SMTL ID : 1kby.1

Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 16 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, T.182 Chain B: F.90, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.2, BPH.4, BPH.8, SPO.10 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:F.90, B:L.160, B:L.183, A:I.177, A:I.177, A:T.182 pi-Stacking: B:H.182, B:H.182 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 BCL.2: 26 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, F.181, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.1, BCL.3, BPH.5, BPH.8 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, A:A.127, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, A:F.181, B:Y.210 Hydrogen bonds: A:S.244 pi-Stacking: A:H.173, A:H.173 Metal complexes: A:H.173 BCL.3: 16 residues within 4Å: Chain A: I.49, Y.128, L.131, F.146, I.150, H.153, L.154 Chain B: F.197, G.203, I.206, A.207, Y.210, L.214 Ligands: BCL.2, BPH.5, BPH.8 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.49, A:Y.128, A:L.131, A:F.146, A:L.154, B:F.197, B:I.206, B:A.207, B:L.214 pi-Stacking: A:H.153, B:Y.210 pi-Cation interactions: A:H.153 Metal complexes: A:H.153

3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 21 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, W.129, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.1, BPH.8 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.67, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277, A:F.181, A:A.184, A:L.189 pi-Stacking: B:F.150 BPH.5: 26 residues within 4Å: Chain A: I.46, 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, T.255, M.256 Ligands: BCL.2, BCL.3 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:I.46, A:A.93, A:F.97, 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 BPH.8: 24 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: A.153, L.156, W.157, T.186, N.187, F.189, S.190, L.196, F.197, L.202, S.205, I.206, L.209, Y.210, T.277, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.3, BPH.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.186, B:F.189, B:L.196, B:F.197, B:F.197, B:L.202, B:I.206, B:L.209, B:Y.210, B:T.277

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: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.190, A:H.230, B:E.234, B:E.234, B:H.266

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

U10.9: 20 residues within 4Å: Chain A: G.35, T.38, F.39, W.100 Chain B: L.214, 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 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.214, 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:F.39, A:W.100 Hydrogen bonds: B:T.222, B:A.260

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.10: 21 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, W.75, W.115, S.119, F.120, M.122, F.123, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.1 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.67, B:F.68, B:I.70, B:W.75, B:W.115, B:F.120, B:F.120, B:F.123, B:F.123, B:W.157, B:L.160, B:F.162, B:F.162, B:F.162, B:W.171, B:V.175, B:Y.177, B:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.11: 19 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, S.152, W.155, R.267, I.270, W.271, V.274, L.278, I.282 Chain C: I.22, F.23, G.26, L.27, Y.30 19 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:W.155, B:I.270, B:W.271, B:V.274, B:L.278, B:I.282, C:I.22, C:F.23, C:Y.30 Hydrogen bonds: B:K.144, A:N.199 Water bridges: B:K.144 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Camara-Artigas, A. et al., The structure of the heterodimer reaction center from Rhodobacter sphaeroides at 2.55 a resolution. Photosynth.Res. (2002)

Release Date

2002-11-13

Peptides

PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN: A
PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN: B
PHOTOSYNTHETIC 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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PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN

PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN

PHOTOSYNTHETIC REACTION CENTER PROTEIN H CHAIN

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