SMTL ID : 7rzw.1

CryoEM structure of Arabidopsis thaliana phytochrome B

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 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: 27 residues within 4Å: Chain A: Y.104, I.108, M.274, Y.276, V.286, Y.298, Y.303, T.306, D.307, P.309, S.312, L.315, F.316, R.322, R.352, P.354, H.355, C.357, H.358, Y.361, M.365, A.372, V.401, H.403, R.578, P.581, R.582 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.104, A:I.108, A:Y.276, A:V.286, A:Y.298, A:Y.303, A:Y.303, A:F.316, A:H.355, A:Y.361, A:A.372, A:V.401, A:R.578, A:P.581 Hydrogen bonds: A:D.307 Salt bridges: A:R.322, A:R.322, A:R.352, A:H.358 pi-Stacking: A:H.358 O6E.2: 25 residues within 4Å: Chain B: Y.104, I.108, M.274, Y.276, T.306, D.307, I.308, P.309, S.312, F.316, R.322, I.324, R.352, P.354, H.355, C.357, H.358, Y.361, M.365, S.370, A.372, L.399, V.401, H.403, R.578 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.104, B:Y.104, B:I.108, B:Y.276, B:Y.276, B:I.308, B:P.309, B:F.316, B:Y.361, B:L.399, B:V.401 Hydrogen bonds: B:H.355, B:S.370 Salt bridges: B:R.322, B:R.352, B:H.358 pi-Stacking: B:H.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Plant phytochrome B is an asymmetric dimer with unique signalling potential. Nature (2022)

Release Date

2022-04-13

Peptides

Phytochrome B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phytochrome B