Urea cycle — five hepatic enzymes (NAGS and ORNT1 named, not pages)
Ammonia is packaged as urea. CPS1 and OTC run in the matrix; ASS1, ASL, and ARG1 run in the cytosol. N-acetylglutamate is the CPS1 on-switch (Regulation). Ornithine returns via ORNT1 — named, not a sixth simulator.
Carbamoyl-phosphate synthase I CPS1
HCO₃⁻ + NH₄⁺ + 2 ATP → carbamoyl phosphate
Two ATP on 5DOU. Occupancy is ADP×2 + Pi + NAG, not ATP and not CP. NAG stays as the allosteric on-switch. Ni at His337 is a purification artifact.
EC 6.3.4.16 · PDB 5DOU
▶ OPEN SIMULATOROrnithine transcarbamylase OTC
carbamoyl phosphate + L-ornithine → L-citrulline
Transfer on 1C9Y. Occupancy is CP + norvaline — never label NVA as ornithine. Phe101 is the current canonical residue. Arg270 vs UniProt Gln270 is a genuine SEQADV.
EC 2.1.3.3 · PDB 1C9Y
▶ OPEN SIMULATORArgininosuccinate synthase ASS1
L-citrulline + L-aspartate + ATP → argininosuccinate
Adenylation on 2NZ2. Occupancy is citrulline + aspartate, not ATP. Citrullyl-AMP is schematic. No covalent Asp intermediate is drawn.
EC 6.3.4.5 · PDB 2NZ2
▶ OPEN SIMULATORArgininosuccinate lyase ASL
argininosuccinate → fumarate + L-arginine
β-elimination on 1K62 Q286R, empty pocket. His160 is the acceptor. Residue 281 is SER — UniProt ACT_SITE donor, named not starred. Do not pin His281.
EC 4.3.2.1 · PDB 1K62
▶ OPEN SIMULATORArginase-1 ARG1
L-arginine + H₂O → urea + L-ornithine
Dimanganese hydrolase on 3GMZ. Occupancy is product ornithine, not arginine. His141 is the compiled proton shuttle. Ornithine returns to OTC via ORNT1 (named, not a page).
EC 3.5.3.1 · PDB 3GMZ
▶ OPEN SIMULATOR