The molecule-metal interface formed by pyridine-2,5-dicarboxylic acid chemically bonded to the Cu(110) surface is investigated by scanning tunneling microscopy and first-principles calculations. Our current-voltage spectroscopy studies reveal an electronic mapping of molecular orbitals as a function of tip position. By combining experimental and theoretical investigations, individual molecular orbitals are characterized by their energy and spatial distribution. The importance of adsorption geometries and conformational changes on the electron transport properties is highlighted.