SMTL ID : 2hg3.1

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with brominated phosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: F.24, W.25, V.26 Chain C: E.94, F.96 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.25, A:W.25 Water bridges: C:E.94 PO4.2: 3 residues within 4Å: Chain A: E.72, Y.73, K.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.73 Salt bridges: A:K.82 PO4.15: 3 residues within 4Å: Chain B: Y.134, L.135, Q.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.134, B:Q.138, B:Q.138 PO4.16: 4 residues within 4Å: Chain B: N.25, N.28, G.53, S.54 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.25, B:N.28, B:S.54, B:S.54 Water bridges: B:Y.51, B:L.55

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.3: 29 residues within 4Å: Chain A: 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 B: Y.210 Ligands: BCL.4, BPH.5, BCL.17, BCL.18, U10.20, PC9.22 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:F.97, A:A.124, A:A.127, A:V.157, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.4: 23 residues within 4Å: Chain A: I.46, I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.3, BPH.5, HTO.7, BCL.18, U10.20, PC9.22 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:I.206, B:L.214, A:I.46, A:I.49, A:Y.128, A:L.131, A:F.146, A:L.154 pi-Stacking: B:Y.210 Metal complexes: A:H.153 BCL.17: 19 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.3, U10.6, BCL.18, BPH.19, PC9.23, LDA.25 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.160, B:I.179, B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.18: 28 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, M.122, 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.3, BCL.4, BCL.17, BPH.19, PC9.23 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:W.66, B:A.153, B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:I.206, B:L.209, B:Y.210, B:V.276 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.5: 32 residues within 4Å: Chain A: F.41, G.45, I.49, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, F.146, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.3, BCL.4, U10.20 20 PLIP interactions: 4 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:Y.210, B:A.213, B:L.214, B:A.217, A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:Y.128, A:F.146, A:Y.148, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241 Hydrogen bonds: A:E.104 BPH.19: 23 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, F.216, L.219, V.220 Chain B: S.59, L.60, G.63, L.64, A.125, V.126, W.129, T.146, A.149, F.150, A.153, T.277 Ligands: BCL.17, BCL.18, PC9.23 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:A.184, A:L.185, A:A.188, A:L.189, B:L.60, B:L.64, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150, B:A.153, B:T.277

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

U10.6: 22 residues within 4Å: Chain A: P.171, I.175, S.178, F.179, T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, L.232, W.263 Ligands: BCL.17, PC9.23 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.171, A:I.175, A:F.179, A:T.182, A:L.189, A:L.193, A:I.224, A:I.229, A:L.232, A:W.263 Hydrogen bonds: A:I.224, A:G.225 U10.20: 25 residues within 4Å: Chain A: F.29, G.35, T.38, W.100, R.103 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 Ligands: BCL.3, BCL.4, BPH.5, PC9.22 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.29, A:T.38, A:W.100, A:W.100, B:L.214, B:M.218, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:H.219, B:A.260

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

HTO.7: 7 residues within 4Å: Chain A: W.151 Chain B: P.200, G.203, L.204, A.207 Ligands: BCL.4, LDA.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.151, B:P.200

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

LDA.8: 6 residues within 4Å: Chain A: Q.62 Chain C: I.17, W.21 Ligands: HTO.7, LDA.29, LDA.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.62 LDA.9: 6 residues within 4Å: Chain A: A.101, V.105, Y.115, P.118, A.122 Ligands: LDA.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.101, A:A.122 LDA.10: 7 residues within 4Å: Chain A: H.116, F.119 Chain B: A.1, E.2, Q.4, I.6 Ligands: LDA.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.119, A:F.119, A:F.119, A:F.119, B:I.6 LDA.11: 6 residues within 4Å: Chain A: G.76, G.77, Q.87, T.90, L.133, W.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.90, A:L.133, A:W.142, A:W.142 Hydrogen bonds: A:G.77 LDA.24: 3 residues within 4Å: Chain B: S.8, W.41, F.42 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.41, B:F.42, B:F.42 pi-Cation interactions: B:W.41 LDA.25: 10 residues within 4Å: Chain B: I.70, M.122, W.157, F.162, V.175, P.176, Y.177, G.178, I.179 Ligands: BCL.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.162, B:V.175, B:Y.177 LDA.27: 6 residues within 4Å: Chain C: A.25, I.28, Y.29 Ligands: CDL.21, LDA.28, LDA.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.28 LDA.28: 5 residues within 4Å: Chain C: Y.29, P.55, F.56 Ligands: PC9.22, LDA.27 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.29, C:P.55, C:F.56 LDA.29: 8 residues within 4Å: Chain C: Y.18, W.21, A.25, I.28 Ligands: LDA.8, PC9.22, LDA.27, LDA.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21, C:I.28 LDA.30: 4 residues within 4Å: Chain C: W.21 Ligands: LDA.8, PC9.22, LDA.29 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.21 Hydrogen bonds: C:W.21 pi-Cation interactions: C:W.21, C:W.21

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 9 residues within 4Å: Chain A: S.52, S.65, V.66, Y.67, L.80, A.81, G.83, L.85, W.86 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.52, A:Y.67, A:L.80, A:G.83, A:W.86 Water bridges: A:S.65 GOL.13: 5 residues within 4Å: Chain A: A.198, N.199, P.200 Chain C: T.63, F.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:N.199, A:G.203, C:T.63 GOL.31: 11 residues within 4Å: Chain B: S.227, R.228, F.229, G.230, R.233 Chain C: R.177, F.178, P.192, Q.194, E.230, C.234 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.177, C:R.177, C:Q.194, B:R.228, B:G.230, B:R.233 GOL.32: 2 residues within 4Å: Chain C: Q.199, R.202 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.199, C:R.202, C:R.202

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

FE.14: 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:H.219, B:E.234, B:H.266

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 19 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, L.278, I.282 Chain C: A.16, S.19, F.23, G.26, L.27, Y.30 Ligands: LDA.27 22 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.155, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278, B:L.278, B:I.282, C:F.23, C:F.23, C:Y.30 Hydrogen bonds: B:K.144 Water bridges: B:K.144, A:N.199, C:Y.30 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

2 x PC9: (7R,14S)-14,15-DIBROMO-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC9.22: 25 residues within 4Å: Chain A: P.28, F.29 Chain B: R.253, M.256, G.257, F.258, W.268, W.271, M.272 Chain C: I.28, L.31, Q.32, Y.40, L.42, N.52, Q.53, G.54, P.55, F.56 Ligands: BCL.3, BCL.4, U10.20, LDA.28, LDA.29, LDA.30 12 PLIP interactions: 4 interactions with chain C, 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.31, C:Q.32, C:F.56, B:F.258, B:F.258, B:F.258, B:W.268, B:W.271, A:F.29 Hydrogen bonds: C:N.52 Water bridges: B:R.253, B:R.253 PC9.23: 13 residues within 4Å: Chain A: V.220, G.221, Y.222 Chain B: S.30, G.31, V.32, G.33, G.48, W.129 Ligands: U10.6, BCL.17, BCL.18, BPH.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.129, A:V.220 Hydrogen bonds: B:G.31, B:G.31

1 x K: POTASSIUM ION(Non-covalent)

K.26: 3 residues within 4Å: Chain C: M.134, A.137, F.140 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.134, C:A.137, C:F.140, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roszak, A.W. et al., Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides. Biochemistry (2007)

Release Date

2007-03-27

Peptides

Reaction center protein L chain: A
Reaction center protein M chain: B
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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Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

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