SMTL ID : 1yst.1

STRUCTURE OF THE PHOTOCHEMICAL REACTION CENTER OF A SPHEROIDENE CONTAINING PURPLE BACTERIUM, RHODOBACTER SPHAEROIDES Y, AT 3 ANGSTROMS RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 22 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, V.157, F.167, H.168, H.173, I.177, F.180, S.244, C.247, M.248 Chain B: F.197, Y.210 Ligands: BCL.2, BPH.3, BCL.6, BCL.7, U10.10 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:A.124, A:A.127, A:Y.128, A:V.157, A:F.167, A:F.167, A:I.177, A:F.180, A:F.180, B:F.197 pi-Stacking: A:H.173, A:H.173 Metal complexes: A:H.173 BCL.2: 16 residues within 4Å: Chain A: P.61, Y.128, L.131, F.146, H.153, L.154, W.156 Chain B: F.197, G.203, I.206, A.207, Y.210, L.214 Ligands: BCL.1, BPH.3, U10.10 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:L.131, A:F.146, A:L.154, A:W.156, B:F.197, B:I.206, B:L.214 pi-Stacking: A:H.153, A:H.153 pi-Cation interactions: A:H.153, A:H.153 Metal complexes: A:H.153 BCL.6: 16 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: L.160, V.175, H.182, L.183, T.186 Ligands: BCL.1, U10.4, BCL.7, BPH.8, SPO.9 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:I.177, A:F.181, B:L.160, B:V.175, B:L.183, B:T.186 pi-Stacking: B:H.182, B:H.182 Metal complexes: B:H.182 BCL.7: 25 residues within 4Å: Chain A: H.168, F.181 Chain B: M.122, V.126, 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, G.280, I.284 Ligands: BCL.1, U10.4, BCL.6, BPH.8 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:L.156, B:F.189, B:F.197, B:F.197, B:I.206, B:L.209, B:Y.210, A:F.181 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 22 residues within 4Å: Chain A: A.42, I.46, I.89, A.93, A.96, W.100, E.104, I.117, A.120, F.121, F.123, A.124, F.146, Y.148, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218 Ligands: BCL.1, BCL.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.42, A:I.46, A:I.89, A:A.93, A:A.96, A:I.117, A:F.121, A:F.121, A:F.123, A:F.146, A:Y.148, A:Y.148, A:L.238, A:V.241, B:Y.210, B:A.213 BPH.8: 22 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, L.219 Chain B: G.63, L.64, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: U10.4, BCL.6, BCL.7, SPO.9 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.64, B:F.67, B:F.67, B:F.150, B:F.150, B:F.150, A:F.181, A:A.184, A:A.188, A:L.189

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

U10.4: 16 residues within 4Å: Chain A: A.186, L.189, H.190, L.193, E.212, D.213, F.216, V.220, S.223, I.224, G.225, I.229, L.232 Ligands: BCL.6, BCL.7, BPH.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.189, A:H.190, A:F.216, A:V.220, A:I.229, A:I.229, A:L.232 Hydrogen bonds: A:E.212, A:I.224, A:G.225 pi-Stacking: A:F.216 U10.10: 16 residues within 4Å: Chain A: F.29 Chain B: L.215, M.218, H.219, T.222, A.248, A.249, W.252, M.256, N.259, A.260, T.261, I.265, W.268 Ligands: BCL.1, BCL.2 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.215, B:M.218, B:I.265, B:W.268, B:W.268, A:F.29 Hydrogen bonds: B:T.222, B:N.259, B:A.260

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 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 SPO: SPHEROIDENE(Non-covalent)

SPO.9: 19 residues within 4Å: Chain B: W.66, F.67, F.68, I.70, F.74, W.75, F.85, W.115, S.119, M.122, F.123, W.157, G.161, F.162, V.175, Y.177, G.178 Ligands: BCL.6, BPH.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.66, B:F.67, B:F.67, B:I.70, B:F.74, B:F.85, B:W.115, B:F.123, B:F.123, B:F.123, B:W.157, B:W.157, B:F.162, B:F.162, B:V.175, B:Y.177, B:Y.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnoux, B. et al., Structure of the photochemical reaction centre of a spheroidene-containing purple-bacterium, Rhodobacter sphaeroides Y, at 3 A resolution. Acta Crystallogr.,Sect.D (1995)

Release Date

1995-02-27

Peptides

PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT): A
PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT): B
PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT): 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 (L SUBUNIT)

PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)

PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)

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