SMTL ID : 1rg5.1

Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 24 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, C.247, M.248 Chain B: Y.210 Ligands: BCL.2, BPH.3, BCL.7, BCL.8 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:A.124, A:A.127, A:V.157, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.2: 18 residues within 4Å: Chain A: Y.128, L.131, F.146, I.150, H.153, L.154 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.1, BPH.3, BCL.8, U10.10, LDA.13 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:I.206, B:L.214, A:L.131, A:L.154 pi-Stacking: B:Y.210 Metal complexes: A:H.153 BCL.7: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, T.182 Chain B: M.122, W.157, I.179, H.182, L.183, T.186 Ligands: BCL.1, U10.4, BCL.8, BPH.9, LDA.15, LDA.17 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.8: 25 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: 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, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.7, BPH.9, LDA.17 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:I.206, B:Y.210, B:V.276 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 22 residues within 4Å: Chain A: A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.148, G.149, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, W.252, M.256 Ligands: BCL.1, BCL.2 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:A.213, B:L.214, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:Y.148, A:L.238, A:V.241 Hydrogen bonds: A:E.104 BPH.9: 19 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219 Chain B: S.59, G.63, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.7, BCL.8 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.67, B:W.129, B:F.150, B:F.150, B:A.153, B:T.277, A:A.184, A:L.189 pi-Stacking: B:F.150

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

U10.4: 17 residues within 4Å: Chain A: S.178, T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 Ligands: BCL.7, LDA.16 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.182, A:L.189, A:L.193, A:F.216, A:F.216, A:F.216, A:F.216, A:I.224, A:I.229 Hydrogen bonds: A:I.224, A:G.225 U10.10: 19 residues within 4Å: Chain A: G.35, T.38, W.100, R.103 Chain B: M.218, H.219, T.222, I.223, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, I.265, W.268 Ligands: BCL.2 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.218, B:W.252, B:M.256, B:F.258, B:I.265, B:W.268, B:W.268, A:W.100 Hydrogen bonds: B:A.260

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

HTO.5: 4 residues within 4Å: Chain A: L.102, P.118, F.119, A.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.118 HTO.11: 1 residues within 4Å: Chain B: T.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.289

1 x FE: FE (III) ION(Non-covalent)

FE.6: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.219, B:E.234, B:H.266, A:H.190, A:H.230

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 14 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, L.278 Chain C: I.22, F.23, G.26, L.27, Y.30 16 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:L.278, C:I.22, C:F.23, C:F.23 Hydrogen bonds: B:K.144, A:N.199 Water bridges: B:K.144, B:R.267, C:Y.30 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

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

LDA.13: 5 residues within 4Å: Chain B: L.204, A.207, M.272 Ligands: BCL.2, LDA.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.207 LDA.14: 3 residues within 4Å: Chain B: M.256, G.257 Ligands: LDA.18 No protein-ligand interaction detected (PLIP) LDA.15: 5 residues within 4Å: Chain A: V.220 Chain B: G.31, V.32, G.33 Ligands: BCL.7 No protein-ligand interaction detected (PLIP) LDA.16: 5 residues within 4Å: Chain B: F.7, L.38, L.39, W.41 Ligands: U10.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.7, B:L.38, B:L.39 pi-Cation interactions: B:W.41, B:W.41 LDA.17: 11 residues within 4Å: Chain B: I.70, W.115, G.161, A.174, V.175, P.176, Y.177, G.178, I.179 Ligands: BCL.7, BCL.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.115, B:A.174, B:V.175, B:V.175, B:Y.177 LDA.18: 10 residues within 4Å: Chain B: R.253, G.257, F.258 Chain C: Q.32, Y.40, L.42, Q.53, F.56 Ligands: LDA.13, LDA.14 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.56, B:F.258 Hydrogen bonds: B:R.253, B:R.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roszak, A.W. et al., Protein Regulation of Carotenoid Binding: Gatekeeper and Locking Amino Acid Residues in Reaction Centers of Rhodobacter sphaeroides. STRUCTURE (2004)

Release Date

2004-04-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
H

Membrane

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

Reaction center protein M chain

Reaction center protein H chain

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