SMTL ID : 2uwt.1

X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 6.5 in the charge-separated state 2nd dataset

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: E.34, R.37, K.62 Chain B: N.199 Chain C: R.267 Ligands: GOL.10 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.34, A:R.37, B:N.199 Water bridges: A:Y.30, A:E.34 GOL.2: 3 residues within 4Å: Chain A: A.25, Y.29, F.56 No protein-ligand interaction detected (PLIP) GOL.3: 2 residues within 4Å: Chain A: W.21 Ligands: GOL.23 No protein-ligand interaction detected (PLIP) GOL.10: 7 residues within 4Å: Chain A: K.62, T.63, F.64 Chain B: A.198, N.199, P.200 Ligands: GOL.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.63, B:P.200 Water bridges: A:T.63, A:T.63, B:G.203 GOL.23: 3 residues within 4Å: Chain B: I.150 Ligands: GOL.3, LDA.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.62

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.4: 28 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, 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 C: Y.210 Ligands: BCL.5, BPH.6, BCL.11, BCL.12, U10.21 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:F.97, B:A.127, B:V.157, B:Y.162, B:F.167, B:A.176, B:I.177, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.5: 18 residues within 4Å: Chain B: I.49, Y.128, L.131, F.146, I.150, H.153, L.154 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.4, BPH.6, BCL.12, LDA.13 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:I.49, B:Y.128, B:L.131, B:F.146, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.11: 17 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, T.182 Chain C: F.67, M.122, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.4, BCL.12, BPH.20, SPO.22 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:F.67, C:L.160, C:V.175, C:L.183, B:I.177, B:I.177 Metal complexes: C:H.182 Hydrogen bonds: B:T.182 Water bridges: B:S.178 pi-Stacking: B:F.181 BCL.12: 28 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: 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, V.276, G.280, I.284 Ligands: BCL.4, BCL.5, BCL.11, BPH.20 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.126, C:L.156, C:T.186, C:F.189, C:L.196, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276, B:V.157 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.6: 33 residues within 4Å: Chain B: T.38, F.41, A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, Y.148, G.149, I.150, H.153, S.237, L.238, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.4, BCL.5, U10.21 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.42, B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:Y.148, B:Y.148, B:I.150, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214, C:A.217 BPH.20: 26 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, F.216, L.219, V.220 Chain C: 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, A.273, V.274, T.277 Ligands: BCL.11, BCL.12, LDA.18 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.60, C:L.64, C:F.67, C:A.125, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:T.277, B:F.181, B:A.184, B:L.189

1 x UQ2: UBIQUINONE-2(Non-covalent)

UQ2.7: 13 residues within 4Å: Chain B: L.189, H.190, L.193, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 Ligands: LDA.17 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.189, B:L.193, B:F.216, B:Y.222, B:I.224, B:I.224, B:I.229 Hydrogen bonds: B:H.190, B:I.224, B:G.225

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain B: E.72, Y.73, K.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.73, B:Y.73 Salt bridges: B:K.82

1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.9: 6 residues within 4Å: Chain B: Q.87, T.90, I.91, T.94, L.133, W.142 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.91, B:T.94, B:L.133 Hydrogen bonds: B:Q.87

6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.13: 9 residues within 4Å: Chain A: W.21 Chain C: P.200, G.203, L.204, A.207, W.268 Ligands: BCL.5, LDA.15, GOL.23 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.204, C:W.268 Hydrogen bonds: C:P.200 LDA.14: 4 residues within 4Å: Chain C: F.7, L.38, W.41, F.42 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.7, C:F.7, C:L.38, C:W.41, C:F.42 pi-Cation interactions: C:W.41 LDA.15: 9 residues within 4Å: Chain A: Q.32, Y.40, F.56 Chain C: R.253, F.258, W.268 Ligands: LDA.13, LDA.16, U10.21 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.258, C:F.258, C:F.258, C:F.258, C:F.258, C:W.268, A:F.56 Hydrogen bonds: C:R.253, C:R.253, A:Y.40 LDA.16: 6 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: LDA.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.258, C:F.258 LDA.17: 6 residues within 4Å: Chain B: V.220 Chain C: V.32, G.33, L.47 Ligands: UQ2.7, LDA.18 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.47 Water bridges: C:G.31 LDA.18: 4 residues within 4Å: Chain C: L.52, W.129 Ligands: LDA.17, BPH.20 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.129

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

FE.19: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.219, C:E.234, C:H.266

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

U10.21: 23 residues within 4Å: Chain B: F.29, Y.30, G.35, W.100, R.103 Chain C: 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.4, BPH.6, LDA.15 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:F.29, B:W.100, C:M.218, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:I.265, C:W.268, C:W.268 Hydrogen bonds: C:T.222, C:A.260

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.22: 21 residues within 4Å: Chain C: F.67, I.70, G.71, F.74, W.75, F.85, L.89, W.115, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, I.179, H.182 Ligands: BCL.11 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:F.74, C:F.74, C:F.85, C:L.89, C:W.115, C:W.157, C:L.160, C:F.162, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koepke, J. et al., Ph Modulates the Quinone Position in the Photosynthetic Reaction Center from Rhodobacter Sphaeroides in the Neutral and Charge Separated States. J.Mol.Biol. (2007)

Release Date

2007-07-03

Peptides

REACTION CENTER PROTEIN H CHAIN: A
REACTION CENTER PROTEIN L CHAIN: B
REACTION CENTER PROTEIN M CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

We predict this structure to be a membrane protein.
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REACTION CENTER PROTEIN H CHAIN

REACTION CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

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