SMTL ID : 2hj6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 30 residues within 4Å: Chain A: F.97, F.121, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, G.161, 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.8, BCL.9, U10.11 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.121, A:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, 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.46, 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.9, U10.11, LDA.16 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.46, A:L.131, A:F.146, A:L.154, B:F.197, B:I.206, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.8: 20 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, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, U10.4, BCL.9, BPH.10, PS2.14, LDA.19 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.160, B:V.175, B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.9: 30 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, M.122, V.126, A.153, L.156, 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, T.277, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.8, BPH.10, LDA.19 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.66, B:V.126, B:A.153, B:L.156, B:T.186, B:F.189, B:L.196, B:I.206, B:L.209, B:Y.210, B:V.276 Hydrogen bonds: B:S.205 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 30 residues within 4Å: Chain A: F.41, A.42, G.45, 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 B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.1, BCL.2, U10.11 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.42, A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214 Hydrogen bonds: A:E.104 BPH.10: 26 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, V.274, T.277 Ligands: BCL.8, BCL.9, PS2.14 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:A.125, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150, B:F.150, A:A.184, A:L.185, A:A.188, A:L.189

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

U10.4: 20 residues within 4Å: Chain A: S.178, F.179, T.182, L.189, H.190, L.193, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, L.232, W.263 Chain B: F.90 Ligands: BCL.8, PS2.14 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.179, A:T.182, A:L.189, A:L.193, A:F.216, A:I.224, A:I.229, A:I.229, A:L.232, A:W.263, B:F.90 Hydrogen bonds: A:I.224, A:G.225 U10.11: 26 residues within 4Å: Chain A: F.29, Y.30, G.35, T.38, W.100, R.103 Chain B: 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.15, LDA.22 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:M.218, B:W.252, B:M.256, B:F.258, B:I.265, B:W.268, B:W.268, B:W.268, A:F.29, A:T.38, A:W.100, A:W.100 Hydrogen bonds: B:A.260

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

FE.5: 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

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

PO4.6: 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:S.54, B:S.54, B:S.54, B:S.54 Water bridges: B:L.55 PO4.7: 2 residues within 4Å: Chain B: Y.134, Q.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.134, B:Q.138

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

HTO.12: 2 residues within 4Å: Chain B: F.123, W.127 No protein-ligand interaction detected (PLIP)

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 17 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: A.16, I.22, F.23, G.26, L.27, Y.30 22 PLIP interactions: 4 interactions with chain C, 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:I.22, C:F.23, C:F.23, B:W.148, B:W.148, B:W.148, B:W.148, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278 Water bridges: C:Y.30, B:K.144, B:R.267 Hydrogen bonds: B:K.144, A:N.199, A:N.199 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

1 x PS2: O-[{[(2R)-2-{[(9S,10S)-9,10-DIBROMOOCTADECANOYL]OXY}-3-(PALMITOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE(Non-covalent)

PS2.14: 13 residues within 4Å: Chain A: L.185, V.220, G.221 Chain B: A.27, R.29, S.30, G.31, L.47, G.48, W.129 Ligands: U10.4, BCL.8, BPH.10 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.129, B:W.129, A:L.185, A:V.220 Hydrogen bonds: B:N.28, B:G.31

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

LDA.15: 9 residues within 4Å: Chain B: R.253, F.258 Chain C: Q.32, Y.40, Q.53, F.56 Ligands: U10.11, LDA.16, LDA.22 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.258, B:F.258, B:F.258, C:Q.32, C:F.56 Hydrogen bonds: B:R.253, B:R.253 Water bridges: C:Q.32 LDA.16: 8 residues within 4Å: Chain B: P.200, F.208, W.268, M.272 Chain C: W.21 Ligands: BCL.2, LDA.15, LDA.24 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.208, B:W.268, C:W.21 Water bridges: B:G.203 LDA.17: 6 residues within 4Å: Chain A: A.101, V.105, Y.115, F.119 Chain B: Q.4 Ligands: GOL.20 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.101, A:V.105, A:Y.115, A:F.119 Hydrogen bonds: B:Q.4 LDA.18: 4 residues within 4Å: Chain B: F.7, L.38, W.41, F.42 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.38, B:W.41, B:F.42 pi-Cation interactions: B:W.41 LDA.19: 11 residues within 4Å: Chain B: I.70, F.74, W.115, W.157, G.161, A.174, V.175, G.178, I.179 Ligands: BCL.8, BCL.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.115, B:A.174, B:I.179 LDA.22: 7 residues within 4Å: Chain A: F.29 Chain B: M.256, G.257 Chain C: N.52, Q.53 Ligands: U10.11, LDA.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.52 Hydrophobic interactions: A:F.29 LDA.23: 1 residues within 4Å: Chain C: A.25 No protein-ligand interaction detected (PLIP) LDA.24: 4 residues within 4Å: Chain C: Y.18, W.21, I.28 Ligands: LDA.16 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.21, C:I.28

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 8 residues within 4Å: Chain A: I.113, G.114, Y.115 Chain B: E.2, Q.4, R.228 Chain C: L.241 Ligands: LDA.17 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.4, B:Q.4, B:R.228, B:R.228, A:Y.115 GOL.25: 2 residues within 4Å: Chain C: N.201, R.202 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.201, C:N.201, C:R.202, C:R.202

1 x K: POTASSIUM ION(Non-covalent)

K.21: 3 residues within 4Å: Chain C: M.134, A.137, F.140 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:M.134

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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