SMTL ID : 5nfx.1

Deinococcus radiodurans BphP PAS-GAF Y263F mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 2 residues within 4Å: Chain A: L.167, I.201 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.201 ACT.2: 4 residues within 4Å: Chain A: R.186, L.209, V.283, H.304 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.283, A:H.304 Salt bridges: A:R.186, A:H.210, A:H.304 ACT.3: 3 residues within 4Å: Chain A: T.197, R.216, F.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.197, A:R.216

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 2 residues within 4Å: Chain A: P.272, Q.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.276

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.5: 26 residues within 4Å: Chain A: T.34, T.35, C.38, E.41, I.43, M.188, Y.190, F.212, F.217, S.220, D.221, I.222, P.223, A.226, Y.230, R.268, T.270, S.271, M.273, H.274, F.277, S.286, L.287, S.288, L.300, H.304 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.43, A:Y.190, A:F.212, A:F.217, A:F.217, A:D.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:D.221, A:D.221, A:Y.230, A:S.271, A:S.286 Water bridges: A:R.268, A:R.268, A:L.287, A:L.287, A:H.304 Salt bridges: A:R.268, A:H.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takala, H. et al., On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome. J. Biol. Chem. (2018)

Release Date

2018-04-18

Peptides

Bacteriophytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacteriophytochrome