SMTL ID : 6upp.1

Radiation Damage Test of PixJ Pb state crystals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 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 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.27, A:Y.29, A:P.59, A:T.86, 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:H.89, A:N.101, A:H.119 Water bridges: A:H.64, A:H.89, A:N.101 Salt bridges: A:H.64, A:R.73 pi-Stacking: A:H.89 pi-Cation interactions: A:H.89 VRB.6: 25 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 Ligands: EDO.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.27, B:Y.29, B:P.59, B:H.89, B:L.96, B:V.103, B:I.117 Hydrogen bonds: B:D.58, B:D.58, B:W.65, B:Y.69, B:Y.69, B:Q.75, B:H.89, B:N.101, B:H.119 Salt bridges: B:H.64, B:R.73 pi-Stacking: B:H.89 pi-Cation interactions: B:H.89

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.147, H.150 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.147, A:H.150, H2O.1, H2O.1, H2O.2 MG.4: 4 residues within 4Å: Chain A: D.5, H.150 Chain B: D.5, H.150 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.137 Chain B: L.20, Q.134 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: E.147, H.150 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.147, B:H.150, H2O.7, H2O.9, H2O.9, H2O.10

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: R.18, A.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.18, A:R.18 EDO.7: 8 residues within 4Å: Chain B: Q.75, T.77, I.80, L.85, H.89, L.93, N.101 Ligands: VRB.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.77, B:H.89, B:N.101 EDO.9: 7 residues within 4Å: Chain B: A.76, T.77, T.78, R.125, Q.126, W.127, I.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.127, B:W.127

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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