SMTL ID : 6pry.1

X-ray crystal structure of the blue-light absorbing state of PixJ from Thermosynechococcus elongatus by serial femtosecond crystallographic analysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x VRB: Phycoviolobilin, blue light-absorbing form(Covalent)

VRB.1: 24 residues within 4Å: Chain A: I.27, Y.29, I.56, D.58, P.59, C.60, F.61, H.64, W.65, Y.69, R.73, Q.75, L.85, T.86, C.88, H.89, Q.92, L.93, L.96, V.98, N.101, V.103, I.117, H.119 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.56, A:P.59, A:H.89, A:L.93, A:L.96, A:V.103, A:I.117 Hydrogen bonds: A:D.58, A:D.58, A:W.65, A:Y.69, A:N.101, A:H.119 Water bridges: A:H.89 Salt bridges: A:H.64, A:R.73 pi-Stacking: A:H.89 pi-Cation interactions: A:H.89 VRB.5: 24 residues within 4Å: Chain B: I.27, Y.29, I.56, D.58, P.59, C.60, F.61, H.64, W.65, Y.69, R.73, Q.75, L.85, T.86, C.88, H.89, Q.92, L.93, L.96, V.98, N.101, V.103, I.117, H.119 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.27, B:Y.29, B:P.59, B:H.89, B:L.96, B:V.103 Hydrogen bonds: B:D.58, B:D.58, B:W.65, B:Y.69, B:Y.69, B:N.101, B:H.119 Water bridges: B:T.86, B:H.89 Salt bridges: B:H.64, B:R.73 pi-Stacking: B:H.89, B:H.89

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: S.1, D.5 Chain B: D.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.5, H2O.6 MG.7: 2 residues within 4Å: Chain B: E.63, H.64 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.64, H2O.8, H2O.8 MG.8: 2 residues within 4Å: Chain B: L.20, Q.134 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: G.47 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: S.43, V.44 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: Y.35, V.66, R.70, Q.111, L.112 Ligand excluded by PLIP

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

PEG.6: 8 residues within 4Å: Chain B: W.48, I.80, F.81, R.94, K.97, V.98, R.99, A.121 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2019-12-18

Peptides

Methyl-accepting chemotaxis protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyl-accepting chemotaxis protein

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