SMTL ID : 1f6n.1

CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT REACTION CENTER PRO L209-> TYR FROM THE PHOTOSYNTHETIC PURPLE BACTERIUM RHODOBACTER SPHAEROIDES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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, T.182 Chain B: F.67, M.122, W.157, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.2, BCL.9, BPH.10, SPO.12 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.67, B:V.175, B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 BCL.2: 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, 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.1, BCL.3, BPH.4, 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:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 pi-Cation interactions: A:H.173 Metal complexes: A:H.173 BCL.3: 18 residues within 4Å: Chain A: I.46, Y.128, L.131, F.146, I.150, H.153, L.154, W.156 Chain B: F.197, G.203, I.206, A.207, Y.210 Ligands: BCL.2, BPH.4, BCL.9, U10.11, LDA.13 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.46, A:Y.128, A:L.131, A:F.146, A:F.146, A:L.154, A:W.156, B:F.197, B:I.206, B:I.206, B:Y.210 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.9: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: M.122, V.126, A.153, L.156, W.157, L.160, W.185, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.3, BPH.10 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.126, B:L.156, B:W.157, B:W.157, B:W.185, B:T.186, B:N.187, B:F.189, B:F.197, B:F.197, B:F.197, B:I.206, B:I.206, B:Y.210, B:V.276, B:I.284, A:V.157 Hydrogen bonds: B:S.205 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 28 residues within 4Å: Chain A: T.38, F.41, A.42, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.148, 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, U10.11 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.42, A:A.96, A:F.97, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.148, A:L.238, B:Y.210, B:A.213, B:L.214, B:L.214, B:A.217 BPH.10: 21 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189 Chain B: 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, U10.5, BCL.9 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.181, A:A.184, A:L.185, A:A.188, A:L.189, B:L.64, B:F.67, B:A.149, B:F.150, B:F.150, 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: 17 residues within 4Å: Chain A: L.189, H.190, L.193, Y.209, E.212, D.213, F.216, V.220, S.223, I.224, G.225, T.226, I.229, L.232 Chain B: L.52, W.129 Ligands: BPH.10 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.189, A:L.193, A:F.216, A:F.216, A:V.220, A:I.229, A:L.232, B:L.52, B:W.129, B:W.129 Hydrogen bonds: A:I.224, A:G.225 U10.11: 25 residues within 4Å: Chain A: F.29, G.35, T.38, F.39, W.100 Chain B: 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.2, BCL.3, BPH.4, LDA.6, LDA.15 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.29, A:T.38, A:F.39, A:W.100, B:M.218, B:W.252, B:M.256, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:T.222, B:A.260

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

LDA.6: 7 residues within 4Å: Chain A: P.28, F.29 Chain B: R.253, G.257 Chain C: L.42 Ligands: U10.11, LDA.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.253 Hydrophobic interactions: A:P.28, A:F.29 LDA.13: 6 residues within 4Å: Chain B: P.200, L.204, W.268, M.272 Chain C: I.28 Ligands: BCL.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.268, C:I.28 LDA.14: 7 residues within 4Å: Chain B: H.145, W.148, R.267, I.270, W.271 Ligands: PO4.8, LDA.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.270, B:W.271 LDA.15: 10 residues within 4Å: Chain B: R.253, G.257, F.258 Chain C: I.28, Q.32, Y.40, Q.53, F.56 Ligands: LDA.6, U10.11 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.258, B:F.258, C:I.28, C:F.56 Hydrogen bonds: B:R.253, C:Y.40 LDA.16: 5 residues within 4Å: Chain C: F.23, G.26, L.27, Y.30 Ligands: LDA.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.23, C:F.23, C:Y.30 pi-Cation interactions: C:Y.30

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

FE.7: 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 4 residues within 4Å: Chain A: N.199 Chain B: H.145, R.267 Ligands: LDA.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.199 Salt bridges: B:H.145, B:R.267

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.12: 18 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, W.75, W.115, S.119, F.120, F.123, W.157, G.161, F.162, W.171, Y.177, G.178, I.179, H.182 Ligands: BCL.1 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:W.75, B:W.115, B:F.120, B:F.123, B:F.123, B:W.157, B:F.162, B:F.162, B:F.162, B:W.171, B:Y.177, B:Y.177, B:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuglstatter, A. et al., X-ray structure analyses of photosynthetic reaction center variants from Rhodobacter sphaeroides: structural changes induced by point mutations at position L209 modulate electron and proton transfer. Biochemistry (2001)

Release Date

2001-04-18

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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