SMTL ID : 4tqq.1

Photosynthetic Reaction Center from R. sphaeroides Analyzed at Room Temperature on an X-ray Transparent Microfluidic Chip

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.1: 25 residues within 4Å: Chain B: T.38, F.41, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, G.149, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.2, BCL.3 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.49, B:A.93, B:F.121, B:F.121, B:F.121, B:A.124, B:Y.148, B:Y.148, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214 Hydrogen bonds: B:E.104 BPH.9: 22 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219 Chain C: S.59, G.63, W.66, F.67, G.71, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.7, BCL.8 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:A.125, C:W.129, C:A.149, C:F.150, C:F.150, C:A.153, C:T.277, B:A.184, B:L.189 pi-Stacking: C:F.150

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 17 residues within 4Å: Chain B: I.49, Y.128, L.131, F.146, H.153, L.154 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BPH.1, BCL.3, U10.6, BCL.7 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.3: 28 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, 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 C: Y.210 Ligands: BPH.1, BCL.2, U10.6, BCL.7, BCL.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.7: 26 residues within 4Å: Chain B: V.157, Y.162, F.181 Chain C: 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.2, BCL.3, BCL.8, BPH.9 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:V.126, C:A.153, C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:I.206, C:L.209, C:Y.210, C:V.276 Metal complexes: C:H.202 BCL.8: 16 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, T.182, L.185 Chain C: M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.3, BCL.7, BPH.9 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.160, C:L.183, B:I.177, B:I.177, B:L.185 Metal complexes: C:H.182

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.4: 11 residues within 4Å: Chain B: H.190, L.193, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.216, B:F.216, B:I.224, B:I.229 Hydrogen bonds: B:I.224, B:G.225 pi-Stacking: B:F.216

1 x FE2: FE (II) ION(Non-covalent)

FE2.5: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.219, C:E.234, C:H.266

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

U10.6: 25 residues within 4Å: Chain A: S.83 Chain B: F.29, G.35, V.36, F.39, W.100, R.103 Chain C: M.218, H.219, T.222, I.223, 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.2, BCL.3 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:F.29, B:F.39, B:W.100 Hydrogen bonds: C:T.222, C:A.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khvostichenko, D.S. et al., X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination. Cryst.Growth Des. (2014)

Release Date

2014-07-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

We predict this structure to be a membrane protein.
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Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

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