SMTL ID : 6tc5.1

Phytochromobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x O6E: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid(Covalent)

O6E.1: 22 residues within 4Å: Chain A: Y.5, Y.181, Y.208, T.211, D.212, I.213, P.214, S.217, F.221, R.227, I.229, R.257, P.259, H.260, C.262, H.263, Y.266, M.270, S.275, V.277, V.307, H.309 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.5, A:Y.208, A:Y.208, A:D.212, A:F.221 Hydrogen bonds: A:D.212, A:D.212, A:H.260, A:S.275 Water bridges: A:R.227, A:R.227, A:H.263, A:V.277, A:H.309, A:H.309 Salt bridges: A:R.227, A:R.227, A:R.257, A:H.263 pi-Cation interactions: A:H.263

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain A: Q.10, R.11, C.250, V.252 No protein-ligand interaction detected (PLIP) BME.3: 5 residues within 4Å: Chain A: F.18, A.230, P.313, R.314, C.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagano, S. et al., Structural insights into photoactivation and signalling in plant phytochromes. Nat.Plants (2020)

Release Date

2020-05-06

Peptides

Phytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Phytochrome