Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to position 3 of glucosamine residues in heparan (PubMed:8900198, PubMed:9346953, PubMed:9988768). Catalyzes the rate limiting step in the biosynthesis of heparan sulfate (HSact) (PubMed:8900198, PubMed:9988768). This modification is a crucial step in the biosynthesis of anticoagulant heparan sulfate as it completes the structure of the antithrombin pentasaccharide binding site (PubMed:8900198, PubMed:9988768). {ECO:0000269|PubMed:8900198, ECO:0000269|PubMed:9346953, ECO:0000269|PubMed:9988768}. This is the function of HS3ST1 (heparan sulfate-glucosamine 3-sulfotransferase 1, ENSG00000002587).