SMTL ID : 2hhk.1

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylglycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 28 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.2, BPH.3, BCL.13, BCL.14, U10.16 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: 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.2: 20 residues within 4Å: Chain A: I.49, 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, G.211, L.214 Ligands: BCL.1, BPH.3, BCL.14, U10.16, PGT.24 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:I.49, A:L.131, A:F.146, A:L.154, B:F.197, B:I.206, B:I.206, B:Y.210, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.13: 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.1, U10.4, BCL.14, BPH.15, PGK.18, LDA.21 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:L.160, B:L.183, A:I.177, A:I.177, A:T.182 Metal complexes: B:H.182 Hydrogen bonds: A:S.178 pi-Stacking: A:F.181 BCL.14: 28 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, 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.1, BCL.2, BCL.13, BPH.15, PGK.18 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.66, B:V.126, 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, B:I.284 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 30 residues within 4Å: Chain A: T.38, F.41, A.42, I.49, A.93, 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 B: Y.210, A.213, L.214, M.218, W.252, T.255, M.256 Ligands: BCL.1, BCL.2, U10.16 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.49, A:A.120, A:F.121, A:F.121, A:F.123, A:Y.128, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213 Hydrogen bonds: A:E.104 pi-Stacking: A:F.121 BPH.15: 25 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.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.13, BCL.14, PGK.18 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:A.125, B:W.129, B:W.129, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277, A:A.184, A:A.188, A:L.189 pi-Stacking: B:F.150

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

U10.4: 20 residues within 4Å: Chain A: M.174, 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 Ligands: BCL.13, PGK.18 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.182, A:L.189, A:L.193, A:F.216, A:Y.222, A:I.224, A:I.224, A:I.229, A:L.232, A:L.232 Hydrogen bonds: A:I.224, A:G.225 U10.16: 24 residues within 4Å: Chain A: F.29, Y.30, 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.1, BCL.2, BPH.3, LDA.25 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.214, B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:I.265, B:W.268, B:W.268, B:W.268, A:F.29, A:F.29, A:W.100, A:W.100 Hydrogen bonds: B:H.219, B:A.260

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: S.52, L.55, S.65, Y.67, L.80, A.81, L.85 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.55, A:S.65, A:Y.67 Water bridges: A:G.83, A:G.83 GOL.6: 5 residues within 4Å: Chain A: A.198, N.199, P.200 Chain C: T.63, F.64 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:N.199, C:T.63, C:T.63 GOL.7: 9 residues within 4Å: Chain A: C.108, R.109, G.112, I.113, G.114, Y.115 Chain B: E.2, R.228 Chain C: L.241 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.112, B:E.2, B:E.2, B:R.228, B:R.228 Water bridges: A:G.112 GOL.28: 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

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

FE.8: 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.9: 3 residues within 4Å: Chain B: S.36, T.37, L.38 Ligand excluded by PLIP

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

PO4.10: 5 residues within 4Å: Chain B: Y.3, Q.4, N.5, I.6, F.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.4, B:N.5, B:I.6, B:F.7, B:F.7 PO4.11: 4 residues within 4Å: Chain B: N.25, N.28, G.53, S.54 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.25, B:N.28, B:S.54, B:S.54 Water bridges: B:Y.51, B:S.54, B:L.55 PO4.12: 2 residues within 4Å: Chain B: Y.134, Q.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.138 PO4.23: 1 residues within 4Å: Chain C: R.202 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.201 Water bridges: C:N.201 Salt bridges: C:R.202

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 16 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 Chain C: I.22, F.23, G.26, Y.30 Ligands: LDA.27 20 PLIP interactions: 5 interactions with chain C, 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:I.22, C:F.23, C:F.23, C:Y.30, B:W.148, B:W.148, B:W.155, B:I.270, B:W.271, B:L.278 Hydrogen bonds: C:Y.30, B:K.144, A:N.199, A:N.199 Water bridges: B:K.144, B:R.267 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

1 x PGK: (1R)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (9S,10S)-9,10-DIBROMOOCTADECANOATE(Non-covalent)

PGK.18: 18 residues within 4Å: Chain A: L.185, V.220, G.221, Y.222 Chain B: L.26, A.27, R.29, S.30, G.31, V.32, G.33, L.47, G.48, W.129 Ligands: U10.4, BCL.13, BCL.14, BPH.15 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.129, B:W.129, A:L.185, A:V.220, A:Y.222 Hydrogen bonds: B:L.26, B:G.31

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

LDA.19: 6 residues within 4Å: Chain A: P.28, F.29 Chain B: M.256, G.257, F.258 Ligands: LDA.26 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.258, A:F.29 LDA.20: 5 residues within 4Å: Chain B: F.7, S.8, L.38, W.41, F.42 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.7, B:W.41, B:W.41, B:F.42 pi-Cation interactions: B:W.41 LDA.21: 10 residues within 4Å: Chain B: I.70, W.115, G.161, A.174, V.175, P.176, Y.177, G.178, I.179 Ligands: BCL.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.115, B:A.174, B:V.175, B:V.175, B:Y.177, B:Y.177, B:I.179 LDA.25: 9 residues within 4Å: Chain B: F.258, W.268 Chain C: Q.32, Y.40, Q.53, F.56 Ligands: U10.16, PGT.24, LDA.26 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.56, B:F.258, B:F.258, B:F.258, B:F.258, B:W.268 LDA.26: 8 residues within 4Å: Chain C: Y.18, W.21, A.25, I.28 Ligands: LDA.19, PGT.24, LDA.25, LDA.27 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21, C:A.25, C:I.28 LDA.27: 5 residues within 4Å: Chain C: A.25, G.26, Y.29 Ligands: CDL.17, LDA.26 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.22: 3 residues within 4Å: Chain C: M.134, A.137, F.140 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.134, C:A.137, C:F.140, H2O.16, H2O.16

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.24: 15 residues within 4Å: Chain A: P.61, Q.62, Y.148 Chain B: G.203, L.204, A.207, F.208, W.268, W.271, M.272 Chain C: W.21, L.31 Ligands: BCL.2, LDA.25, LDA.26 7 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: A:P.61, C:L.31, B:L.204, B:F.208, B:W.268, B:W.268, B:W.271

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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