SMTL ID : 6tby.1

Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 22 residues within 4Å: Chain A: Y.17, Y.193, V.203, Y.220, T.223, D.224, I.225, P.226, S.229, F.233, R.239, I.241, R.269, P.271, H.272, C.274, H.275, Y.278, M.282, V.289, V.319, H.321 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.17, A:Y.193, A:V.203, A:Y.220, A:Y.220, A:D.224, A:I.225, A:I.225, A:F.233 Hydrogen bonds: A:D.224, A:D.224, A:H.272, A:S.287, A:S.287 Water bridges: A:R.239, A:R.239, A:H.275, A:V.289, A:H.321 Salt bridges: A:R.239, A:R.239, A:R.269, A:H.275 pi-Cation interactions: A:H.275

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.230, F.231, R.234, K.313, L.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.230, A:R.230, A:R.234, A:L.314

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

BME.3: 4 residues within 4Å: Chain A: Q.22, R.23, C.262, V.264 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.22 BME.4: 5 residues within 4Å: Chain A: F.30, R.137, P.325, R.326, C.327 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.137

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: L.76, D.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.254 PEG.6: 6 residues within 4Å: Chain A: D.79, R.81, L.82, P.86, A.89, R.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.81, A:R.112

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