SMTL ID : 4zrr.1

Crystal Structure of Monomeric Bacteriophytochrome mutant D207L Y263F at 1.5 A resolution Using a home source.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x LBV: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid(Covalent)

LBV.1: 33 residues within 4Å: Chain A: T.34, T.35, C.38, E.41, I.43, M.188, Y.190, V.200, F.212, F.217, S.220, L.221, I.222, P.223, Q.225, A.226, Y.230, R.236, R.268, T.270, S.271, M.273, H.274, F.277, L.278, M.281, S.286, L.287, S.288, L.300, A.302, H.304 Ligands: LBW.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:T.35, A:Y.190, A:F.212, A:F.217, A:F.217, A:L.221, A:I.222, A:I.222, A:P.223, A:A.226, A:Y.230, A:T.270, A:F.277, A:F.277, A:L.300 Hydrogen bonds: A:L.221, A:L.221, A:L.221, A:Y.230, A:S.271, A:S.286, A:H.304 Water bridges: A:R.268, A:H.274, A:H.274, A:L.287, A:L.287 Salt bridges: A:R.268, A:H.274 pi-Stacking: A:H.274

1 x LBW: 3-[2-[(Z)-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E,4R)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid(Covalent)

LBW.2: 34 residues within 4Å: Chain A: I.33, T.34, T.35, C.38, E.41, I.43, M.188, Y.190, V.200, F.212, F.217, S.220, L.221, I.222, P.223, Q.225, A.226, Y.230, R.236, R.268, T.270, S.271, M.273, H.274, F.277, L.278, M.281, S.286, L.287, S.288, L.300, A.302, H.304 Ligands: LBV.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.43, A:F.212, A:F.217, A:F.217, A:L.221, A:L.221, A:I.222, A:I.222, A:P.223, A:A.226, A:Y.230, A:M.273, A:H.274, A:F.277, A:F.277 Hydrogen bonds: A:L.221, A:L.221, A:L.221, A:Y.230, A:S.271, A:S.286, A:H.304 Water bridges: A:R.268, A:H.274, A:H.274, A:L.287, A:L.287 Salt bridges: A:R.268, A:H.274 pi-Stacking: A:H.274

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

PO4.3: 3 residues within 4Å: Chain A: R.179, R.206, E.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.207 Salt bridges: A:R.179

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: L.26, G.29, G.30, P.31, E.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.32, A:E.32 PEG.5: 8 residues within 4Å: Chain A: F.192, A.193, P.194, D.195, A.196, R.227, Q.296, L.297 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.196, A:L.297 Water bridges: A:R.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lehtivuori, H. et al., Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor. Front Mol Biosci (2015)

Release Date

2016-01-20

Peptides

Bacteriophytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacteriophytochrome

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