SMTL ID : 3s7q.1

Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: 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, H.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 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:I.43, A:Y.190, A:F.212, A:F.217, A:F.217, A:H.221, A:I.222, A:I.222, A:P.223, A:A.226, A:Y.230, A:H.274, A:F.277, A:F.277, A:L.300 Hydrogen bonds: A:H.221, A:H.221, A:H.221, A:Y.230, A:S.271, A:S.286, A:H.304 Water bridges: A:R.268, 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, H.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 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:I.43, A:Y.190, A:F.212, A:F.217, A:F.217, A:H.221, A:I.222, A:I.222, A:P.223, A:A.226, A:Y.230, A:H.274, A:F.277, A:F.277, A:L.300 Hydrogen bonds: A:H.221, A:H.221, A:H.221, A:Y.230, A:S.271, A:S.286, A:H.304 Water bridges: A:R.268, 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: R.186, L.209, H.210, F.212, M.281, G.282, V.283, H.304, Q.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.186, A:R.186, A:G.282, A:H.304 Water bridges: A:Q.306 GOL.4: 12 residues within 4Å: Chain A: H.44, I.45, D.109, H.130, V.132, L.229, R.232, H.233, P.261, L.262, G.263, G.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.109, A:R.232, A:H.233, A:G.263, A:G.264

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

PO4.5: 3 residues within 4Å: Chain A: R.179, R.206, E.207 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.207 Water bridges: A:E.207, A:E.207 Salt bridges: A:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Auldridge, M.E. et al., Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein. J.Biol.Chem. (2012)

Release Date

2012-01-11

Peptides

Bacteriophytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacteriophytochrome