A novel three-dimensional (3D) metal–organic framework of silver(I)-pyrazine-2,3-dicarboxylate (pzdc) with ethylenediamine ligand (en), {[Ag₄(μ₄-pzdc)₂(μ-en)₂]·H₂O}_n (1), was synthesized and structurally characterized by spectral methods (FT-IR and photoluminescence), elemental analysis, thermal analysis (TG, DTG, DTA) and single crystal X-ray diffraction techniques. X-ray crystallographic study of 1 revealed that the pzdc ligand adopts a new coordination mode. Four Ag(I) atoms with different coordination geometries are linked together with carboxylate groups to form 1D tetranuclear building block. The adjacent 1D blocks are connected through the en ligand to form a 2D layer structure, which is further connected to a 3D framework by argentophilic interaction (Ag1⋯Ag2 = 3.096 and Ag3⋯Ag4 = 3.3070 Å). The complex exhibits C–H⋯Ag, N–H⋯Ag intermolecular multicenter heteroacceptor (IMH) hydrogen-bonding interactions between the Ag(I) ions and hydrogen atoms of the en ligand and (O–H)⋯Ag interaction of the pseudo-agostic (IPA) between the Ag(I) ion and hydrogen atoms of the water molecule. In order to assess the potential of 1 in gas storage applications, we performed atomically detailed simulations. Furthermore, 1 exhibits green and unusual yellow luminescence in the solid state at room temperature. Complex 1 has also good antimicrobial activity (36–63 μg mL⁻¹) on studied microorganisms.