SMTL ID : 8c3i.1

Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 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)(Non-covalent)

LBV.1: 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, H.274, Y.277, M.281, S.286, L.287, S.288, H.304 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.35, 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:R.236 Hydrogen bonds: A:D.221, A:D.221, A:Y.230, A:S.271, A:H.274, A:S.286, A:S.288 Water bridges: A:I.43, A:R.268, A:R.268, A:L.287, A:L.287, A:H.304 Salt bridges: A:R.268, A:H.274 pi-Stacking: A:H.274 LBV.2: 26 residues within 4Å: Chain B: T.34, 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, H.274, Y.277, M.281, S.286, L.287, S.288, H.304 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.43, B:Y.190, B:F.212, B:F.217, B:F.217, B:D.221, B:I.222, B:I.222, B:P.223, B:A.226, B:Y.230, B:R.236 Hydrogen bonds: B:D.221, B:D.221, B:S.271, B:S.286, B:S.288 Water bridges: B:I.43, B:R.268, B:R.268, B:L.287, B:H.304, B:H.304 Salt bridges: B:R.268, B:H.274 pi-Stacking: B:H.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madan Kumar, S. et al., Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome. To Be Published

Release Date

2024-01-10

Peptides

Bacteriophytochrome: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Bacteriophytochrome

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