Among more than fifty blazars detected in very high energy (VHE, E>100GeV) gamma-rays, only three belong to the subclass of Flat Spectrum Radio Quasars (FSRQs). MAGIC observed FSRQ PKS 1510-089 in February-April 2012 during a high activity state in the high energy (HE, E>100 MeV) gamma-ray band observed by AGILE and Fermi. MAGIC observations result in the detection of a source with significance of 6.0 sigma. In agreement with the previous VHE observations of the source, we find no statistically significant variability during the MAGIC observations in daily, weekly or monthly time scales. The other two known VHE FSRQs have shown daily scale to sub-hour variability. We study the multifrequency behaviour of the source at the epoch of MAGIC observation, collecting quasi-simultaneous data at radio and optical (GASP-WEBT and F-Gamma collaborations, REM, Steward, Perkins, Liverpool, OVRO and VLBA telescopes), X-ray (Swift satellite) and HE gamma-ray frequencies. The gamma-ray SED combining AGILE, Fermi and MAGIC data joins smoothly and shows no hint of a break. The multifrequency light curves suggest a common origin for the millimeter radio and HE gamma-ray emission and the HE gamma-ray flaring starts when the new component is ejected from the 43GHz VLBA core. The quasi-simultaneous multifrequency SED is modelled with a one-zone inverse Compton model. We study two different origins of the seed photons for the inverse Compton scattering, namely the infra-red torus and a slow sheath surrounding the jet around the VLBA core. Both models fit the data well. However, the fast HE gamma-ray variability requires that within the modelled large emitting region, there must exist more compact regions. We suggest that these observed signatures would be most naturally explained by a turbulent plasma flowing at a relativistic speed down the jet and crossing a standing conical shock.