SMTL ID : 1z9j.1

Photosynthetic Reaction Center from Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 16 residues within 4Å: Chain A: M.174, I.177, S.178, F.181, T.182, L.185 Chain B: F.67, I.70, M.122, H.160, H.182, T.186 Ligands: BCL.2, U10.4, BCL.7, BPH.9 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:F.67, B:I.70, A:I.177, A:I.177, A:L.185 pi-Stacking: B:H.182, B:H.182, A:F.181 pi-Cation interactions: B:H.182 BCL.2: 23 residues within 4Å: Chain A: F.97, A.124, A.127, Y.128, H.131, V.157, Y.162, F.167, H.168, H.173, I.177, F.180, V.241, S.244, A.245, C.247, M.248 Chain B: L.209, Y.210 Ligands: BCL.1, BPH.3, BCL.7, BCL.8 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.97, A:A.124, A:A.127, A:Y.128, A:V.157, A:Y.162, A:F.167, A:F.167, A:I.177, A:F.180, A:F.180, B:L.209, B:Y.210 Hydrogen bonds: A:S.244 Salt bridges: A:H.131 pi-Stacking: A:H.173 Metal complexes: A:H.173 BCL.7: 25 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: M.122, A.153, L.156, W.157, H.160, T.186, N.187, S.190, L.196, H.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.8, BPH.9 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:A.153, B:W.157, B:T.186, B:L.196, B:I.206, B:I.206, B:L.209, B:Y.210, B:V.276 pi-Stacking: B:H.202, B:H.202 pi-Cation interactions: B:H.202 Metal complexes: B:H.202 BCL.8: 15 residues within 4Å: Chain A: I.46, F.97, Y.128, H.131, F.146, H.153, L.154 Chain B: H.197, G.203, I.206, A.207, Y.210 Ligands: BCL.2, BPH.3, BCL.7 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.46, A:F.97, A:F.146, A:L.154 pi-Stacking: A:H.153, A:H.153, B:Y.210, B:Y.210 pi-Cation interactions: A:H.153 Metal complexes: A:H.153

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 27 residues within 4Å: Chain A: F.41, A.42, G.45, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, G.149, I.150, H.153, S.237, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252 Ligands: BCL.2, BCL.8, U10.10 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.42, A:A.93, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.121, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213 BPH.9: 17 residues within 4Å: Chain A: F.181, A.184, L.185 Chain B: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, A.149, F.150, A.273, T.277 Ligands: BCL.1, BCL.7 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:F.67, B:A.125, B:A.149, B:F.150, B:F.150, B:T.277, A:F.181, A:A.184, A:L.185 pi-Stacking: B:F.150

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

U10.4: 12 residues within 4Å: Chain A: T.182, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, I.229, L.232 Ligands: BCL.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.216, A:F.216, A:Y.222, A:L.232 Hydrogen bonds: A:I.224, A:G.225 pi-Stacking: A:F.216 U10.10: 21 residues within 4Å: Chain A: G.35, T.38, F.39, W.100, R.103 Chain B: L.215, M.218, H.219, T.222, A.248, A.249, W.252, M.256, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Ligands: BPH.3 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.39, A:W.100, A:W.100, A:W.100, B:L.215, B:M.218, B:W.252, B:A.260, B:I.265, B:I.265, B:I.265, B:W.268 Hydrogen bonds: B:A.260 pi-Stacking: B:W.252

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

FE.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 MN: MANGANESE (II) ION(Non-covalent)

MN.6: 5 residues within 4Å: Chain B: E.168, E.173, V.192, H.193, D.288 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.193, B:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thielges, M. et al., Design of a Redox-Linked Active Metal Site: Manganese Bound to Bacterial Reaction Centers at a Site Resembling That of Photosystem II. Biochemistry (2005)

Release Date

2005-06-07

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
A

B
B

C
C

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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