SMTL ID : 1m3x.1

Photosynthetic Reaction Center From Rhodobacter Sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 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, M.174, I.177, S.178, T.182 Chain B: M.122, W.157, L.160, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.2, PC1.6, BCL.9, BPH.10, SPO.12 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:I.177, B:L.160, B:L.183, B:W.185 Hydrogen bonds: A:T.182 pi-Stacking: B:H.182 pi-Cation interactions: B:H.182 Metal complexes: B:H.182 BCL.2: 29 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, T.160, G.161, 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: T.186, Y.210 Ligands: BCL.1, BCL.3, BPH.4, BCL.9, GGD.14 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, A:A.127, A:T.160, A:Y.162, A:F.167, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 pi-Stacking: A:H.173, A:H.173 Metal complexes: A:H.173 BCL.3: 18 residues within 4Å: Chain A: 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, L.214 Ligands: BCL.2, BPH.4, BCL.9, U10.11, GGD.14 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:L.214, A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157 pi-Stacking: B:Y.210, B:Y.210, A:H.153 pi-Cation interactions: A:H.153 Metal complexes: A:H.153 BCL.9: 26 residues within 4Å: Chain A: V.157, Y.162, 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, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.3, BPH.10 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.126, B:L.156, B:T.186, B:F.189, B:L.196, B:F.197, B:F.197, B:I.206, B:Y.210, B:V.276, B:I.284 pi-Stacking: B:H.202 pi-Cation interactions: B:H.202 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 28 residues within 4Å: Chain A: A.42, I.46, 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, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.2, BCL.3, U10.11 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.210, B:A.213, B:L.214, B:A.217, A:A.42, A:I.46, A:A.120, A:F.121, A:F.121, A:F.121, A:Y.148, A:L.238, A:V.241, A:V.241 BPH.10: 22 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219 Chain B: S.59, G.63, L.64, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.1, PC1.6, BCL.9 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.64, B:F.67, 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)

U10.5: 11 residues within 4Å: Chain A: L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, I.229, L.232 Ligands: PC1.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.222 Hydrogen bonds: A:I.224 Water bridges: A:G.225 U10.11: 23 residues within 4Å: Chain A: 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.3, BPH.4, GGD.14 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.39, A:W.100, B:M.218, B:W.252, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:T.222, B:A.260

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 10 residues within 4Å: Chain A: V.220, Y.222, L.235, L.236 Chain B: F.7, F.42, W.129 Ligands: BCL.1, U10.5, BPH.10 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.7, B:F.42, B:F.42, A:Y.222, A:L.235, A:L.236

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: 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 CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain B: T.21 Ligand excluded by PLIP

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.12: 22 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, W.75, F.85, W.115, L.116, 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.1 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:F.68, B:F.68, B:I.70, B:F.85, B:W.115, B:L.116, B:F.120, 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, V.274, L.278, I.282 Chain C: S.19, I.22, G.26, Y.30 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.155, B:W.271, B:V.274, B:I.282, C:I.22, C:Y.30 Hydrogen bonds: B:K.144 Water bridges: B:K.144 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

1 x GGD: NONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY] -1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER(Non-covalent)

GGD.14: 19 residues within 4Å: Chain A: P.28 Chain B: A.207, F.208, R.253, M.256, G.257, F.258, W.268, L.275 Chain C: W.21, L.24, L.27, I.28, Q.32, Y.40, L.42 Ligands: BCL.2, BCL.3, U10.11 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.40, C:L.42, B:F.258, B:F.258, B:F.258, B:F.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Camara-Artigas, A. et al., Interactions between lipids and bacterial reaction centers determined by protein crystallography. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-08-28

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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