SMTL ID : 7z9e.1

Deinococcus radiodurans BphP PAS-GAF H260A/Y263F mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 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.3: 4 residues within 4Å: Chain A: T.197, R.216, F.217, P.218 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.197, A:R.216 ACT.4: 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:L.209, A:V.283, A:H.304 Salt bridges: A:R.186, A:H.304

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

MPD.2: 1 residues within 4Å: Chain A: P.194 No protein-ligand interaction detected (PLIP) MPD.5: 3 residues within 4Å: Chain A: P.272, M.273, 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.6: 27 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.236, R.268, T.270, S.271, M.273, A.274, F.277, S.286, L.287, S.288, L.300, H.304 29 PLIP interactions: 29 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:T.270, A:M.273, A:A.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:S.286, A:L.287, A:L.287, A:H.304 Salt bridges: A:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lehtivuori, H. et al., Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome. Photochem Photobiol Sci (2022)

Release Date

2022-08-10

Peptides

Bacteriophytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bacteriophytochrome