SMTL ID : 6tc7.1

PAS-GAF bidomain of Glycine max phytochromeA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 24 residues within 4Å: Chain A: Y.21, M.25, M.191, Y.193, V.203, Y.220, T.223, D.224, I.225, P.226, S.229, F.233, R.239, I.241, R.269, A.270, P.271, H.272, C.274, H.275, Y.278, M.282, V.289, H.321 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.21, A:Y.193, A:Y.193, A:V.203, A:Y.220, A:Y.220, A:D.224, A:P.226, A:F.233, A:H.272 Hydrogen bonds: A:D.224, A:D.224, A:H.272, A:H.275, A:S.287, A:S.287 Water bridges: A:R.269, A:R.269, A:H.275, A:S.284, A:V.289, A:H.321, A:H.321 Salt bridges: A:R.239, A:R.239, A:R.269, A:H.275 pi-Stacking: A:H.275 CYC.3: 23 residues within 4Å: Chain B: Y.21, M.25, M.191, Y.193, V.203, Y.220, T.223, D.224, I.225, P.226, S.229, F.233, R.239, R.269, P.271, H.272, C.274, H.275, Y.278, S.287, V.289, V.319, H.321 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:Y.21, B:Y.193, B:V.203, B:Y.220, B:Y.220, B:Y.220, B:D.224, B:I.225, B:P.226, B:F.233, B:H.272 Hydrogen bonds: B:D.224, B:D.224, B:H.272, B:S.287 Water bridges: B:H.275, B:H.275, B:S.284, B:S.287, B:V.289, B:V.289, B:H.321, B:H.321 Salt bridges: B:R.239, B:R.239, B:R.269, B:H.275 pi-Cation interactions: B:H.275

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

PEG.2: 5 residues within 4Å: Chain A: Y.119, V.136, E.140, M.143, P.329 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.140 PEG.4: 9 residues within 4Å: Chain B: Y.119, E.134, P.135, V.136, E.140, F.327, P.329, F.330, R.333 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.134, B:E.134, B:F.330, B:R.333

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Phytochrome