SMTL ID : 5mfu.1

PA3825-EAL Mn-pGpG Structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: E.35, N.94, E.126, D.156 Ligands: NA.2, G.3, G.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:E.126, A:D.156, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: N.94, D.156, D.157 Ligands: MN.1, G.3, G.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.94

2 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

G.3: 17 residues within 4Å: Chain A: Q.21, E.35, R.39, R.49, N.94, D.156, D.157, Q.180, E.213, G.214, E.216, G.234, Y.235, P.240 Ligands: MN.1, NA.2, G.4 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Q.21, A:M.38, A:R.39, A:N.94, A:N.94, A:D.156, A:D.157, A:Q.180, A:Y.235 Water bridges: A:R.49, A:R.49, A:D.51, A:T.67, A:S.96, A:D.157, A:D.157, A:Q.233, A:Y.235, A:Y.235 Salt bridges: A:R.39, A:R.49, A:E.216 pi-Stacking: A:Y.235 pi-Cation interactions: A:Y.235 G.4: 11 residues within 4Å: Chain A: L.37, M.38, R.39, R.49, P.50, D.51, L.70, N.94 Ligands: MN.1, NA.2, G.3 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellini, D. et al., Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases. Sci Rep (2017)

Release Date

2017-03-01

Peptides

Diguanylate phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diguanylate phosphodiesterase