SMTL ID : 6i7i.1

Crystal structure of dimeric FICD mutant K256A complexed with MgATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.265 Ligands: ATP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.2 MG.4: 2 residues within 4Å: Chain B: D.265 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.3, H2O.3, H2O.5

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 19 residues within 4Å: Chain A: T.128, I.131, E.132, V.214, H.217, V.258, H.261, D.265, G.266, N.267, G.268, R.269, R.272, Y.297, Y.298, L.301, E.302, N.305 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:I.131, A:D.265, A:D.265, A:G.266, A:N.267, A:N.267, A:G.268, A:R.269, A:R.272, A:Y.297, A:Y.297, A:N.305 Water bridges: A:R.269, A:Y.298 Salt bridges: A:H.261, A:R.269, A:R.269, A:R.272 ATP.5: 19 residues within 4Å: Chain B: T.128, I.131, E.132, V.214, H.217, V.258, H.261, D.265, G.266, N.267, G.268, R.269, R.272, Y.297, Y.298, L.301, E.302, N.305 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.131, B:E.132, B:D.265, B:G.266, B:N.267, B:N.267, B:G.268, B:R.269, B:R.272, B:Y.297, B:N.305 Water bridges: B:R.269 Salt bridges: B:H.261, B:R.269, B:R.269, B:R.272

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.3: 7 residues within 4Å: Chain A: F.232, W.235, L.252, Y.255, K.256, Y.259, V.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.256 P33.6: 7 residues within 4Å: Chain B: F.232, W.235, L.252, Y.255, K.256, Y.259, V.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perera, L.A. et al., An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP. Embo J. (2019)

Release Date

2019-09-25

Peptides

Adenosine monophosphate-protein transferase FICD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Adenosine monophosphate-protein transferase FICD