SMTL ID : 4rcr.1

STRUCTURE OF THE REACTION CENTER FROM RHODOBACTER SPHAEROIDES R-26 AND 2.4.1: PROTEIN-COFACTOR (BACTERIOCHLOROPHYLL, BACTERIOPHEOPHYTIN, AND CAROTENOID) INTERACTIONS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 18 residues within 4Å: Chain A: H.168, H.173, M.174, I.177, S.178, F.181, T.182 Chain B: F.90, L.160, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.2, BOG.5, BCL.7, BPH.9 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.160, B:W.185, A:I.177 Metal complexes: B:H.182 Hydrogen bonds: A:H.173, A:T.182 BCL.2: 25 residues within 4Å: Chain A: F.97, A.124, A.127, Y.128, L.131, W.156, V.157, S.158, G.161, Y.162, F.167, H.168, H.173, I.177, F.180, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.1, BPH.3, BCL.7, BCL.8, U10.10 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.97, A:F.97, A:A.127, A:Y.128, A:W.156, A:Y.162, A:F.167, A:F.167, A:F.167, A:I.177, A:F.180, A:F.180 Metal complexes: A:H.173 BCL.7: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: W.66, M.122, V.126, A.153, I.154, L.156, W.157, L.160, T.186, N.187, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, G.283, I.284 Ligands: BCL.1, BCL.2, BCL.8, BPH.9 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:W.66, B:W.66, B:V.126, B:I.154, B:L.156, B:W.157, B:T.186, B:N.187, B:F.197, B:I.206, B:L.209, B:Y.210, B:I.284, A:V.157, A:F.181 Hydrogen bonds: B:S.205 Metal complexes: B:H.202 BCL.8: 15 residues within 4Å: Chain A: Y.128, L.131, F.146, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210 Ligands: BCL.2, BPH.3, BCL.7, U10.10 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:I.206, A:F.146, A:V.157 Salt bridges: A:H.153

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 25 residues within 4Å: Chain A: F.41, A.42, I.89, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.2, BCL.8, U10.10 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:Y.210, B:A.213, B:L.214, A:A.42, A:A.96, A:F.97, A:W.100, A:A.120, A:F.121, A:F.121, A:F.121, A:A.124, A:Y.148, A:V.241, A:V.241 BPH.9: 21 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, L.219 Chain B: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153 Ligands: BCL.1, BCL.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:L.64, B:F.67, B:A.125, B:F.150, B:F.150, B:F.150, B:A.153, A:A.184, A:L.189 Hydrogen bonds: B:W.129 pi-Stacking: B:F.150

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

U10.4: 15 residues within 4Å: Chain A: L.189, H.190, L.193, E.212, D.213, F.216, V.220, S.223, I.224, G.225, T.226, I.229, L.232 Chain B: L.60, W.129 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.189, A:L.189, A:L.193, A:F.216, A:F.216, A:V.220, A:I.229, A:L.232, B:L.60, B:L.60, B:W.129 Hydrogen bonds: A:I.224 U10.10: 22 residues within 4Å: Chain A: F.29, V.31, G.35, V.36, T.38, 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, I.265, W.268 Ligands: BCL.2, BPH.3, BCL.8 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.29, A:F.29, A:V.31, A:V.36, A:T.38, A:W.100, B:W.252, B:W.252, B:F.258, B:F.258, B:W.268, B:W.268 Hydrogen bonds: B:A.260

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.5: 11 residues within 4Å: Chain B: W.66, F.67, I.70, F.74, G.161, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.1 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.66, B:Y.177, B:Y.177 Hydrogen bonds: B:F.67, B:G.71

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

FE.6: 6 residues within 4Å: Chain A: H.190, V.194, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeates, T.O. et al., Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions. Proc.Natl.Acad.Sci.USA (1988)

Release Date

1993-10-31

Peptides

PHOTOSYNTHETIC REACTION CENTER: A
PHOTOSYNTHETIC REACTION CENTER: B
PHOTOSYNTHETIC REACTION CENTER: 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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PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

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