3VPK
Crystal Structure of 6-Guanidinohexanoyl Trypsin
Summary for 3VPK
| Entry DOI | 10.2210/pdb3vpk/pdb |
| Descriptor | Cationic trypsin, 6-carbamimidamidohexanoic acid, CALCIUM ION, ... (5 entities in total) |
| Functional Keywords | acyl-enzyme intermediate, serine protease inhibitor, trypsin, serine protease, digestion, anti-pancreatitis drug, leaving group, catalytic water molecule, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor |
| Biological source | Bos taurus (bovine) |
| Cellular location | Secreted, extracellular space: P00760 |
| Total number of polymer chains | 1 |
| Total formula weight | 23703.75 |
| Authors | Masuda, Y.,Nitanai, Y.,Mizutani, R.,Noguchi, S. (deposition date: 2012-03-05, release date: 2012-05-23, Last modification date: 2024-11-20) |
| Primary citation | Masuda, Y.,Nitanai, Y.,Mizutani, R.,Noguchi, S. Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated Proteins, 2012 Cited by PubMed Abstract: The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation. PubMed: 23161653DOI: 10.1002/prot.24206 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.94 Å) |
Structure validation
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