SMTL ID : 2ux3.1

X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 9 in the neutral state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.34, R.37, K.62 Chain B: N.199 Chain C: R.267 Ligands: GOL.12, CDL.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.34, A:R.37 Water bridges: A:E.34 GOL.2: 3 residues within 4Å: Chain A: A.25, I.28, F.56 No protein-ligand interaction detected (PLIP) GOL.3: 2 residues within 4Å: Chain A: W.21, A.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.21 GOL.4: 1 residues within 4Å: Chain A: W.21 No protein-ligand interaction detected (PLIP) GOL.12: 7 residues within 4Å: Chain A: K.62, T.63, F.64 Chain B: A.198, N.199, P.200 Ligands: GOL.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.200, A:T.63 Water bridges: B:G.203 GOL.13: 5 residues within 4Å: Chain B: G.77, A.78, L.80, Q.87 Ligands: HTO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.78, B:A.78

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.5: 18 residues within 4Å: Chain B: I.49, Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BPH.7, BCL.9, LDA.17 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain B, Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214, B:I.49, B:Y.128, B:L.131, B:F.146, B:F.146, B:L.154, B:V.157 pi-Stacking: C:Y.210 Metal complexes: B:H.153 BCL.9: 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.7, BCL.15, BCL.16, U10.26 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:T.160, 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.15: 18 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, F.181, T.182 Chain C: F.67, M.122, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.9, BCL.16, LDA.23, BPH.25, SPO.27 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.67, C:L.160, C:L.183, B:I.177, B:I.177 Metal complexes: C:H.182 Hydrogen bonds: B:T.182 pi-Stacking: B:F.181 BCL.16: 29 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, N.195, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284 Ligands: BCL.9, BCL.15, LDA.22, BPH.25 13 PLIP interactions: 12 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, C:I.284, B:V.157 Metal complexes: C:H.202

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

LDA.6: 1 residues within 4Å: Chain B: Y.148 No protein-ligand interaction detected (PLIP) LDA.14: 2 residues within 4Å: Chain B: F.179 Ligands: UQ2.8 No protein-ligand interaction detected (PLIP) LDA.17: 8 residues within 4Å: Chain C: P.200, L.204, A.207, F.208, W.268, M.272 Ligands: BCL.5, LDA.19 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.208, C:W.268 Hydrogen bonds: C:P.200 LDA.18: 5 residues within 4Å: Chain C: F.7, L.38, L.39, W.41, F.42 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.39, C:W.41, C:F.42, C:F.42 pi-Cation interactions: C:W.41 LDA.19: 8 residues within 4Å: Chain A: Q.32, Y.40, F.56 Chain C: R.253, F.258 Ligands: LDA.17, LDA.20, U10.26 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.258, C:F.258, C:F.258, C:F.258, A:Q.32, A:F.56 Hydrogen bonds: C:R.253, C:R.253, A:Y.40 LDA.20: 5 residues within 4Å: Chain B: P.28 Chain C: M.256, G.257 Ligands: LDA.19, U10.26 No protein-ligand interaction detected (PLIP) LDA.21: 7 residues within 4Å: Chain B: V.220, G.221 Chain C: G.31, V.32, G.33, L.47 Ligands: LDA.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.47 LDA.22: 6 residues within 4Å: Chain B: V.220 Chain C: L.52, W.129 Ligands: BCL.16, LDA.21, BPH.25 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.129 LDA.23: 2 residues within 4Å: Chain B: W.263 Ligands: BCL.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.263

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.7: 32 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, L.238, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.5, BCL.9, U10.26 19 PLIP interactions: 16 interactions with chain B, 3 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:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:A.217 Hydrogen bonds: B:E.104 BPH.25: 22 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219 Chain C: S.59, G.63, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.15, BCL.16, LDA.22 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.66, C:F.67, C:A.125, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, B:F.181, B:A.184, B:L.185

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

UQ2.8: 15 residues within 4Å: Chain B: T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, S.223, I.224, G.225, T.226, I.229, L.232 Ligands: LDA.14 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.182, B:L.189, B:L.189, B:L.193, B:F.216, B:F.216, B:I.224, B:I.229, B:L.232 Hydrogen bonds: B:H.190, B:I.224, B:G.225

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

PO4.10: 3 residues within 4Å: Chain B: E.72, Y.73, K.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.73, B:Y.73, B:Y.73 Salt bridges: B:K.82

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

HTO.11: 5 residues within 4Å: Chain B: Q.87, T.94, L.133, W.142 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.133

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

FE.24: 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)

U10.26: 24 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: BPH.7, BCL.9, LDA.19, LDA.20 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:F.29, B:F.29, B:W.100, 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.27: 23 residues within 4Å: Chain C: F.67, I.70, G.71, F.74, W.75, L.89, F.105, 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.15 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:I.70, C:F.74, C:L.89, C:F.105, C:W.115, C:F.123, C:W.157, C:L.160, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.28: 15 residues within 4Å: Chain A: I.22, F.23, G.26, Y.30 Chain B: N.199, P.200 Chain C: G.143, K.144, H.145, W.148, W.155, R.267, W.271, L.278 Ligands: GOL.1 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.148, C:W.148, C:W.148, C:W.155, C:W.271, C:L.278, A:I.22, A:F.23 Hydrogen bonds: C:K.144 Water bridges: C:K.144, C:K.144 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267

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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