SMTL ID : 1pcr.1

STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTRE FROM RHODOBACTER SPHAEROIDES AT 2.65 ANGSTROMS RESOLUTION: COFACTORS AND PROTEIN-COFACTOR INTERACTIONS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: M.122, V.175, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.2, BCL.11, BPH.12, SPO.14 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:V.175, B:L.183, B:W.185, A:I.177, A:F.181 Metal complexes: B:H.182 BCL.2: 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, F.181, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.1, BCL.3, BPH.4, BCL.11 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:I.177, A:I.177, A:F.180, A:F.181, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.3: 18 residues within 4Å: Chain A: 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, L.214 Ligands: BCL.2, BPH.4, BCL.11, U10.13, LDA.15 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.11: 29 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, M.122, V.126, L.156, W.157, L.160, W.185, 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.1, BCL.2, BCL.3, BPH.12 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:W.66, B:V.126, B:L.156, B:W.157, B:W.185, B:T.186, B:N.187, B:F.189, B:L.196, B:F.197, B:I.206, B:L.209, B:Y.210, B:V.276, B:I.284, A:V.157 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 25 residues within 4Å: Chain A: F.41, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, 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.2, BCL.3, U10.13 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.96, A:F.97, A:A.120, A:F.121, A:F.121, A:F.121, A:A.124, A:Y.148, A:L.238, B:Y.210, B:A.213, B:L.214, B:A.217 BPH.12: 21 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189 Chain B: S.59, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.1, BCL.11 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.181, A:A.184, A:L.185, A:L.189, B:L.64, B:F.67, B:A.149, B:F.150, B:A.153, B:T.277 Hydrogen bonds: B:T.133 pi-Stacking: B:F.150

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

U10.5: 16 residues within 4Å: Chain A: I.175, F.179, T.182, L.193, F.216, Y.222, S.223, I.224, G.225, I.229, L.232, F.243, I.250, W.259, W.262 Ligands: LDA.16 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.179, A:F.179, A:T.182, A:F.216, A:L.232, A:F.243, A:F.243, A:I.250, A:W.259 Hydrogen bonds: A:I.224, A:G.225 U10.13: 24 residues within 4Å: Chain A: G.35, T.38, F.39, W.100 Chain B: L.214, M.218, H.219, T.222, A.245, A.248, A.249, W.252, M.256, F.258, N.259, A.260, M.262, I.265, W.268, M.272 Ligands: BCL.3, BPH.4, LDA.17, LDA.18 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.214, B:M.218, B:W.252, B:M.256, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268, A:F.39, A:W.100, A:W.100, A:W.100 Hydrogen bonds: B:T.222, B:A.260

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

LDA.6: 5 residues within 4Å: Chain A: I.49, P.61, Q.62, Y.148, I.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.49, A:I.150 LDA.7: 4 residues within 4Å: Chain A: L.44, L.48, I.88, I.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.44, A:I.88 LDA.8: 9 residues within 4Å: Chain A: L.75, G.76, G.77, Q.87, T.90, I.91, T.94, L.133, W.142 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.90, A:T.94, A:L.133, A:W.142 LDA.15: 10 residues within 4Å: Chain B: P.200, L.204, A.207, F.208, W.268, M.272 Chain C: W.21, I.28 Ligands: BCL.3, LDA.17 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.204, B:A.207, B:F.208, B:W.268, C:I.28 LDA.16: 5 residues within 4Å: Chain B: F.7, L.38, W.41, F.42 Ligands: U10.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.42 LDA.17: 9 residues within 4Å: Chain B: R.253, G.257, F.258 Chain C: Q.32, Y.40, Q.53 Ligands: U10.13, LDA.15, LDA.18 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.258, B:F.258, B:F.258, B:F.258 Hydrogen bonds: B:R.253, C:Y.40, C:Y.40 LDA.18: 4 residues within 4Å: Chain B: M.256, G.257 Ligands: U10.13, LDA.17 No protein-ligand interaction detected (PLIP) LDA.19: 9 residues within 4Å: Chain B: H.145, W.148, W.155, R.267, I.270, W.271, V.274, L.278 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.155, B:I.270, B:W.271, B:W.271, B:V.274 LDA.20: 5 residues within 4Å: Chain B: M.65, T.69, I.72, L.114, I.117 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.72

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

FE.9: 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 4 residues within 4Å: Chain A: N.199 Chain B: H.145, R.267 Ligands: LDA.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.267 Salt bridges: B:H.145, B:R.267 Hydrogen bonds: A:N.199

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.14: 19 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, W.75, L.116, S.119, F.120, F.123, W.157, L.160, G.161, F.162, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.1 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.68, B:I.70, B:L.116, B:F.120, B:F.120, B:F.123, B:F.123, B:W.157, B:L.160, B:F.162, B:F.162, B:F.162, B:V.175, B:V.175, B:Y.177, B:Y.177, B:I.179, B:H.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ermler, U. et al., Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: cofactors and protein-cofactor interactions. Structure (1994)

Release Date

1995-02-07

Peptides

PHOTOSYNTHETIC REACTION CENTER: A
PHOTOSYNTHETIC REACTION CENTER: B
PHOTOSYNTHETIC REACTION CENTER: 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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PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

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