D:S.55, D:S.55, D:S.134, D:S.134 Water bridges: D:G.56, D:R.135 PO4.19: 4 residues within 4Å: Chain B: Y.31 Chain C: N.200 Chain D: H.144, R.266 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:H.144, D:R.266 Hydrogen bonds: B:Y.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wohri, A.B. et al., Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface. Biochemistry (2009)

Release Date

2009-09-22

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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