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 C: R.267 Chain B: N.199 Ligands: GOL.12, CDL.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.34, A:R.37 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: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.63, B:P.200 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 C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Chain B: I.49, Y.128, L.131, F.146, I.150, H.153, L.154, V.157 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 C: Y.210 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 Ligands: BCL.5, BPH.7, BCL.15, BCL.16, U10.26 15 PLIP interactions: 1 interactions with chain C, 14 interactions with chain B, Hydrophobic interactions: C:Y.210, 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 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.15: 18 residues within 4Å: Chain C: F.67, M.122, L.160, I.179, H.182, L.183, T.186 Chain B: H.168, M.174, I.177, S.178, F.181, T.182 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 Hydrogen bonds: B:T.182 Metal complexes: C:H.182 pi-Stacking: B:F.181 BCL.16: 29 residues within 4Å: 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 Chain B: V.157, Y.162, H.168, F.181 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: 3 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Q.32, A:F.56, C:F.258, C:F.258, C:F.258, C:F.258 Hydrogen bonds: A:Y.40, C:R.253, C:R.253 LDA.20: 5 residues within 4Å: Chain C: M.256, G.257 Chain B: P.28 Ligands: LDA.19, U10.26 No protein-ligand interaction detected (PLIP) LDA.21: 7 residues within 4Å: Chain C: G.31, V.32, G.33, L.47 Chain B: V.220, G.221 Ligands: LDA.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.47 LDA.22: 6 residues within 4Å: Chain C: L.52, W.129 Chain B: V.220 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 C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 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 Ligands: BCL.5, BCL.9, U10.26 20 PLIP interactions: 3 interactions with chain C, 17 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:A.217, 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 Hydrogen bonds: B:W.100, B:E.104 BPH.25: 22 residues within 4Å: 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 Chain B: F.181, A.184, L.185, L.189, L.219 Ligands: BCL.15, BCL.16, LDA.22 13 PLIP interactions: 10 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 Hydrogen bonds: C:W.129

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 C: H.219, E.234, H.266 Chain B: H.190, H.230 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.219, C:E.234, C:H.266, B:H.190, B:H.230

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

U10.26: 24 residues within 4Å: 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 Chain B: F.29, Y.30, G.35, W.100, R.103 Ligands: BPH.7, BCL.9, LDA.19, LDA.20 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: 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, B:F.29, B:F.29, B:W.100, B:W.100 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 21 PLIP interactions: 21 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 Hydrogen bonds: C:W.75

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.28: 15 residues within 4Å: Chain A: I.22, F.23, G.26, Y.30 Chain C: G.143, K.144, H.145, W.148, W.155, R.267, W.271, L.278 Chain B: N.199, P.200 Ligands: GOL.1 16 PLIP interactions: 2 interactions with chain A, 14 interactions with chain C Hydrophobic interactions: A:I.22, A:F.23, C:W.148, C:W.148, C:W.148, C:W.155, C:W.271, C:L.278 Hydrogen bonds: C:K.144, C:W.148 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267 Water bridges: C:K.144, C:K.144

Links

RCSB   PDBe   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

REACTION CENTER PROTEIN H CHAIN

REACTION CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

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