SMTL ID : 1ogv.1

Lipidic cubic phase crystal structure of the photosynthetic reaction centre from Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 27 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: BCL.2, BPH.3, BCL.4, BCL.5 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:Y.128, B:V.157, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.2: 21 residues within 4Å: Chain B: I.46, I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.1, BPH.3, BCL.5, U10.7 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:L.214, B:I.46, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154 pi-Stacking: C:Y.210 Metal complexes: B:H.153 BCL.4: 17 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain C: W.157, L.160, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.1, BCL.5, BPH.6 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, Hydrophobic interactions: B:I.177, B:I.177, B:F.181, B:L.185, C:L.160, C:L.183, C:W.185 Metal complexes: C:H.182 BCL.5: 27 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: W.66, A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.4, BPH.6 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:W.66, C:L.156, C:T.186, C:F.189, C:L.196, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276, B:V.157 Hydrogen bonds: C:Y.210 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 32 residues within 4Å: Chain B: T.38, A.42, G.45, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, F.146, Y.148, G.149, I.150, H.153, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.1, BCL.2, U10.7 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.42, B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:F.146, B:Y.148, B:Y.148, B:H.153, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214, C:A.217 Hydrogen bonds: B:E.104 pi-Stacking: B:F.121 BPH.6: 20 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219 Chain C: S.59, G.63, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.4, BCL.5 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.125, C:W.129, C:A.149, C:F.150, C:F.150, C:T.277, B:A.184, B:L.189 pi-Stacking: C:F.150

1 x U10: UBIQUINONE-10(Non-covalent)

U10.7: 21 residues within 4Å: Chain B: F.29, W.100 Chain C: L.214, M.218, H.219, T.222, I.223, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Ligands: BCL.2, BPH.3 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:W.252, C:M.256, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, C:W.268, B:F.29, B:W.100, B:W.100 Hydrogen bonds: C:T.222, C:A.260

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 15 residues within 4Å: Chain A: I.12, F.13, G.16, L.17, Y.20 Chain B: N.199 Chain C: G.143, K.144, H.145, W.148, W.155, R.267, W.271, V.274, L.278 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain C Hydrophobic interactions: A:I.12, A:F.13, A:F.13, A:L.17, A:Y.20, C:W.155, C:W.155, C:W.155, C:W.155, C:W.271, C:V.274, C:L.278 Water bridges: A:Y.20, C:K.144 Hydrogen bonds: C:K.144, C:W.148 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267

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

FE2.9: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.219, C:E.234, C:H.266, B:H.190, B:H.230

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 5 residues within 4Å: Chain C: G.53, L.55, G.56, R.132, R.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katona, G. et al., Lipidic Cubic Phase Crystal Structure of the Photosynthetic Reaction Centre from Rhodobacter Sphaeroides at 2.35 A Resolution. J.Mol.Biol. (2003)

Release Date

2003-08-05

Peptides

Reaction center protein H chain: A
Reaction center protein L chain: B
Reaction center protein M chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

We predict this structure to be a membrane protein.
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Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

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