SMTL ID : 1rqk.1

Structure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with 3,4-dihydrospheroidene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 26 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, T.160, 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 B: Y.210 Ligands: BCL.2, BPH.3, BCL.8, BCL.9 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:T.160, 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: 20 residues within 4Å: Chain A: I.46, Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.1, BPH.3, BCL.9, U10.11, LDA.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:I.46, A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.8: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, T.182 Chain B: M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, BCL.9, BPH.10, SP2.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.160, B:V.175, B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.9: 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.8, BPH.10, LDA.17 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:F.197, B:I.206, B:Y.210, B:V.276, A:V.157 Hydrogen bonds: B:S.205, B:Y.210 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 27 residues within 4Å: Chain A: I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.1, BCL.2, LDA.5, U10.11 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.210, B:A.213, B:L.214, A:I.49, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:Y.148, A:I.150, A:L.238, A:V.241 BPH.10: 24 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 Chain B: S.59, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.8, BCL.9, LDA.17 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.64, B:F.67, B:W.129, B:W.129, B:A.149, B:F.150, B:F.150, B:T.277, A:F.181, A:A.184 pi-Stacking: B:F.150

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

U10.4: 18 residues within 4Å: Chain A: F.123, 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, L.232, L.235, S.239, F.242 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.123, A:L.189, A:L.193, A:F.216, A:F.216, A:I.224, A:I.229, A:I.229, A:L.232, A:L.235, A:F.242 Hydrogen bonds: A:I.224, A:G.225 U10.11: 24 residues within 4Å: Chain A: Y.30, G.35, T.38, F.39, W.100, R.103 Chain B: M.218, H.219, T.222, 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, LDA.18 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.218, B:W.252, B:M.256, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268, A:W.100 Hydrogen bonds: B:A.260

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

LDA.5: 6 residues within 4Å: Chain A: I.49, P.61, I.64, Y.148, G.149 Ligands: BPH.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.61 Hydrogen bonds: A:Y.148 Water bridges: A:I.150 LDA.6: 2 residues within 4Å: Chain A: A.101, Y.115 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.101 LDA.14: 7 residues within 4Å: Chain B: P.200, L.204, F.208, W.268, M.272 Chain C: I.28 Ligands: BCL.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.28, B:F.208, B:W.268 LDA.15: 4 residues within 4Å: Chain A: P.28 Chain B: M.256, G.257 Ligands: LDA.18 No protein-ligand interaction detected (PLIP) LDA.16: 4 residues within 4Å: Chain A: V.220 Chain B: S.30, G.31 Ligands: LDA.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.31 LDA.17: 4 residues within 4Å: Chain B: S.30 Ligands: BCL.9, BPH.10, LDA.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.31 LDA.18: 7 residues within 4Å: Chain C: I.28, Q.32, Y.40, Q.53, F.56 Ligands: U10.11, LDA.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.28, C:I.28, C:Q.32, C:F.56

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

FE.7: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.190, A:H.230, B:H.219, B:E.234, B:H.266

1 x SP2: 3,4-DIHYDROSPHEROIDENE(Non-covalent)

SP2.12: 21 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, W.75, F.105, W.115, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.67, B:I.70, B:F.74, B:F.105, B:W.115, B:W.157, B:L.160, B:F.162, B:F.162, B:F.162, B:W.171, B:V.175, B:V.175, B:Y.177, B:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 16 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, W.271, L.278 Chain C: A.16, I.22, F.23, G.26, L.27, Y.30 16 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.155, B:W.271, B:W.271, B:L.278, C:I.22, C:F.23 Hydrogen bonds: B:K.144, A:P.200 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267 Water bridges: C:Y.30

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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